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CHEBI ONTOLOGY - ANNOTATIONS

The Chemical Entities of Biological Interest (ChEBI) ontology is downloaded weekly from EMBL-EBI at http://www.ebi.ac.uk/chebi/. The data is made available under the Creative Commons License (CC BY 3.0, http://creativecommons.org/licenses/by/3.0/). For more information see: Degtyarenko et al. (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344–D350.
Term:berberine
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Accession:CHEBI:16118 term browser browse the term
Definition:A botanical anti-fungal agent that has formula C20H18NO4.
Synonyms:exact_synonym: 9,10-dimethoxy-5,6-dihydro[1,3]dioxolo[4,5-g]isoquino[3,2-a]isoquinolin-7-ium
 related_synonym: 5,6-dihydro-9,10-dimethoxy-1,3-benzodioxolo[5,6-a]benzo[g]quinolizinium;   7,8,13,13a-tetradehydro-9,10-dimethoxy-2,3-[methylenebis(oxy)]berbinium;   9,10-dimethoxy-2,3-(methylenedioxy)-7,8,13,13a-tetradehydroberbinium;   Berberin;   Formula=C20H18NO4;   InChI=1S/C20H18NO4/c1-22-17-4-3-12-7-16-14-9-19-18(24-11-25-19)8-13(14)5-6-21(16)10-15(12)20(17)23-2/h3-4,7-10H,5-6,11H2,1-2H3/q+1;   InChIKey=YBHILYKTIRIUTE-UHFFFAOYSA-N;   SMILES=COc1ccc2cc3-c4cc5OCOc5cc4CC[n+]3cc2c1OC;   Umbellatine
 alt_id: CHEBI:13893;   CHEBI:22753;   CHEBI:3066;   CHEBI:41098
 xref: Beilstein:3570374;   CAS:2086-83-1;   Chemspider:2263;   DrugBank:DB04115;   FooDB:FDB023165;   HMDB:HMDB0003409;   KEGG:C00757;   KNApSAcK:C00001819;   LINCS:LSM-6553
 xref_mesh: MESH:D001599
 xref: MetaCyc:BERBERINE;   PDBeChem:BER;   PMID:11860742;   PMID:12232209;   PMID:12428952;   PMID:12433089;   PMID:12468268;   PMID:15040083;   PMID:15531889;   PMID:15739507;   PMID:15768991;   PMID:16379555;   PMID:16448624;   PMID:16505103;   PMID:17089049;   PMID:17295371;   PMID:17531424;   PMID:18537696;   PMID:19014947;   PMID:19336898;   PMID:19640223;   PMID:19652370;   PMID:19704371;   PMID:20471843;   PMID:20847417;   PMID:21401114;   PMID:21420512;   PMID:21500372;   PMID:21661731;   PMID:23231038;   PMID:26167392;   PMID:8730735;   Pesticides:berberine;   Wikipedia:Berberine


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berberine term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ABCA1 ATP binding cassette subfamily A member 1 increases expression EXP berberine increases expression of abca1 protein in mouse liver and human hepatocytes RGD PMID:29505790 RGD:19165131 NCBI chr 9:104,781,006...104,928,155
Ensembl chr 9:104,781,006...104,928,155 		JBrowse link
G ABCB1 ATP binding cassette subfamily B member 1 increases expression ISO Berberine results in increased expression of ABCB1A mRNA CTD PMID:20410605 NCBI chr 7:87,503,017...87,713,295
Ensembl chr 7:87,503,017...87,713,323 		JBrowse link
G ACADM acyl-CoA dehydrogenase medium chain multiple interactions ISO Berberine inhibits the reaction [Ethanol results in decreased expression of ACADM mRNA] CTD PMID:25455889 NCBI chr 1:75,724,709...75,763,679
Ensembl chr 1:75,724,431...75,787,575 		JBrowse link
G ACAN aggrecan decreases expression EXP Berberine results in decreased expression of ACAN mRNA CTD PMID:26478571 NCBI chr15:88,803,436...88,875,353
Ensembl chr15:88,803,436...88,875,353 		JBrowse link
G ACHE acetylcholinesterase (Yt blood group) multiple interactions
decreases activity		 ISO
EXP		 Berberine inhibits the reaction [[Cadmium co-treated with Aluminum co-treated with Fluorides] results in increased activity of ACHE protein]; Berberine inhibits the reaction [[Cadmium co-treated with Aluminum co-treated with Fluorides] results in increased expression of ACHE mRNA]; Berberine inhibits the reaction [acetamiprid results in increased activity of ACHE protein]
Berberine results in decreased activity of ACHE protein		 CTD PMID:29170048 PMID:33844597 PMID:37350525 NCBI chr 7:100,889,994...100,896,994
Ensembl chr 7:100,889,994...100,896,974 		JBrowse link
G ACOX1 acyl-CoA oxidase 1 multiple interactions ISO Berberine inhibits the reaction [Ethanol results in decreased expression of ACOX1 mRNA] CTD PMID:25455889 NCBI chr17:75,941,507...75,979,166
Ensembl chr17:75,941,507...75,979,177 		JBrowse link
G ACTA2 actin alpha 2, smooth muscle decreases expression
multiple interactions		 ISO Berberine results in decreased expression of ACTA2 protein
Berberine inhibits the reaction [Particulate Matter results in increased expression of ACTA2 mRNA]		 CTD PMID:17973934 PMID:37839514 NCBI chr10:88,935,074...88,991,337
Ensembl chr10:88,934,822...88,991,339 		JBrowse link
G ADIPOQ adiponectin, C1Q and collagen domain containing multiple interactions ISO Berberine inhibits the reaction [Clozapine results in increased expression of ADIPOQ mRNA]; Berberine inhibits the reaction [Risperidone results in increased expression of ADIPOQ mRNA] CTD PMID:20564506 NCBI chr 3:186,842,710...186,858,463
Ensembl chr 3:186,842,704...186,858,463 		JBrowse link
G AGER advanced glycosylation end-product specific receptor multiple interactions ISO Berberine inhibits the reaction [Bortezomib results in increased expression of AGER mRNA] CTD PMID:35121005 NCBI chr 6:32,180,969...32,184,253
Ensembl chr 6:32,180,968...32,184,322 		JBrowse link
G AHR aryl hydrocarbon receptor increases activity ISO
EXP		 Berberine results in increased activity of AHR protein CTD PMID:16046213 NCBI chr 7:17,298,652...17,346,147
Ensembl chr 7:16,916,359...17,346,152 		JBrowse link
G AKT1 AKT serine/threonine kinase 1 multiple interactions
decreases phosphorylation
increases phosphorylation		 EXP
ISO		 Berberine inhibits the reaction [Glucose results in decreased phosphorylation of AKT1 protein]
Berberine results in decreased phosphorylation of AKT1 protein
Berberine inhibits the reaction [Thioacetamide results in increased phosphorylation of AKT1 protein]
Berberine results in increased phosphorylation of AKT1 protein		 CTD PMID:23954465 PMID:30138605 PMID:33325633 NCBI chr14:104,769,349...104,795,748
Ensembl chr14:104,769,349...104,795,759 		JBrowse link
G AKT2 AKT serine/threonine kinase 2 multiple interactions ISO Berberine inhibits the reaction [Dexamethasone results in decreased expression of AKT2 mRNA] CTD PMID:20462044 NCBI chr19:40,230,317...40,285,345
Ensembl chr19:40,230,317...40,285,536 		JBrowse link
G ALB albumin multiple interactions ISO Berberine inhibits the reaction [Thioacetamide results in decreased expression of ALB protein] CTD PMID:30138605 NCBI chr 4:73,404,287...73,421,482
Ensembl chr 4:73,397,114...73,421,482 		JBrowse link
G APP amyloid beta precursor protein multiple interactions ISO Berberine inhibits the reaction [[Cadmium co-treated with Aluminum co-treated with Fluorides] results in increased expression of APP mRNA] CTD PMID:29170048 NCBI chr21:25,880,550...26,171,128
Ensembl chr21:25,880,535...26,171,128 		JBrowse link
G AURKB aurora kinase B decreases expression EXP Berberine results in decreased expression of AURKB mRNA CTD PMID:27311644 NCBI chr17:8,204,731...8,210,575
Ensembl chr17:8,204,733...8,210,600 		JBrowse link
G AURKC aurora kinase C increases expression EXP Berberine results in increased expression of AURKC mRNA CTD PMID:27311644 NCBI chr19:57,231,023...57,235,548
Ensembl chr19:57,231,009...57,235,548 		JBrowse link
G BAX BCL2 associated X, apoptosis regulator multiple interactions
increases expression		 ISO
EXP		 [Berberine co-treated with Thioacetamide] results in increased expression of BAX mRNA; Berberine inhibits the reaction [Chlorpyrifos results in increased expression of BAX mRNA]; Berberine inhibits the reaction [Mercuric Chloride results in increased expression of BAX protein]
Berberine results in increased expression of BAX mRNA; Berberine results in increased expression of BAX protein
[Berberine co-treated with Cisplatin] results in increased expression of BAX protein; [Berberine co-treated with Niacinamide] results in increased expression of BAX protein; Acetylcysteine inhibits the reaction [[Berberine co-treated with Cisplatin] results in increased expression of BAX protein]; SRT1720 inhibits the reaction [Berberine results in increased expression of BAX protein]		 CTD PMID:16505103 PMID:20656010 PMID:25600690 PMID:26712469 PMID:30138605 More... NCBI chr19:48,954,875...48,961,798
Ensembl chr19:48,954,815...48,961,798 		JBrowse link
G BBC3 BCL2 binding component 3 increases expression
multiple interactions		 EXP Berberine results in increased expression of BBC3 mRNA
[Berberine co-treated with Niacinamide] results in increased expression of BBC3 mRNA		 CTD PMID:26712469 NCBI chr19:47,220,824...47,232,860
Ensembl chr19:47,220,822...47,232,766 		JBrowse link
G BCL2 BCL2 apoptosis regulator decreases expression
increases expression
multiple interactions		 EXP
ISO		 Berberine results in decreased expression of BCL2 mRNA; Berberine results in decreased expression of BCL2 protein
Berberine results in increased expression of BCL2 protein
Berberine inhibits the reaction [Chlorpyrifos results in decreased expression of BCL2 mRNA]; Berberine inhibits the reaction [Mercuric Chloride results in decreased expression of BCL2 protein]; Berberine inhibits the reaction [Thioacetamide results in increased expression of BCL2 mRNA]
[Berberine co-treated with Cisplatin] results in decreased expression of BCL2 protein; [Berberine co-treated with Niacinamide] results in decreased expression of BCL2 protein; Berberine inhibits the reaction [Glucose results in decreased expression of BCL2 protein]		 CTD PMID:16505103 PMID:20656010 PMID:23954465 PMID:24751971 PMID:25600690 More... NCBI chr18:63,123,346...63,320,090
Ensembl chr18:63,123,346...63,320,128 		JBrowse link
G BCL2L1 BCL2 like 1 decreases expression EXP Berberine results in decreased expression of BCL2L1 protein CTD PMID:16505103 NCBI chr20:31,664,452...31,723,963
Ensembl chr20:31,664,452...31,723,989 		JBrowse link
G BCL2L11 BCL2 like 11 multiple interactions
increases expression		 EXP [Berberine co-treated with Niacinamide] results in increased expression of BCL2L11 mRNA
Berberine results in increased expression of BCL2L11 mRNA		 CTD PMID:26712469 NCBI chr 2:111,120,914...111,168,445
Ensembl chr 2:111,119,378...111,168,444 		JBrowse link
G BECN1 beclin 1 multiple interactions ISO Berberine inhibits the reaction [Chlorpyrifos results in decreased expression of BECN1 mRNA]
Berberine promotes the reaction [[Water deficiency co-treated with NG-Nitroarginine Methyl Ester co-treated with Indomethacin co-treated with Iohexol] results in increased expression of BECN1 protein]		 CTD PMID:35439518 PMID:38705399 NCBI chr17:42,810,132...42,824,282
Ensembl chr17:42,810,134...42,833,350 		JBrowse link
G BGLAP bone gamma-carboxyglutamate protein increases expression
multiple interactions		 EXP Berberine results in increased expression of BGLAP mRNA; Berberine results in increased expression of BGLAP protein
CTNNB1 mutant form inhibits the reaction [Berberine results in increased expression of BGLAP protein]; DKK1 protein inhibits the reaction [Berberine results in increased expression of BGLAP protein]		 CTD PMID:26478571 NCBI chr 1:156,242,184...156,243,317
Ensembl chr 1:156,242,184...156,243,317 		JBrowse link
G BIRC5 baculoviral IAP repeat containing 5 affects binding EXP Berberine binds to BIRC5 promoter CTD PMID:17968851 NCBI chr17:78,214,253...78,225,635
Ensembl chr17:78,214,186...78,225,636 		JBrowse link
G BNIP3 BCL2 interacting protein 3 multiple interactions
increases expression		 EXP
ISO		 [Cisplatin co-treated with Berberine] results in increased expression of BNIP3 protein
Berberine promotes the reaction [[Water deficiency co-treated with NG-Nitroarginine Methyl Ester co-treated with Indomethacin co-treated with Iohexol] results in increased expression of BNIP3 protein]
Berberine results in increased expression of BNIP3 protein		 CTD PMID:36070022 PMID:38705399 NCBI chr10:131,967,684...131,981,923
Ensembl chr10:131,967,684...131,981,967 		JBrowse link
G BNIP3L BCL2 interacting protein 3 like multiple interactions
increases expression		 EXP [Cisplatin co-treated with Berberine] results in increased expression of BNIP3L protein; BNIP3L protein affects the reaction [[Berberine co-treated with Cisplatin] results in increased lipidation of MAP1LC3B protein]
Berberine results in increased expression of BNIP3L protein		 CTD PMID:36070022 NCBI chr 8:26,383,054...26,413,127
Ensembl chr 8:26,383,054...26,505,636 		JBrowse link
G CASP1 caspase 1 multiple interactions ISO Berberine inhibits the reaction [[Water deficiency co-treated with NG-Nitroarginine Methyl Ester co-treated with Indomethacin co-treated with Iohexol] results in increased expression of and results in increased cleavage of CASP1 protein]; Berberine inhibits the reaction [[Water deficiency co-treated with NG-Nitroarginine Methyl Ester co-treated with Indomethacin co-treated with Iohexol] results in increased expression of CASP1 mRNA] CTD PMID:38705399 NCBI chr11:105,025,443...105,036,686
Ensembl chr11:105,025,397...105,035,250 		JBrowse link
G CASP3 caspase 3 multiple interactions
increases activity
increases cleavage
increases expression		 EXP
ISO		 [Berberine co-treated with Cisplatin] results in increased cleavage of CASP3 protein; [Berberine co-treated with Niacinamide] results in increased cleavage of CASP3 protein; Acetylcysteine inhibits the reaction [[Berberine co-treated with Cisplatin] results in increased cleavage of CASP3 protein]; Berberine results in increased cleavage of and results in increased activity of CASP3 protein
Berberine inhibits the reaction [Particulate Matter results in increased expression of CASP3 protein]
Berberine increases activity of CASP3 protein in colon epithelial cells
Berberine results in increased cleavage of CASP3 protein
[Berberine co-treated with Thioacetamide] results in increased expression of CASP3 mRNA; Berberine inhibits the reaction [Chlorpyrifos results in increased expression of CASP3 mRNA]; Berberine inhibits the reaction [Mercuric Chloride results in increased activity of CASP3 protein]; Berberine inhibits the reaction [Mercuric Chloride results in increased expression of CASP3 mRNA]
Berberine results in increased activity of CASP3 protein
Berberine results in increased expression of CASP3 mRNA		 CTD
RGD		 PMID:16505103 PMID:20656010 PMID:25600690 PMID:26712469 PMID:30138605 More... RGD:152995489 NCBI chr 4:184,627,696...184,649,447
Ensembl chr 4:184,627,696...184,650,062 		JBrowse link
G CASP8 caspase 8 increases activity EXP Berberine results in increased activity of CASP8 protein CTD PMID:20656010 NCBI chr 2:201,233,463...201,287,711
Ensembl chr 2:201,233,443...201,361,836 		JBrowse link
G CASP9 caspase 9 increases cleavage
multiple interactions		 EXP
ISO		 Berberine results in increased cleavage of CASP9 protein
Berberine inhibits the reaction [Particulate Matter results in increased expression of CASP9 protein]
[Berberine co-treated with Thioacetamide] results in increased expression of CASP9 mRNA
[Berberine co-treated with Niacinamide] results in increased cleavage of CASP9 protein		 CTD PMID:16505103 PMID:26712469 PMID:30138605 PMID:37839514 NCBI chr 1:15,491,401...15,524,912
Ensembl chr 1:15,490,832...15,526,534 		JBrowse link
G CAT catalase multiple interactions ISO Berberine affects the reaction [[Streptozocin co-treated with Dietary Carbohydrates co-treated with Dietary Fats] affects the activity of CAT protein]; Berberine inhibits the reaction [acetamiprid results in decreased activity of CAT protein]; Berberine inhibits the reaction [Bortezomib results in decreased expression of CAT protein]; Berberine inhibits the reaction [Chlorpyrifos results in decreased activity of CAT protein]; Berberine inhibits the reaction [Mercuric Chloride results in decreased activity of CAT protein]; Berberine inhibits the reaction [Thioacetamide results in decreased activity of CAT protein]
Berberine inhibits the reaction [[Lipopolysaccharides co-treated with Galactosamine] results in decreased expression of CAT protein]; Berberine inhibits the reaction [Particulate Matter results in decreased expression of CAT protein]		 CTD PMID:20828602 PMID:24751971 PMID:25600690 PMID:30138605 PMID:33460233 More... NCBI chr11:34,438,934...34,472,060
Ensembl chr11:34,438,934...34,472,060 		JBrowse link
G CCL2 C-C motif chemokine ligand 2 multiple interactions EXP
ISO		 Berberine inhibits the reaction [IL1B protein results in increased expression of CCL2 mRNA]; Berberine inhibits the reaction [IL1B protein results in increased secretion of CCL2 protein]; Berberine inhibits the reaction [TNF protein results in increased expression of CCL2 mRNA]; Berberine inhibits the reaction [TNF protein results in increased secretion of CCL2 protein]
Berberine inhibits the reaction [[Lipopolysaccharides co-treated with Galactosamine] results in increased expression of CCL2 protein]; Berberine inhibits the reaction [[Water deficiency co-treated with NG-Nitroarginine Methyl Ester co-treated with Indomethacin co-treated with Iohexol] results in increased expression of CCL2 mRNA]		 CTD PMID:16391493 PMID:35691465 PMID:38705399 NCBI chr17:34,255,285...34,257,203
Ensembl chr17:34,255,274...34,257,208 		JBrowse link
G CCND1 cyclin D1 decreases expression
multiple interactions		 EXP Berberine results in decreased expression of CCND1 protein
Berberine inhibits the reaction [CDK4 mRNA binds to CCND1 mRNA]		 CTD PMID:16505103 PMID:33325633 PMID:36822301 NCBI chr11:69,641,156...69,654,474
Ensembl chr11:69,641,156...69,654,474 		JBrowse link
G CCND2 cyclin D2 decreases expression EXP Berberine results in decreased expression of CCND2 protein CTD PMID:16505103 NCBI chr12:4,273,762...4,305,353
Ensembl chr12:4,269,771...4,305,353 		JBrowse link
G CCNE1 cyclin E1 decreases expression EXP Berberine results in decreased expression of CCNE1 protein CTD PMID:16505103 NCBI chr19:29,811,991...29,824,312
Ensembl chr19:29,811,991...29,824,312 		JBrowse link
G CCNT1 cyclin T1 multiple interactions ISO Berberine affects the reaction [[Streptozocin co-treated with Dietary Carbohydrates co-treated with Dietary Fats] affects the expression of CCNT1 mRNA]; Berberine affects the reaction [[Streptozocin co-treated with Dietary Carbohydrates co-treated with Dietary Fats] affects the expression of CCNT1 protein] CTD PMID:20828602 NCBI chr12:48,688,458...48,716,707
Ensembl chr12:48,688,458...48,716,998 		JBrowse link
G CD36 CD36 molecule (CD36 blood group) multiple interactions
increases expression		 EXP
ISO		 15-deoxyprostaglandin J2 promotes the reaction [Berberine results in increased expression of CD36 mRNA]; 2-(2-amino-3-methoxyphenyl)-4H-1-benzopyran-4-one inhibits the reaction [Berberine results in increased expression of CD36 protein]; Berberine promotes the reaction [15-deoxyprostaglandin J2 results in increased expression of CD36 mRNA]; Berberine results in increased expression of and affects the localization of CD36 protein; CEBPB protein promotes the reaction [Berberine results in increased expression of CD36 mRNA]
Berberine results in increased expression of CD36 mRNA; Berberine results in increased expression of CD36 protein		 CTD PMID:28038998 PMID:29408570 NCBI chr 7:80,602,207...80,679,274
Ensembl chr 7:80,369,575...80,679,277 		JBrowse link
G CDH1 cadherin 1 multiple interactions ISO Berberine inhibits the reaction [Particulate Matter results in decreased expression of CDH1 mRNA] CTD PMID:37839514 NCBI chr16:68,737,292...68,835,537
Ensembl chr16:68,737,292...68,835,537 		JBrowse link
G CDH2 cadherin 2 decreases expression EXP Berberine results in decreased expression of CDH2 mRNA CTD PMID:26478571 NCBI chr18:27,932,879...28,177,130
Ensembl chr18:27,932,879...28,177,946 		JBrowse link
G CDK2 cyclin dependent kinase 2 decreases expression EXP Berberine results in decreased expression of CDK2 protein CTD PMID:16505103 NCBI chr12:55,966,830...55,972,789
Ensembl chr12:55,966,781...55,972,789 		JBrowse link
G CDK4 cyclin dependent kinase 4 decreases expression
multiple interactions		 EXP Berberine results in decreased expression of CDK4 protein
Berberine inhibits the reaction [CDK4 mRNA binds to CCND1 mRNA]		 CTD PMID:16505103 PMID:36822301 NCBI chr12:57,747,727...57,752,310
Ensembl chr12:57,747,727...57,756,013 		JBrowse link
G CDK6 cyclin dependent kinase 6 decreases expression EXP Berberine results in decreased expression of CDK6 protein CTD PMID:16505103 NCBI chr 7:92,604,921...92,836,573
Ensembl chr 7:92,604,921...92,836,573 		JBrowse link
G CDK9 cyclin dependent kinase 9 multiple interactions ISO Berberine affects the reaction [[Streptozocin co-treated with Dietary Carbohydrates co-treated with Dietary Fats] affects the expression of CDK9 mRNA]; Berberine affects the reaction [[Streptozocin co-treated with Dietary Carbohydrates co-treated with Dietary Fats] affects the expression of CDK9 protein] CTD PMID:20828602 NCBI chr 9:127,786,034...127,790,792
Ensembl chr 9:127,785,679...127,790,792 		JBrowse link
G CDKN1A cyclin dependent kinase inhibitor 1A increases expression EXP Berberine results in increased expression of CDKN1A protein CTD PMID:16505103 PMID:23747414 NCBI chr 6:36,676,463...36,687,332
Ensembl chr 6:36,676,460...36,687,337 		JBrowse link
G CDKN1B cyclin dependent kinase inhibitor 1B increases expression EXP Berberine results in increased expression of CDKN1B protein CTD PMID:16505103 NCBI chr12:12,717,368...12,722,369
Ensembl chr12:12,685,498...12,722,369 		JBrowse link
G CDKN1C cyclin dependent kinase inhibitor 1C increases expression EXP Berberine results in increased expression of CDKN1C mRNA CTD PMID:26478571 NCBI chr11:2,883,218...2,885,775
Ensembl chr11:2,883,213...2,885,775 		JBrowse link
G CEBPA CCAAT enhancer binding protein alpha multiple interactions
decreases expression		 ISO
EXP		 Berberine inhibits the reaction [Clozapine results in increased expression of CEBPA mRNA]; Berberine inhibits the reaction [Clozapine results in increased expression of CEBPA protein]; Berberine inhibits the reaction [Risperidone results in increased expression of CEBPA mRNA]; Berberine inhibits the reaction [Risperidone results in increased expression of CEBPA protein]
Berberine results in decreased expression of CEBPA mRNA; Berberine results in decreased expression of CEBPA protein		 CTD PMID:20564506 PMID:26478571 PMID:37511356 NCBI chr19:33,299,934...33,302,534
Ensembl chr19:33,299,934...33,302,534 		JBrowse link
G CEBPB CCAAT enhancer binding protein beta increases expression
affects phosphorylation
multiple interactions		 EXP
ISO		 Berberine results in increased expression of CEBPB mRNA
Berberine affects the phosphorylation of CEBPB protein
2-(2-amino-3-methoxyphenyl)-4H-1-benzopyran-4-one inhibits the reaction [Berberine results in increased phosphorylation of CEBPB protein]; CEBPB protein promotes the reaction [Berberine results in increased expression of CD36 mRNA]		 CTD PMID:28038998 NCBI chr20:50,190,583...50,192,690
Ensembl chr20:50,190,830...50,192,668 		JBrowse link
G CHEK1 checkpoint kinase 1 increases expression EXP Berberine results in increased expression of CHEK1 protein modified form CTD PMID:23747414 NCBI chr11:125,625,136...125,681,124
Ensembl chr11:125,625,163...125,676,255 		JBrowse link
G CHEK2 checkpoint kinase 2 increases expression EXP Berberine results in increased expression of CHEK2 protein modified form CTD PMID:23747414 NCBI chr22:28,687,743...28,741,834
Ensembl chr22:28,687,743...28,742,422 		JBrowse link
G COL10A1 collagen type X alpha 1 chain increases expression EXP Berberine results in increased expression of COL10A1 mRNA CTD PMID:26478571 NCBI chr 6:116,118,909...116,217,144
Ensembl chr 6:116,118,909...116,158,747 		JBrowse link
G COL1A1 collagen type I alpha 1 chain increases expression
multiple interactions		 EXP
ISO		 Berberine results in increased expression of COL1A1 mRNA
Berberine inhibits the reaction [Particulate Matter results in increased expression of COL1A1 mRNA]		 CTD PMID:26478571 PMID:37839514 NCBI chr17:50,184,101...50,201,631
Ensembl chr17:50,184,101...50,201,632 		JBrowse link
G COL2A1 collagen type II alpha 1 chain decreases expression EXP Berberine results in decreased expression of COL2A1 mRNA CTD PMID:26478571 NCBI chr12:47,972,967...48,006,212
Ensembl chr12:47,972,967...48,004,554 		JBrowse link
G COL3A1 collagen type III alpha 1 chain multiple interactions ISO Berberine inhibits the reaction [Particulate Matter results in increased expression of COL3A1 mRNA] CTD PMID:37839514 NCBI chr 2:188,974,373...189,012,746
Ensembl chr 2:188,974,373...189,012,746 		JBrowse link
G COX4I1 cytochrome c oxidase subunit 4I1 multiple interactions ISO Berberine inhibits the reaction [acetamiprid results in decreased expression of COX4I1 mRNA] CTD PMID:37350525 NCBI chr16:85,799,695...85,807,068
Ensembl chr16:85,798,633...85,807,068 		JBrowse link
G CPT1A carnitine palmitoyltransferase 1A multiple interactions ISO Berberine inhibits the reaction [Ethanol results in decreased expression of CPT1A mRNA] CTD PMID:25455889 NCBI chr11:68,754,620...68,844,277
Ensembl chr11:68,754,620...68,844,410 		JBrowse link
G CREB1 cAMP responsive element binding protein 1 multiple interactions ISO Berberine inhibits the reaction [Bortezomib results in decreased expression of CREB1 protein] CTD PMID:35121005 NCBI chr 2:207,529,962...207,605,988
Ensembl chr 2:207,529,737...207,605,988 		JBrowse link
G CREBBP CREB binding protein increases expression EXP Berberine results in increased expression of CREBBP mRNA CTD PMID:27311644 NCBI chr16:3,725,054...3,880,713
Ensembl chr16:3,725,054...3,880,713 		JBrowse link
G CST3 cystatin C multiple interactions ISO Berberine inhibits the reaction [[Water deficiency co-treated with NG-Nitroarginine Methyl Ester co-treated with Indomethacin co-treated with Iohexol] results in increased expression of CST3 protein] CTD PMID:38705399 NCBI chr20:23,626,706...23,637,955
Ensembl chr20:23,626,706...23,638,473 		JBrowse link
G CTNNB1 catenin beta 1 increases expression
multiple interactions		 EXP Berberine results in increased expression of CTNNB1 protein
CTNNB1 mutant form inhibits the reaction [Berberine results in increased expression of BGLAP protein]; CTNNB1 mutant form inhibits the reaction [Berberine results in increased expression of RUNX2 mRNA]; CTNNB1 mutant form inhibits the reaction [Berberine results in increased expression of SPP1 protein]; DKK1 protein inhibits the reaction [Berberine results in increased expression of CTNNB1 protein]		 CTD PMID:26478571 NCBI chr 3:41,199,505...41,240,443
Ensembl chr 3:41,194,741...41,260,096 		JBrowse link
G CTSD cathepsin D multiple interactions
decreases cleavage		 EXP GSK2795039 affects the reaction [Berberine results in decreased cleavage of CTSD protein] CTD PMID:36070022 NCBI chr11:1,752,755...1,763,927
Ensembl chr11:1,752,752...1,764,573 		JBrowse link
G CTSL cathepsin L multiple interactions
decreases cleavage		 EXP Acetylcysteine inhibits the reaction [Berberine results in decreased cleavage of CTSL protein]; GSK2795039 affects the reaction [Berberine results in decreased cleavage of CTSL protein] CTD PMID:36070022 NCBI chr 9:87,726,119...87,731,469
Ensembl chr 9:87,724,051...87,731,469 		JBrowse link
G CXCL8 C-X-C motif chemokine ligand 8 multiple interactions EXP Berberine inhibits the reaction [IL1B protein results in increased expression of CXCL8 mRNA]; Berberine inhibits the reaction [IL1B protein results in increased secretion of CXCL8 protein]; Berberine inhibits the reaction [Mustard Gas results in increased secretion of CXCL8 protein]; Berberine inhibits the reaction [TNF protein results in increased expression of CXCL8 mRNA]; Berberine inhibits the reaction [TNF protein results in increased secretion of CXCL8 protein] CTD PMID:16391493 PMID:28916288 NCBI chr 4:73,740,569...73,743,716
Ensembl chr 4:73,740,519...73,743,716 		JBrowse link
G CYBB cytochrome b-245 beta chain multiple interactions EXP Berberine promotes the reaction [CYBB protein binds to NCF1 protein binds to NCF2 protein binds to RAC2 protein]; Berberine promotes the reaction [CYBB protein binds to NCF1 protein]; Berberine promotes the reaction [CYBB protein binds to NCF2 protein]; Berberine promotes the reaction [CYBB protein binds to RAC2 protein] CTD PMID:36070022 NCBI chr  X:37,780,059...37,813,461
Ensembl chr  X:37,780,018...37,813,461 		JBrowse link
G CYCS cytochrome c, somatic affects localization
multiple interactions		 EXP Berberine affects the localization of CYCS protein
[Berberine co-treated with Cisplatin] results in increased expression of CYCS protein		 CTD PMID:16505103 PMID:36070022 NCBI chr 7:25,118,656...25,125,260
Ensembl chr 7:25,118,656...25,125,260 		JBrowse link
G CYP17A1 cytochrome P450 family 17 subfamily A member 1 multiple interactions ISO Berberine inhibits the reaction [Dexamethasone results in increased expression of CYP17A1 mRNA] CTD PMID:20462044 NCBI chr10:102,830,531...102,837,413
Ensembl chr10:102,830,531...102,837,472 		JBrowse link
G CYP1A1 cytochrome P450 family 1 subfamily A member 1 decreases activity
increases expression
multiple interactions		 EXP
ISO		 Berberine results in decreased activity of CYP1A1 protein
Berberine results in increased expression of CYP1A1 mRNA
Berberine inhibits the reaction [beta-Naphthoflavone results in increased expression of CYP1A1 mRNA]		 CTD PMID:16046213 PMID:22342832 PMID:24583342 NCBI chr15:74,719,542...74,725,528
Ensembl chr15:74,719,542...74,725,536 		JBrowse link
G CYP1A2 cytochrome P450 family 1 subfamily A member 2 multiple interactions ISO Berberine inhibits the reaction [beta-Naphthoflavone results in increased expression of CYP1A2 mRNA] CTD PMID:22342832 NCBI chr15:74,748,845...74,756,607
Ensembl chr15:74,748,845...74,756,607 		JBrowse link
G CYP2B6 cytochrome P450 family 2 subfamily B member 6 multiple interactions
increases expression		 ISO Berberine inhibits the reaction [Streptozocin results in increased expression of CYP2B10 mRNA]; Berberine promotes the reaction [Phenobarbital results in increased expression of CYP2B10 mRNA]
Berberine results in increased expression of CYP2B10 mRNA		 CTD PMID:22342832 NCBI chr19:40,991,282...41,018,398
Ensembl chr19:40,991,282...41,018,398 		JBrowse link
G CYP2E1 cytochrome P450 family 2 subfamily E member 1 decreases expression
multiple interactions		 ISO Berberine results in decreased expression of CYP2E1 mRNA
Berberine inhibits the reaction [Ethanol results in increased expression of CYP2E1 protein]; Berberine inhibits the reaction [Isoniazid results in increased expression of CYP2E1 mRNA]		 CTD PMID:22342832 PMID:25455889 NCBI chr10:133,527,363...133,539,123
Ensembl chr10:133,520,406...133,561,220 		JBrowse link
G CYP3A4 cytochrome P450 family 3 subfamily A member 4 multiple interactions
decreases expression
decreases activity		 EXP
ISO		 [Berberine results in increased activity of NR1I2 protein] which results in increased expression of CYP3A4 mRNA
Berberine results in decreased expression of CYP3A4 mRNA; Berberine results in decreased expression of CYP3A4 protein
Berberine results in decreased activity of CYP3A4 protein
Atorvastatin promotes the reaction [Berberine results in decreased activity of CYP3A4 protein]; Berberine promotes the reaction [Atorvastatin results in decreased activity of CYP3A4 protein]; Berberine promotes the reaction [Atorvastatin results in decreased expression of CYP3A4 mRNA]; Berberine promotes the reaction [Atorvastatin results in decreased expression of CYP3A4 protein]; Berberine promotes the reaction [Simvastatin results in decreased activity of CYP3A4 protein]; Berberine promotes the reaction [Simvastatin results in decreased expression of CYP3A4 protein]; Simvastatin promotes the reaction [Berberine results in decreased activity of CYP3A4 protein]		 CTD PMID:21524698 PMID:30086269 NCBI chr 7:99,756,967...99,784,184
Ensembl chr 7:99,756,960...99,784,248 		JBrowse link
G DKK1 dickkopf WNT signaling pathway inhibitor 1 multiple interactions EXP DKK1 protein inhibits the reaction [Berberine results in increased expression of BGLAP protein]; DKK1 protein inhibits the reaction [Berberine results in increased expression of CTNNB1 protein]; DKK1 protein inhibits the reaction [Berberine results in increased expression of RUNX2 mRNA]; DKK1 protein inhibits the reaction [Berberine results in increased expression of SPP1 protein] CTD PMID:26478571 NCBI chr10:52,314,281...52,317,657
Ensembl chr10:52,314,281...52,318,042 		JBrowse link
G DNMT1 DNA methyltransferase 1 decreases expression EXP Berberine results in decreased expression of DNMT1 mRNA CTD PMID:27311644 NCBI chr19:10,133,346...10,194,953
Ensembl chr19:10,133,342...10,231,286 		JBrowse link
G DNMT3B DNA methyltransferase 3 beta decreases expression EXP Berberine results in decreased expression of DNMT3B mRNA CTD PMID:27311644 NCBI chr20:32,762,385...32,809,356
Ensembl chr20:32,762,385...32,809,359 		JBrowse link
G DZIP3 DAZ interacting zinc finger protein 3 increases expression EXP Berberine results in increased expression of DZIP3 mRNA CTD PMID:27311644 NCBI chr 3:108,589,510...108,694,840
Ensembl chr 3:108,589,705...108,694,840 		JBrowse link
G EGF epidermal growth factor multiple interactions EXP 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one inhibits the reaction [EGF protein inhibits the reaction [Berberine results in decreased activity of MMP2 protein]]; 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one inhibits the reaction [EGF protein inhibits the reaction [Berberine results in decreased activity of MMP9 protein]]; EGF protein inhibits the reaction [Berberine results in decreased activity of MMP2 protein]; EGF protein inhibits the reaction [Berberine results in decreased activity of MMP9 protein] CTD PMID:33325633 NCBI chr 4:109,912,883...110,013,766
Ensembl chr 4:109,912,883...110,013,766 		JBrowse link
G EGFR epidermal growth factor receptor decreases expression EXP Berberine results in decreased expression of EGFR protein CTD PMID:33325633 NCBI chr 7:55,019,017...55,211,628
Ensembl chr 7:55,019,017...55,211,628 		JBrowse link
G EIF4EBP1 eukaryotic translation initiation factor 4E binding protein 1 multiple interactions EXP Berberine results in decreased phosphorylation of and results in increased expression of EIF4EBP1 protein CTD PMID:23363784 NCBI chr 8:38,030,534...38,060,365
Ensembl chr 8:38,030,534...38,060,365 		JBrowse link
G EP300 E1A binding protein p300 increases expression EXP Berberine results in increased expression of EP300 mRNA CTD PMID:27311644 NCBI chr22:41,092,592...41,180,077
Ensembl chr22:41,092,510...41,180,077 		JBrowse link
G ERBB2 erb-b2 receptor tyrosine kinase 2 multiple interactions EXP benzyloxycarbonylleucyl-leucyl-leucine aldehyde inhibits the reaction [Berberine results in decreased expression of ERBB2 protein]; Berberine results in decreased expression of and results in increased ubiquitination of ERBB2 protein CTD PMID:33325633 NCBI chr17:39,688,094...39,728,658
Ensembl chr17:39,687,914...39,730,426 		JBrowse link
G ESR1 estrogen receptor 1 multiple interactions EXP Berberine inhibits the reaction [Estradiol results in increased activity of ESR1 protein] CTD PMID:30818834 NCBI chr 6:151,656,672...152,129,619
Ensembl chr 6:151,656,691...152,129,619 		JBrowse link
G ESRRA estrogen related receptor alpha multiple interactions EXP Berberine inhibits the reaction [XCT790 results in decreased activity of ESRRA protein] CTD PMID:30818834 NCBI chr11:64,305,524...64,316,743
Ensembl chr11:64,305,497...64,316,743 		JBrowse link
G FABP4 fatty acid binding protein 4 decreases expression
increases expression
multiple interactions		 EXP
ISO		 Berberine results in decreased expression of FABP4 mRNA
Berberine results in increased expression of FABP4 mRNA
15-deoxyprostaglandin J2 promotes the reaction [Berberine results in increased expression of FABP4 mRNA]; Berberine promotes the reaction [15-deoxyprostaglandin J2 results in increased expression of FABP4 mRNA]		 CTD PMID:26478571 PMID:29408570 NCBI chr 8:81,478,419...81,483,233
Ensembl chr 8:81,478,419...81,483,236 		JBrowse link
G FAS Fas cell surface death receptor multiple interactions
increases expression		 ISO
EXP		 [Clozapine co-treated with Berberine] results in decreased expression of FAS mRNA; Berberine inhibits the reaction [Risperidone results in increased expression of FAS mRNA]
Berberine results in increased expression of FAS mRNA; Berberine results in increased expression of FAS protein		 CTD PMID:20564506 PMID:20656010 NCBI chr10:88,964,050...89,017,059
Ensembl chr10:88,953,813...89,029,605 		JBrowse link
G FASLG Fas ligand increases expression EXP Berberine results in increased expression of FASLG mRNA; Berberine results in increased expression of FASLG protein CTD PMID:20656010 NCBI chr 1:172,659,103...172,666,876
Ensembl chr 1:172,659,103...172,666,876 		JBrowse link
G FN1 fibronectin 1 multiple interactions ISO Berberine inhibits the reaction [Thioacetamide results in increased expression of FN1 mRNA]
Berberine inhibits the reaction [Particulate Matter results in increased expression of FN1 mRNA]		 CTD PMID:30138605 PMID:37839514 NCBI chr 2:215,360,865...215,436,068
Ensembl chr 2:215,360,440...215,436,073 		JBrowse link
G FOXO1 forkhead box O1 multiple interactions EXP [Berberine co-treated with Niacinamide] results in increased expression of and results in increased acetylation of FOXO1 protein; Berberine results in increased expression of and results in increased acetylation of FOXO1 protein CTD PMID:26712469 NCBI chr13:40,555,667...40,666,641
Ensembl chr13:40,555,667...40,666,641 		JBrowse link
G FOXO3 forkhead box O3 multiple interactions EXP [Berberine co-treated with Niacinamide] results in increased expression of and results in increased acetylation of FOXO3 protein; Berberine results in increased expression of and results in increased acetylation of FOXO3 protein CTD PMID:26712469 NCBI chr 6:108,559,825...108,684,774
Ensembl chr 6:108,559,835...108,684,774 		JBrowse link
G FUNDC1 FUN14 domain containing 1 increases expression
multiple interactions		 EXP Berberine results in increased expression of FUNDC1 protein
[Cisplatin co-treated with Berberine] results in increased expression of FUNDC1 protein; FUNDC1 protein affects the reaction [[Berberine co-treated with Cisplatin] results in increased lipidation of MAP1LC3B protein]		 CTD PMID:36070022 NCBI chr  X:44,523,639...44,542,859
Ensembl chr  X:44,523,639...44,542,859 		JBrowse link
G GATA2 GATA binding protein 2 increases expression ISO Berberine results in increased expression of GATA2 mRNA CTD PMID:37511356 NCBI chr 3:128,479,422...128,493,201
Ensembl chr 3:128,479,427...128,493,201 		JBrowse link
G GATA3 GATA binding protein 3 increases expression ISO Berberine results in increased expression of GATA3 mRNA CTD PMID:37511356 NCBI chr10:8,045,333...8,075,198
Ensembl chr10:8,045,378...8,075,198 		JBrowse link
G GCLC glutamate-cysteine ligase catalytic subunit multiple interactions ISO Berberine inhibits the reaction [Bortezomib results in increased expression of GCLC mRNA] CTD PMID:35121005 NCBI chr 6:53,497,341...53,545,101
Ensembl chr 6:53,497,341...53,616,970 		JBrowse link
G GCLM glutamate-cysteine ligase modifier subunit multiple interactions ISO Berberine inhibits the reaction [Bortezomib results in increased expression of GCLM mRNA] CTD PMID:35121005 NCBI chr 1:93,885,199...93,909,430
Ensembl chr 1:93,885,199...93,909,456 		JBrowse link
G GDF5 growth differentiation factor 5 decreases expression EXP Berberine results in decreased expression of GDF5 mRNA CTD PMID:26478571 NCBI chr20:35,433,347...35,454,749
Ensembl chr20:35,433,347...35,454,746 		JBrowse link
G GFAP glial fibrillary acidic protein multiple interactions ISO Berberine inhibits the reaction [Bortezomib results in increased expression of GFAP mRNA] CTD PMID:35121005 NCBI chr17:44,903,159...44,915,500
Ensembl chr17:44,903,159...44,916,937 		JBrowse link
G GPT glutamic--pyruvic transaminase multiple interactions ISO Berberine inhibits the reaction [Ethanol results in increased activity of GPT protein]
Berberine inhibits the reaction [Mercuric Chloride results in increased activity of GPT protein]; Berberine inhibits the reaction [Thioacetamide results in increased activity of GPT protein]		 CTD PMID:24751971 PMID:25455889 PMID:30138605 NCBI chr 8:144,503,068...144,507,172
Ensembl chr 8:144,502,973...144,507,174 		JBrowse link
G GPX1 glutathione peroxidase 1 multiple interactions ISO Berberine inhibits the reaction [Mercuric Chloride results in decreased expression of GPX1 mRNA] CTD PMID:24751971 PMID:33460233 NCBI chr 3:49,357,176...49,358,353
Ensembl chr 3:49,357,174...49,358,605 		JBrowse link
G GSK3B glycogen synthase kinase 3 beta multiple interactions
increases phosphorylation		 ISO
EXP		 Berberine inhibits the reaction [Dexamethasone results in decreased expression of GSK3B mRNA]
Berberine results in increased phosphorylation of GSK3B protein
Berberine inhibits the reaction [Glucose results in decreased phosphorylation of GSK3B protein]		 CTD PMID:20462044 PMID:23954465 NCBI chr 3:119,821,321...120,094,447
Ensembl chr 3:119,821,321...120,094,994 		JBrowse link
G GSR glutathione-disulfide reductase multiple interactions ISO Berberine inhibits the reaction [Chlorpyrifos results in decreased activity of GSR protein]; Berberine inhibits the reaction [Mercuric Chloride results in decreased activity of GSR protein] CTD PMID:24751971 PMID:25600690 PMID:33460233 PMID:35439518 NCBI chr 8:30,678,066...30,727,846
Ensembl chr 8:30,678,066...30,727,846 		JBrowse link
G H2AC11 H2A clustered histone 11 decreases expression EXP Berberine results in decreased expression of H2AC11 mRNA CTD PMID:27311644 NCBI chr 6:27,133,043...27,133,535
Ensembl chr 6:27,133,043...27,133,535 		JBrowse link
G H2AC12 H2A clustered histone 12 decreases expression EXP Berberine results in decreased expression of H2AC12 mRNA CTD PMID:27311644 NCBI chr 6:27,147,106...27,147,562
Ensembl chr 6:27,147,106...27,147,562 		JBrowse link
G H2AC14 H2A clustered histone 14 decreases expression EXP Berberine results in decreased expression of H2AC14 mRNA CTD PMID:27311644 NCBI chr 6:27,814,302...27,814,777
Ensembl chr 6:27,814,302...27,814,777 		JBrowse link
G H2AC15 H2A clustered histone 15 decreases expression EXP Berberine results in decreased expression of H2AC15 mRNA CTD PMID:27311644 NCBI chr 6:27,837,880...27,838,375
Ensembl chr 6:27,837,880...27,838,375 		JBrowse link
G H2AC17 H2A clustered histone 17 decreases expression EXP Berberine results in decreased expression of H2AC17 mRNA CTD PMID:27311644 NCBI chr 6:27,892,699...27,893,185
Ensembl chr 6:27,892,699...27,893,185 		JBrowse link
G H2AC18 H2A clustered histone 18 decreases expression EXP Berberine results in decreased expression of H2AC18 mRNA CTD PMID:27311644 NCBI chr 1:149,842,218...149,842,750
Ensembl chr 1:149,842,218...149,842,750 		JBrowse link
G H2AC25 H2A clustered histone 25 decreases expression EXP Berberine results in decreased expression of H2AC25 mRNA CTD PMID:27311644 NCBI chr 1:228,457,364...228,457,873
Ensembl chr 1:228,434,777...228,457,873 		JBrowse link
G H2AC4 H2A clustered histone 4 decreases expression EXP Berberine results in decreased expression of H2AC4 mRNA CTD PMID:27311644 NCBI chr 6:26,033,092...26,033,618
Ensembl chr 6:26,033,092...26,033,618 		JBrowse link
G H2AC6 H2A clustered histone 6 decreases expression EXP Berberine results in decreased expression of H2AC6 mRNA CTD PMID:27311644 NCBI chr 6:26,124,172...26,124,690
Ensembl chr 6:26,124,145...26,139,116 		JBrowse link
G H2AC8 H2A clustered histone 8 decreases expression EXP Berberine results in decreased expression of H2AC8 mRNA CTD PMID:27311644 NCBI chr 6:26,216,921...26,217,437
Ensembl chr 6:26,216,921...26,217,437 		JBrowse link
G H2AX H2A.X variant histone increases expression
decreases expression
multiple interactions		 EXP Berberine results in increased expression of H2AX protein modified form
Berberine results in decreased expression of H2AX mRNA; Berberine results in decreased expression of H2AX protein
TOP2A protein affects the reaction [Berberine results in increased expression of H2AX protein modified form]		 CTD PMID:23363784 PMID:23747414 PMID:27311644 NCBI chr11:119,093,874...119,095,465
Ensembl chr11:119,093,874...119,095,465 		JBrowse link
G H2BC11 H2B clustered histone 11 decreases expression EXP Berberine results in decreased expression of H2BC11 mRNA CTD PMID:27311644 NCBI chr 6:27,132,316...27,132,795
Ensembl chr 6:27,125,897...27,132,795 		JBrowse link
G H2BC12 H2B clustered histone 12 decreases expression EXP Berberine results in decreased expression of H2BC12 mRNA CTD PMID:27311644 NCBI chr 6:27,138,293...27,146,858
Ensembl chr 6:27,146,361...27,146,855 		JBrowse link
G H2BC13 H2B clustered histone 13 decreases expression EXP Berberine results in decreased expression of H2BC13 mRNA CTD PMID:27311644 NCBI chr 6:27,807,479...27,807,929
Ensembl chr 6:27,807,479...27,807,929 		JBrowse link
G H2BC14 H2B clustered histone 14 decreases expression EXP Berberine results in decreased expression of H2BC14 mRNA CTD PMID:27311644 NCBI chr 6:27,815,022...27,815,489
Ensembl chr 6:27,815,022...27,815,489 		JBrowse link
G H2BC15 H2B clustered histone 15 decreases expression EXP Berberine results in decreased expression of H2BC15 mRNA CTD PMID:27311644 NCBI chr 6:27,838,569...27,839,110
Ensembl chr 6:27,838,545...27,855,709 		JBrowse link
G H2BC17 H2B clustered histone 17 decreases expression EXP Berberine results in decreased expression of H2BC17 mRNA CTD PMID:27311644 NCBI chr 6:27,893,425...27,893,891
Ensembl chr 6:27,893,425...27,893,891 		JBrowse link
G H2BC4 H2B clustered histone 4 decreases expression EXP Berberine results in decreased expression of H2BC4 mRNA CTD PMID:27311644 NCBI chr 6:26,113,170...26,123,926
Ensembl chr 6:26,086,317...26,123,926 		JBrowse link
G H2BC5 H2B clustered histone 5 decreases expression EXP Berberine results in decreased expression of H2BC5 mRNA CTD PMID:27311644 NCBI chr 6:26,158,121...26,171,349
Ensembl chr 6:26,158,122...26,171,349 		JBrowse link
G H2BC6 H2B clustered histone 6 decreases expression EXP Berberine results in decreased expression of H2BC6 mRNA CTD PMID:27311644 NCBI chr 6:26,183,761...26,184,230
Ensembl chr 6:26,172,059...26,184,655 		JBrowse link
G H2BC7 H2B clustered histone 7 decreases expression EXP Berberine results in decreased expression of H2BC7 mRNA CTD PMID:27311644 NCBI chr 6:26,199,516...26,199,988
Ensembl chr 6:26,199,516...26,199,988 		JBrowse link
G H2BC8 H2B clustered histone 8 decreases expression EXP Berberine results in decreased expression of H2BC8 mRNA CTD PMID:27311644 NCBI chr 6:26,216,200...26,216,688
Ensembl chr 6:26,216,200...26,216,688 		JBrowse link
G H2BC9 H2B clustered histone 9 decreases expression EXP Berberine results in decreased expression of H2BC9 mRNA CTD PMID:27311644 NCBI chr 6:26,251,614...26,252,075
Ensembl chr 6:26,251,614...26,252,075 		JBrowse link
G H2BW2 H2B.W histone 2 decreases expression EXP Berberine results in decreased expression of H2BW2 mRNA CTD PMID:27311644 NCBI chr  X:104,039,956...104,042,454
Ensembl chr  X:104,039,956...104,042,454 		JBrowse link
G H3-3A H3.3 histone A decreases expression EXP Berberine results in decreased expression of H3-3A mRNA CTD PMID:27311644 NCBI chr 1:226,061,831...226,072,019
Ensembl chr 1:226,061,851...226,072,019 		JBrowse link
G H3-4 H3.4 histone, cluster member decreases expression EXP Berberine results in decreased expression of H3-4 mRNA CTD PMID:27311644 NCBI chr 1:228,424,845...228,425,360
Ensembl chr 1:228,424,845...228,425,360 		JBrowse link
G H3C1 H3 clustered histone 1 decreases expression EXP Berberine results in decreased expression of H3C1 mRNA CTD PMID:27311644 NCBI chr 6:26,020,451...26,020,958
Ensembl chr 6:26,020,451...26,020,958 		JBrowse link
G H3C10 H3 clustered histone 10 decreases expression EXP Berberine results in decreased expression of H3C10 mRNA CTD PMID:27311644 NCBI chr 6:27,810,051...27,810,536
Ensembl chr 6:27,810,051...27,811,300 		JBrowse link
G H3C12 H3 clustered histone 12 decreases expression EXP Berberine results in decreased expression of H3C12 mRNA CTD PMID:27311644 NCBI chr 6:27,890,315...27,890,826
Ensembl chr 6:27,890,315...27,893,106 		JBrowse link
G H3C2 H3 clustered histone 2 decreases expression EXP Berberine results in decreased expression of H3C2 mRNA CTD PMID:27311644 NCBI chr 6:26,031,589...26,032,099
Ensembl chr 6:26,031,589...26,032,099 		JBrowse link
G H3C4 H3 clustered histone 4 decreases expression EXP Berberine results in decreased expression of H3C4 mRNA CTD PMID:27311644 NCBI chr 6:26,196,784...26,199,293
Ensembl chr 6:26,196,784...26,197,286 		JBrowse link
G H3C7 H3 clustered histone 7 decreases expression EXP Berberine results in decreased expression of H3C7 mRNA CTD PMID:27311644 NCBI chr 6:26,250,142...26,250,635
Ensembl chr 6:26,250,142...26,250,635 		JBrowse link
G H3C8 H3 clustered histone 8 decreases expression EXP Berberine results in decreased expression of H3C8 mRNA CTD PMID:27311644 NCBI chr 6:26,270,918...26,271,413
Ensembl chr 6:26,270,918...26,271,413 		JBrowse link
G H4C14 H4 clustered histone 14 decreases expression EXP Berberine results in decreased expression of H4C14 mRNA CTD PMID:27311644 NCBI chr 1:149,832,657...149,833,052
Ensembl chr 1:149,832,657...149,839,767 		JBrowse link
G H4C2 H4 clustered histone 2 decreases expression EXP Berberine results in decreased expression of H4C2 mRNA CTD PMID:27311644 NCBI chr 6:26,026,896...26,027,283
Ensembl chr 6:26,026,896...26,027,283 		JBrowse link
G H4C3 H4 clustered histone 3 decreases expression EXP Berberine results in decreased expression of H4C3 mRNA CTD PMID:27311644 NCBI chr 6:26,103,933...26,104,337
Ensembl chr 6:26,103,933...26,104,337 		JBrowse link
G H4C8 H4 clustered histone 8 decreases expression EXP Berberine results in decreased expression of H4C8 mRNA CTD PMID:27311644 NCBI chr 6:26,285,126...26,285,534
Ensembl chr 6:26,277,609...26,285,638 		JBrowse link
G H4C9 H4 clustered histone 9 decreases expression EXP Berberine results in decreased expression of H4C9 mRNA CTD PMID:27311644 NCBI chr 6:27,139,282...27,139,678
Ensembl chr 6:27,139,282...27,139,678 		JBrowse link
G HAT1 histone acetyltransferase 1 increases expression EXP Berberine results in increased expression of HAT1 mRNA CTD PMID:27311644 NCBI chr 2:171,922,461...171,983,686
Ensembl chr 2:171,922,448...171,983,686 		JBrowse link
G HDAC2 histone deacetylase 2 decreases expression EXP Berberine results in decreased expression of HDAC2 mRNA CTD PMID:27311644 NCBI chr 6:113,933,028...113,971,148
Ensembl chr 6:113,933,028...114,011,308 		JBrowse link
G HDAC5 histone deacetylase 5 increases expression EXP Berberine results in increased expression of HDAC5 mRNA CTD PMID:27311644 NCBI chr17:44,076,753...44,123,641
Ensembl chr17:44,076,746...44,123,702 		JBrowse link
G HDAC8 histone deacetylase 8 decreases expression EXP Berberine results in decreased expression of HDAC8 mRNA CTD PMID:27311644 NCBI chr  X:72,329,516...72,572,843
Ensembl chr  X:72,329,516...72,573,101 		JBrowse link
G HDAC9 histone deacetylase 9 decreases expression
increases expression		 EXP Berberine results in decreased expression of HDAC9 mRNA
Berberine results in increased expression of HDAC9 mRNA		 CTD PMID:27311644 NCBI chr 7:18,086,825...19,002,416
Ensembl chr 7:18,086,949...19,002,416 		JBrowse link
G HGF hepatocyte growth factor multiple interactions
increases expression		 ISO
EXP		 Berberine inhibits the reaction [Bleomycin results in decreased expression of HGF mRNA]
15-deoxyprostaglandin J2 promotes the reaction [Berberine results in increased expression of HGF mRNA]; 15-deoxyprostaglandin J2 promotes the reaction [Berberine results in increased expression of HGF protein]; 2-chloro-5-nitrobenzanilide inhibits the reaction [Berberine results in increased expression of HGF protein]; Berberine promotes the reaction [15-deoxyprostaglandin J2 results in increased expression of HGF mRNA]; Berberine promotes the reaction [15-deoxyprostaglandin J2 results in increased expression of HGF protein]; Dactinomycin inhibits the reaction [Berberine results in increased expression of HGF protein]; PPARG mRNA promotes the reaction [Berberine results in increased expression of HGF protein]
Berberine results in increased expression of HGF mRNA; Berberine results in increased expression of HGF protein		 CTD PMID:29408570 NCBI chr 7:81,699,010...81,770,047
Ensembl chr 7:81,699,010...81,770,438 		JBrowse link
G HMGB1 high mobility group box 1 multiple interactions ISO Berberine inhibits the reaction [[Water deficiency co-treated with NG-Nitroarginine Methyl Ester co-treated with Indomethacin co-treated with Iohexol] results in increased expression of HMGB1 protein] CTD PMID:38705399 NCBI chr13:30,456,704...30,617,597
Ensembl chr13:30,456,704...30,617,597 		JBrowse link
G HMOX1 heme oxygenase 1 increases expression
multiple interactions		 EXP
ISO		 Berberine results in increased expression of HMOX1 protein
Berberine results in increased expression of HMOX1 mRNA; Berberine results in increased expression of HMOX1 protein
Berberine inhibits the reaction [Particulate Matter results in decreased expression of HMOX1 protein]
Berberine inhibits the reaction [Bortezomib results in increased expression of HMOX1 mRNA]
Berberine promotes the reaction [Glucose results in increased expression of HMOX1 protein]; NFE2L2 mutant form inhibits the reaction [Berberine results in increased expression of HMOX1 protein]		 CTD PMID:23954465 PMID:35121005 PMID:37511356 PMID:37839514 NCBI chr22:35,381,096...35,394,207
Ensembl chr22:35,380,361...35,394,214 		JBrowse link
G HNF4A hepatocyte nuclear factor 4 alpha multiple interactions ISO Berberine inhibits the reaction [Fructose results in decreased expression of HNF4A mRNA]; Berberine inhibits the reaction [Fructose results in decreased expression of HNF4A protein]
Berberine inhibits the reaction [Ethanol results in decreased expression of HNF4 protein]		 CTD PMID:18563319 PMID:25455889 NCBI chr20:44,355,699...44,434,596
Ensembl chr20:44,355,699...44,432,845 		JBrowse link
G IDH3A isocitrate dehydrogenase (NAD(+)) 3 catalytic subunit alpha decreases expression EXP Berberine results in decreased expression of IDH3A mRNA CTD PMID:30818834 NCBI chr15:78,149,362...78,171,945
Ensembl chr15:78,131,498...78,171,945 		JBrowse link
G IFNG interferon gamma multiple interactions ISO Berberine inhibits the reaction [Thioacetamide results in increased expression of IFNG mRNA] CTD PMID:30138605 NCBI chr12:68,154,768...68,159,740
Ensembl chr12:68,154,768...68,159,740 		JBrowse link
G IGF1R insulin like growth factor 1 receptor multiple interactions
increases expression		 EXP Berberine inhibits the reaction [Glucose results in decreased expression of IGF1R protein]
Berberine results in increased expression of IGF1R protein		 CTD PMID:23954465 NCBI chr15:98,648,539...98,964,530
Ensembl chr15:98,648,539...98,964,530 		JBrowse link
G IGF2BP3 insulin like growth factor 2 mRNA binding protein 3 multiple interactions
decreases expression		 EXP
ISO		 [Chloroquine co-treated with Berberine] results in decreased expression of IGF2BP3 protein; Berberine promotes the reaction [IGF2BP3 protein binds to TRIM21 protein]; Cycloheximide promotes the reaction [Berberine results in decreased expression of IGF2BP3 protein]
Berberine inhibits the reaction [[Dextran Sulfate co-treated with azomethane] results in increased expression of IGF2BP3 protein]		 CTD PMID:36822301 NCBI chr 7:23,310,209...23,470,491
Ensembl chr 7:23,310,209...23,470,491 		JBrowse link
G IL10 interleukin 10 multiple interactions
increases expression		 ISO Berberine affects the reaction [Lipopolysaccharides affects the expression of IL10 mRNA]
[Berberine co-treated with Thioacetamide] results in increased expression of IL10 mRNA
Berberine results in increased expression of IL10 mRNA		 CTD PMID:21867779 PMID:30138605 NCBI chr 1:206,767,602...206,772,494
Ensembl chr 1:206,767,602...206,774,541 		JBrowse link
G IL1B interleukin 1 beta multiple interactions EXP
ISO		 Berberine inhibits the reaction [IL1B protein results in increased expression of CCL2 mRNA]; Berberine inhibits the reaction [IL1B protein results in increased expression of CXCL8 mRNA]; Berberine inhibits the reaction [IL1B protein results in increased secretion of CCL2 protein]; Berberine inhibits the reaction [IL1B protein results in increased secretion of CXCL8 protein]
Berberine inhibits the reaction [[Lipopolysaccharides co-treated with Galactosamine] results in increased expression of IL1B mRNA]; Berberine inhibits the reaction [[Lipopolysaccharides co-treated with Galactosamine] results in increased expression of IL1B protein]; Berberine inhibits the reaction [[Water deficiency co-treated with NG-Nitroarginine Methyl Ester co-treated with Indomethacin co-treated with Iohexol] results in increased expression of IL1B mRNA]; Berberine inhibits the reaction [[Water deficiency co-treated with NG-Nitroarginine Methyl Ester co-treated with Indomethacin co-treated with Iohexol] results in increased expression of IL1B protein]; Berberine inhibits the reaction [Particulate Matter results in increased expression of IL1B protein]
Berberine inhibits the reaction [[Cadmium co-treated with Aluminum co-treated with Fluorides] results in increased expression of IL1B protein]; Berberine inhibits the reaction [Bortezomib results in increased expression of IL1B mRNA]; Berberine inhibits the reaction [Thioacetamide results in increased expression of IL1B mRNA]		 CTD PMID:16391493 PMID:29170048 PMID:30138605 PMID:35121005 PMID:35691465 More... NCBI chr 2:112,829,751...112,836,779
Ensembl chr 2:112,829,751...112,836,816 		JBrowse link
G IL2 interleukin 2 increases expression ISO Berberine results in increased expression of IL2 mRNA CTD PMID:21867779 NCBI chr 4:122,451,470...122,456,725
Ensembl chr 4:122,451,470...122,456,725 		JBrowse link
G IL23A interleukin 23 subunit alpha multiple interactions ISO Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased expression of IL23A mRNA]; Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased secretion of IL23A protein] CTD PMID:30240693 NCBI chr12:56,338,884...56,340,410
Ensembl chr12:56,334,174...56,340,410 		JBrowse link
G IL4 interleukin 4 multiple interactions
increases expression		 ISO Berberine inhibits the reaction [Lipopolysaccharides results in decreased expression of IL4 mRNA]
Berberine results in increased expression of IL4 mRNA		 CTD PMID:21867779 NCBI chr 5:132,673,989...132,682,678
Ensembl chr 5:132,673,986...132,682,678 		JBrowse link
G IL6 interleukin 6 multiple interactions ISO
EXP		 Berberine inhibits the reaction [[Cadmium co-treated with Aluminum co-treated with Fluorides] results in increased expression of IL6 protein]; Berberine inhibits the reaction [Bortezomib results in increased expression of IL6 mRNA]; Berberine inhibits the reaction [Thioacetamide results in increased expression of IL6 mRNA]; Berberine inhibits the reaction [Thioacetamide results in increased expression of IL6 protein]
Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased expression of IL6 mRNA]; Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased secretion of IL6 protein]; Berberine inhibits the reaction [[Lipopolysaccharides co-treated with Galactosamine] results in increased expression of IL6 mRNA]; Berberine inhibits the reaction [[Lipopolysaccharides co-treated with Galactosamine] results in increased expression of IL6 protein]; Berberine inhibits the reaction [[Water deficiency co-treated with NG-Nitroarginine Methyl Ester co-treated with Indomethacin co-treated with Iohexol] results in increased expression of IL6 mRNA]; Berberine inhibits the reaction [Particulate Matter results in increased expression of IL6 protein]
Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of IL6 protein]; Berberine inhibits the reaction [Mustard Gas results in increased secretion of IL6 protein]; KPNA4 protein inhibits the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of IL6 protein]]; LINC00943 inhibits the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of IL6 protein]]; MIR142 affects the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of IL6 protein]]		 CTD PMID:28916288 PMID:29170048 PMID:30138605 PMID:30240693 PMID:34427876 More... NCBI chr 7:22,727,200...22,731,998
Ensembl chr 7:22,725,884...22,732,002 		JBrowse link
G ITGA1 integrin subunit alpha 1 increases expression EXP Berberine results in increased expression of ITGA1 mRNA CTD PMID:26478571 NCBI chr 5:52,787,916...52,959,209
Ensembl chr 5:52,787,916...52,959,209 		JBrowse link
G ITGB4 integrin subunit beta 4 increases expression EXP berberine increases expression of ITGB4 protein in colon epithelial cells RGD PMID:29564000 RGD:152995489 NCBI chr17:75,721,459...75,757,818
Ensembl chr17:75,721,328...75,757,818 		JBrowse link
G JUN Jun proto-oncogene, AP-1 transcription factor subunit affects localization
multiple interactions		 ISO Berberine affects the localization of JUN protein
arsenic trioxide promotes the reaction [Berberine affects the localization of JUN protein]		 CTD PMID:18294404 NCBI chr 1:58,780,791...58,784,047
Ensembl chr 1:58,776,845...58,784,048 		JBrowse link
G KCNH2 potassium voltage-gated channel subfamily H member 2 decreases activity
multiple interactions		 ISO Berberine results in decreased activity of KCNH2 protein
Berberine promotes the reaction [Atorvastatin results in decreased activity of KCNH2 protein]; Berberine promotes the reaction [Simvastatin results in decreased activity of KCNH2 protein]		 CTD PMID:30086269 NCBI chr 7:150,944,961...150,978,321
Ensembl chr 7:150,944,961...150,978,321 		JBrowse link
G KDM1A lysine demethylase 1A increases expression EXP Berberine results in increased expression of KDM1A mRNA CTD PMID:27311644 NCBI chr 1:23,019,468...23,083,689
Ensembl chr 1:23,019,443...23,083,689 		JBrowse link
G KDM4A lysine demethylase 4A increases expression EXP Berberine results in increased expression of KDM4A mRNA CTD PMID:27311644 NCBI chr 1:43,650,149...43,705,518
Ensembl chr 1:43,650,149...43,705,518 		JBrowse link
G KDM5B lysine demethylase 5B increases expression EXP Berberine results in increased expression of KDM5B mRNA CTD PMID:27311644 NCBI chr 1:202,724,495...202,808,421
Ensembl chr 1:202,724,495...202,808,487 		JBrowse link
G KDM6A lysine demethylase 6A increases expression EXP Berberine results in increased expression of KDM6A mRNA CTD PMID:27311644 NCBI chr  X:44,873,188...45,112,779
Ensembl chr  X:44,873,188...45,112,779 		JBrowse link
G KDM6B lysine demethylase 6B increases expression EXP Berberine results in increased expression of KDM6B mRNA CTD PMID:27311644 NCBI chr17:7,834,217...7,854,796
Ensembl chr17:7,834,217...7,854,796 		JBrowse link
G KMT5A lysine methyltransferase 5A increases expression EXP Berberine results in increased expression of KMT5A mRNA CTD PMID:27311644 NCBI chr12:123,384,132...123,409,353
Ensembl chr12:123,384,132...123,409,353 		JBrowse link
G KPNA4 karyopherin subunit alpha 4 multiple interactions EXP Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of KPNA4 protein]; KPNA4 protein inhibits the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of IL6 protein]]; KPNA4 protein inhibits the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of KPNA4 protein]]; KPNA4 protein inhibits the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of TNF protein]]; KPNA4 protein inhibits the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased phosphorylation of NFKBIA protein]]; KPNA4 protein inhibits the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased phosphorylation of RELA protein]]; LINC00943 inhibits the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of KPNA4 protein]]; MIR142 affects the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of KPNA4 protein]] CTD PMID:34427876 NCBI chr 3:160,495,007...160,565,571
Ensembl chr 3:160,495,007...160,565,571 		JBrowse link
G LDLR low density lipoprotein receptor multiple interactions
increases expression		 ISO Berberine inhibits the reaction [Clozapine results in increased expression of LDLR mRNA]; Berberine inhibits the reaction [Risperidone results in increased expression of LDLR mRNA]
Berberine results in increased expression of LDLR mRNA
Berberine promotes the reaction [Simvastatin results in increased expression of LDLR mRNA]; Simvastatin promotes the reaction [Berberine results in increased expression of LDLR mRNA]		 CTD PMID:18640378 PMID:20564506 NCBI chr19:11,089,463...11,133,820
Ensembl chr19:11,089,418...11,133,820 		JBrowse link
G LINC00943 long intergenic non-protein coding RNA 943 multiple interactions EXP Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of LINC00943 mRNA]; LINC00943 inhibits the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of IL6 protein]]; LINC00943 inhibits the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of KPNA4 protein]]; LINC00943 inhibits the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of TNF protein]] CTD PMID:34427876 NCBI chr12:126,737,007...126,746,256
Ensembl chr12:126,723,412...126,749,027 		JBrowse link
G MAP1LC3B microtubule associated protein 1 light chain 3 beta multiple interactions
increases localization		 EXP
ISO		 [Berberine co-treated with Cisplatin] results in increased lipidation of MAP1LC3B protein; Berberine results in increased expression of and results in increased lipidation of MAP1LC3B protein; BNIP3L protein affects the reaction [[Berberine co-treated with Cisplatin] results in increased lipidation of MAP1LC3B protein]; FUNDC1 protein affects the reaction [[Berberine co-treated with Cisplatin] results in increased lipidation of MAP1LC3B protein]
Berberine results in increased localization of MAP1LC3B protein
Berberine inhibits the reaction [Chlorpyrifos results in decreased expression of MAP1LC3B mRNA]		 CTD PMID:35439518 PMID:36070022 NCBI chr16:87,392,336...87,404,774
Ensembl chr16:87,383,953...87,404,779 		JBrowse link
G MAP3K5 mitogen-activated protein kinase kinase kinase 5 multiple interactions ISO Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in decreased expression of and results in increased phosphorylation of MAP3K5 protein] CTD PMID:30240693 NCBI chr 6:136,557,046...136,793,091
Ensembl chr 6:136,557,046...136,793,097 		JBrowse link
G MAPK1 mitogen-activated protein kinase 1 decreases phosphorylation ISO Berberine results in decreased phosphorylation of MAPK1 protein CTD PMID:18294404 NCBI chr22:21,759,657...21,867,680
Ensembl chr22:21,759,657...21,867,680 		JBrowse link
G MAPK3 mitogen-activated protein kinase 3 decreases phosphorylation
multiple interactions		 ISO Berberine results in decreased phosphorylation of MAPK3 protein
Berberine inhibits the reaction [Dexamethasone results in decreased expression of MAPK3 mRNA]		 CTD PMID:18294404 PMID:20462044 NCBI chr16:30,114,105...30,123,220
Ensembl chr16:30,114,105...30,123,506 		JBrowse link
G MAPK8 mitogen-activated protein kinase 8 multiple interactions EXP [Berberine co-treated with Cisplatin] results in increased phosphorylation of MAPK8 protein; Acetylcysteine inhibits the reaction [[Berberine co-treated with Cisplatin] results in increased phosphorylation of MAPK8 protein] CTD PMID:36070022 NCBI chr10:48,306,677...48,439,360
Ensembl chr10:48,306,639...48,439,360 		JBrowse link
G MAPT microtubule associated protein tau multiple interactions ISO Berberine inhibits the reaction [[Cadmium co-treated with Aluminum co-treated with Fluorides] results in increased expression of MAPT mRNA] CTD PMID:29170048 NCBI chr17:45,894,554...46,028,334
Ensembl chr17:45,894,527...46,028,334 		JBrowse link
G MCM2 minichromosome maintenance complex component 2 multiple interactions ISO Berberine inhibits the reaction [Dexamethasone results in increased expression of MCM2 mRNA] CTD PMID:20462044 NCBI chr 3:127,598,411...127,622,436
Ensembl chr 3:127,598,223...127,622,436 		JBrowse link
G MIR142 microRNA 142 multiple interactions EXP Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in decreased expression of MIR142 mRNA]; MIR142 affects the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of IL6 protein]]; MIR142 affects the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of KPNA4 protein]]; MIR142 affects the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of TNF protein]] CTD PMID:34427876 NCBI chr17:58,331,232...58,331,318
Ensembl chr17:58,331,232...58,331,318 		JBrowse link
G MIR19A microRNA 19a decreases expression EXP Berberine results in decreased expression of MIR19A mRNA CTD PMID:29687521 NCBI chr13:91,350,891...91,350,972
Ensembl chr13:91,350,891...91,350,972 		JBrowse link
G MIR21 microRNA 21 decreases expression EXP berberine decreases expression of MIR21 RNA in colon epithelial cell RGD PMID:29564000 RGD:152995489 NCBI chr17:59,841,266...59,841,337
Ensembl chr17:59,841,266...59,841,337 		JBrowse link
G MIR92A1 microRNA 92a-1 decreases expression EXP Berberine results in decreased expression of MIR92A1 mRNA CTD PMID:29687521 NCBI chr13:91,351,314...91,351,391
Ensembl chr13:91,351,314...91,351,391 		JBrowse link
G MMP13 matrix metallopeptidase 13 increases expression EXP Berberine results in increased expression of MMP13 mRNA CTD PMID:26478571 NCBI chr11:102,942,995...102,955,732
Ensembl chr11:102,942,995...102,955,732 		JBrowse link
G MMP14 matrix metallopeptidase 14 multiple interactions
decreases expression		 ISO arsenic trioxide promotes the reaction [Berberine results in decreased expression of MMP14 protein] CTD PMID:18294404 NCBI chr14:22,836,585...22,847,758
Ensembl chr14:22,836,560...22,849,041 		JBrowse link
G MMP2 matrix metallopeptidase 2 multiple interactions
decreases activity
decreases expression		 EXP
ISO		 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one inhibits the reaction [EGF protein inhibits the reaction [Berberine results in decreased activity of MMP2 protein]]; Arsenic Trioxide promotes the reaction [Berberine results in decreased activity of MMP2 protein]; Berberine promotes the reaction [Arsenic Trioxide results in decreased activity of MMP2 protein]; EGF protein inhibits the reaction [Berberine results in decreased activity of MMP2 protein]
Berberine results in decreased expression of MMP2 protein
arsenic trioxide promotes the reaction [Berberine results in decreased activity of MMP2 protein]; arsenic trioxide promotes the reaction [Berberine results in decreased expression of MMP2 protein]; Berberine promotes the reaction [arsenic trioxide results in decreased activity of MMP2 protein]		 CTD PMID:18294404 PMID:33325633 NCBI chr16:55,478,830...55,506,691
Ensembl chr16:55,389,700...55,506,691 		JBrowse link
G MMP9 matrix metallopeptidase 9 multiple interactions
decreases activity		 EXP 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one inhibits the reaction [EGF protein inhibits the reaction [Berberine results in decreased activity of MMP9 protein]]; EGF protein inhibits the reaction [Berberine results in decreased activity of MMP9 protein] CTD PMID:33325633 NCBI chr20:46,008,908...46,016,561
Ensembl chr20:46,008,908...46,016,561 		JBrowse link
G MPO myeloperoxidase multiple interactions ISO Berberine inhibits the reaction [Lipopolysaccharides results in increased expression of MPO protein] CTD PMID:21963898 NCBI chr17:58,269,855...58,280,935
Ensembl chr17:58,269,855...58,280,935 		JBrowse link
G MT-CO1 mitochondrially encoded cytochrome c oxidase I multiple interactions ISO Berberine inhibits the reaction [acetamiprid results in decreased expression of COX1 mRNA] CTD PMID:37350525 NCBI chr MT:5,904...7,445
Ensembl chr MT:5,904...7,445 		JBrowse link
G MT-ND1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 multiple interactions ISO Berberine inhibits the reaction [acetamiprid results in decreased expression of ND1 mRNA] CTD PMID:37350525 NCBI chr MT:3,307...4,262
Ensembl chr MT:3,307...4,262 		JBrowse link
G MT-ND2 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 2 multiple interactions ISO Berberine inhibits the reaction [acetamiprid results in decreased expression of ND2 mRNA] CTD PMID:37350525 NCBI chr MT:4,470...5,511
Ensembl chr MT:4,470...5,511 		JBrowse link
G MTOR mechanistic target of rapamycin kinase multiple interactions ISO Berberine inhibits the reaction [Chlorpyrifos results in increased expression of MTOR mRNA]; Berberine inhibits the reaction [Chlorpyrifos results in increased expression of MTOR protein] CTD PMID:35439518 NCBI chr 1:11,106,535...11,262,551
Ensembl chr 1:11,106,535...11,262,556 		JBrowse link
G MTTP microsomal triglyceride transfer protein multiple interactions ISO Berberine inhibits the reaction [Ethanol results in decreased expression of MTTP protein] CTD PMID:25455889 NCBI chr 4:99,564,130...99,623,997
Ensembl chr 4:99,564,081...99,623,997 		JBrowse link
G MYC MYC proto-oncogene, bHLH transcription factor multiple interactions
affects localization		 ISO arsenic trioxide promotes the reaction [Berberine affects the localization of MYC protein] CTD PMID:18294404 NCBI chr 8:127,735,434...127,742,951
Ensembl chr 8:127,735,434...127,742,951 		JBrowse link
G NAMPT nicotinamide phosphoribosyltransferase multiple interactions
decreases expression		 EXP [Berberine co-treated with Niacinamide] results in decreased expression of NAMPT protein; SRT1720 inhibits the reaction [Berberine results in decreased expression of NAMPT protein] CTD PMID:26712469 NCBI chr 7:106,248,298...106,285,888
Ensembl chr 7:106,248,298...106,285,966 		JBrowse link
G NCF1 neutrophil cytosolic factor 1 multiple interactions EXP Berberine promotes the reaction [CYBB protein binds to NCF1 protein binds to NCF2 protein binds to RAC2 protein]; Berberine promotes the reaction [CYBB protein binds to NCF1 protein] CTD PMID:36070022 NCBI chr 7:74,774,011...74,789,315
Ensembl chr 7:74,774,011...74,789,315 		JBrowse link
G NCF2 neutrophil cytosolic factor 2 multiple interactions EXP Berberine promotes the reaction [CYBB protein binds to NCF1 protein binds to NCF2 protein binds to RAC2 protein]; Berberine promotes the reaction [CYBB protein binds to NCF2 protein] CTD PMID:36070022 NCBI chr 1:183,555,562...183,601,849
Ensembl chr 1:183,554,461...183,590,905 		JBrowse link
G NFE2L2 NFE2 like bZIP transcription factor 2 increases expression
multiple interactions
increases activity		 EXP
ISO		 Berberine results in increased expression of NFE2L2 protein
Berberine inhibits the reaction [Particulate Matter results in decreased expression of NFE2L2 protein]
Berberine results in increased activity of NFE2L2 protein
Berberine inhibits the reaction [Bortezomib results in increased expression of NFE2L2 mRNA]; Berberine promotes the reaction [Bleomycin results in increased expression of NFE2L2 protein]
NFE2L2 mutant form inhibits the reaction [Berberine inhibits the reaction [Glucose results in increased abundance of Reactive Oxygen Species]]; NFE2L2 mutant form inhibits the reaction [Berberine results in increased expression of HMOX1 protein]; NFE2L2 mutant form inhibits the reaction [Berberine results in increased expression of NGF protein]		 CTD PMID:23523906 PMID:23954465 PMID:30818834 PMID:35121005 PMID:37839514 NCBI chr 2:177,230,303...177,264,727
Ensembl chr 2:177,218,667...177,392,756 		JBrowse link
G NFKB1 nuclear factor kappa B subunit 1 multiple interactions ISO Berberine inhibits the reaction [Bortezomib results in increased expression of NFKB1 mRNA] CTD PMID:35121005 NCBI chr 4:102,501,359...102,617,302
Ensembl chr 4:102,501,330...102,617,302 		JBrowse link
G NFKBIA NFKB inhibitor alpha multiple interactions ISO
EXP		 Berberine inhibits the reaction [Lipopolysaccharides results in increased phosphorylation of NFKBIA protein]
Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased phosphorylation of NFKBIA protein]; KPNA4 protein inhibits the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased phosphorylation of NFKBIA protein]]		 CTD PMID:21963898 PMID:34427876 NCBI chr14:35,401,513...35,404,749
Ensembl chr14:35,401,079...35,404,749 		JBrowse link
G NGF nerve growth factor multiple interactions EXP Berberine inhibits the reaction [Glucose results in decreased expression of NGF protein]; NFE2L2 mutant form inhibits the reaction [Berberine results in increased expression of NGF protein] CTD PMID:23954465 NCBI chr 1:115,285,917...115,338,249
Ensembl chr 1:115,285,904...115,338,770 		JBrowse link
G NLRP3 NLR family pyrin domain containing 3 multiple interactions ISO Berberine inhibits the reaction [Bortezomib results in increased expression of NLRP3 mRNA]
Berberine inhibits the reaction [[Water deficiency co-treated with NG-Nitroarginine Methyl Ester co-treated with Indomethacin co-treated with Iohexol] results in increased expression of NLRP3 mRNA]; Berberine inhibits the reaction [[Water deficiency co-treated with NG-Nitroarginine Methyl Ester co-treated with Indomethacin co-treated with Iohexol] results in increased expression of NLRP3 protein]		 CTD PMID:35121005 PMID:38705399 NCBI chr 1:247,416,077...247,448,817
Ensembl chr 1:247,332,331...247,449,108 		JBrowse link
G NOS2 nitric oxide synthase 2 multiple interactions ISO Berberine inhibits the reaction [Carbon Tetrachloride results in increased expression of NOS2 protein]
Berberine inhibits the reaction [Bleomycin results in increased expression of NOS2 protein]		 CTD PMID:21095217 PMID:23523906 NCBI chr17:27,756,766...27,800,529
Ensembl chr17:27,756,766...27,800,529 		JBrowse link
G NQO1 NAD(P)H quinone dehydrogenase 1 multiple interactions ISO Berberine reverses reaction [Carbontetrachloride decreases Nqo1 mRNA in liver]
Berberine inhibits the reaction [Bortezomib results in increased expression of NQO1 mRNA]		 CTD
RGD		 PMID:35121005 PMID:31432116 RGD:25823187 NCBI chr16:69,709,401...69,726,560
Ensembl chr16:69,706,996...69,726,668 		JBrowse link
G NR1H3 nuclear receptor subfamily 1 group H member 3 increases localization EXP Berberine increases localization of NR1H3 protein in macrophage nucleus RGD PMID:20506155 RGD:401827279 NCBI chr11:47,248,300...47,269,033
Ensembl chr11:47,248,300...47,269,033 		JBrowse link
G NR1I2 nuclear receptor subfamily 1 group I member 2 increases activity
multiple interactions		 EXP Berberine results in increased activity of NR1I2 protein
[Berberine results in increased activity of NR1I2 protein] which results in increased expression of CYP3A4 mRNA		 CTD PMID:21524698 NCBI chr 3:119,782,101...119,818,487
Ensembl chr 3:119,780,484...119,818,487 		JBrowse link
G NR1I3 nuclear receptor subfamily 1 group I member 3 increases activity EXP Berberine results in increased activity of NR1I3 protein CTD PMID:30818834 NCBI chr 1:161,229,669...161,238,203
Ensembl chr 1:161,229,666...161,238,244 		JBrowse link
G NSD2 nuclear receptor binding SET domain protein 2 decreases expression EXP Berberine results in decreased expression of NSD2 mRNA CTD PMID:27311644 NCBI chr 4:1,871,393...1,982,192
Ensembl chr 4:1,871,393...1,982,207 		JBrowse link
G ODC1 ornithine decarboxylase 1 multiple interactions
decreases expression		 ISO arsenic trioxide promotes the reaction [Berberine results in decreased expression of ODC1 protein] CTD PMID:18294404 NCBI chr 2:10,439,968...10,448,327
Ensembl chr 2:10,439,968...10,448,327 		JBrowse link
G OMD osteomodulin increases expression EXP Berberine results in increased expression of OMD mRNA CTD PMID:26478571 NCBI chr 9:92,412,380...92,424,471
Ensembl chr 9:92,412,380...92,424,471 		JBrowse link
G P2RX7 purinergic receptor P2X 7 multiple interactions EXP Berberine affects the reaction [3'-O-(4-benzoyl)benzoyladenosine 5'-triphosphate results in increased activity of P2RX7 protein] CTD PMID:21320518 NCBI chr12:121,132,876...121,188,032
Ensembl chr12:121,132,819...121,188,032 		JBrowse link
G PARP1 poly(ADP-ribose) polymerase 1 increases cleavage
multiple interactions		 EXP Berberine results in increased cleavage of PARP1 protein
[Berberine co-treated with Cisplatin] results in increased cleavage of PARP1 protein; [Berberine co-treated with Niacinamide] results in increased cleavage of PARP1 protein; Acetylcysteine inhibits the reaction [[Berberine co-treated with Cisplatin] results in increased cleavage of PARP1 protein]		 CTD PMID:16505103 PMID:26712469 PMID:36070022 NCBI chr 1:226,360,691...226,408,093
Ensembl chr 1:226,360,210...226,408,154 		JBrowse link
G PDCD4 programmed cell death 4 increases expression EXP Berberine increases expression of PDCD4 protein in colon epithelial cells RGD PMID:29564000 RGD:152995489 NCBI chr10:110,871,928...110,900,006
Ensembl chr10:110,871,795...110,900,006 		JBrowse link
G PDK4 pyruvate dehydrogenase kinase 4 increases expression ISO Berberine results in increased expression of PDK4 mRNA CTD PMID:37511356 NCBI chr 7:95,583,499...95,596,516
Ensembl chr 7:95,583,499...95,596,516 		JBrowse link
G PPARA peroxisome proliferator activated receptor alpha multiple interactions ISO Berberine inhibits the reaction [Ethanol results in decreased expression of PPARA mRNA] CTD PMID:25455889 NCBI chr22:46,150,526...46,243,756
Ensembl chr22:46,150,521...46,243,755 		JBrowse link
G PPARD peroxisome proliferator activated receptor delta increases activity
increases expression		 ISO Berberine results in increased activity of PPARD protein
Berberine results in increased expression of PPARD mRNA; Berberine results in increased expression of PPARD protein		 CTD PMID:37511356 NCBI chr 6:35,342,558...35,428,178
Ensembl chr 6:35,342,558...35,428,191 		JBrowse link
G PPARG peroxisome proliferator activated receptor gamma multiple interactions
decreases expression
increases response to substance
increases expression		 ISO
EXP		 Berberine inhibits the reaction [Clozapine results in increased expression of PPARG mRNA]; Berberine inhibits the reaction [Clozapine results in increased expression of PPARG protein]; Berberine inhibits the reaction [Particulate Matter results in decreased expression of PPARG mRNA]; Berberine inhibits the reaction [Risperidone results in increased expression of PPARG mRNA]; Berberine inhibits the reaction [Risperidone results in increased expression of PPARG protein]
Berberine results in decreased expression of PPARG mRNA; Berberine results in decreased expression of PPARG protein
PPARG mRNA results in increased susceptibility to Berberine
15-deoxyprostaglandin J2 promotes the reaction [Berberine affects the localization of and results in increased activity of PPARG protein]; Berberine inhibits the reaction [Bleomycin binds to PPARG protein]; Berberine promotes the reaction [15-deoxyprostaglandin J2 affects the localization of and results in increased activity of PPARG protein]; Berberine results in increased activity of and affects the localization of PPARG protein; PPARG mRNA promotes the reaction [Berberine results in increased expression of HGF protein]
Berberine results in increased expression of PPARG mRNA		 CTD PMID:20564506 PMID:26478571 PMID:29408570 PMID:37511356 PMID:37839514 NCBI chr 3:12,287,368...12,434,344
Ensembl chr 3:12,287,368...12,434,356 		JBrowse link
G PPARGC1A PPARG coactivator 1 alpha multiple interactions ISO Berberine inhibits the reaction [Ethanol results in decreased expression of PPARGC1A mRNA] CTD PMID:25455889 NCBI chr 4:23,792,021...24,472,905
Ensembl chr 4:23,755,041...23,904,089 		JBrowse link
G PRG4 proteoglycan 4 decreases expression EXP Berberine results in decreased expression of PRG4 mRNA CTD PMID:26478571 NCBI chr 1:186,296,273...186,314,567
Ensembl chr 1:186,296,279...186,314,567 		JBrowse link
G PRKAA1 protein kinase AMP-activated catalytic subunit alpha 1 increases phosphorylation ISO Berberine results in increased phosphorylation of PRKAA1 protein CTD PMID:28298333 NCBI chr 5:40,759,389...40,798,374
Ensembl chr 5:40,759,389...40,798,374 		JBrowse link
G PRKCA protein kinase C alpha multiple interactions ISO arsenic trioxide promotes the reaction [Berberine results in decreased activity of PRKCA protein]; Berberine results in decreased activity of and affects the localization of PRKCA protein CTD PMID:18294404 NCBI chr17:66,302,613...66,810,743
Ensembl chr17:66,302,613...66,810,743 		JBrowse link
G PRKCE protein kinase C epsilon multiple interactions
decreases activity		 ISO arsenic trioxide promotes the reaction [Berberine results in decreased activity of PRKCE protein]; Berberine results in decreased activity of and affects the localization of PRKCE protein CTD PMID:18294404 NCBI chr 2:45,651,279...46,187,990
Ensembl chr 2:45,651,345...46,187,990 		JBrowse link
G PRMT1 protein arginine methyltransferase 1 decreases expression EXP Berberine results in decreased expression of PRMT1 mRNA CTD PMID:27311644 NCBI chr19:49,676,153...49,688,447
Ensembl chr19:49,675,786...49,689,029 		JBrowse link
G PRMT2 protein arginine methyltransferase 2 increases expression EXP Berberine results in increased expression of PRMT2 mRNA CTD PMID:27311644 NCBI chr21:46,635,674...46,665,124
Ensembl chr21:46,635,595...46,665,124 		JBrowse link
G PRMT5 protein arginine methyltransferase 5 increases expression EXP Berberine results in increased expression of PRMT5 mRNA CTD PMID:27311644 NCBI chr14:22,920,529...22,929,376
Ensembl chr14:22,920,525...22,929,408 		JBrowse link
G PRMT6 protein arginine methyltransferase 6 increases expression EXP Berberine results in increased expression of PRMT6 mRNA CTD PMID:27311644 NCBI chr 1:107,056,674...107,059,294
Ensembl chr 1:107,056,674...107,067,636 		JBrowse link
G PRMT7 protein arginine methyltransferase 7 increases expression EXP Berberine results in increased expression of PRMT7 mRNA CTD PMID:27311644 NCBI chr16:68,311,019...68,360,870
Ensembl chr16:68,310,951...68,360,852 		JBrowse link
G PRMT8 protein arginine methyltransferase 8 increases expression EXP Berberine results in increased expression of PRMT8 mRNA CTD PMID:27311644 NCBI chr12:3,381,349...3,593,973
Ensembl chr12:3,381,349...3,593,973 		JBrowse link
G PTEN phosphatase and tensin homolog multiple interactions
increases expression		 ISO ((3Z)-N-(3-chlorophenyl)-3-((3,5-dimethyl-4-((4-methylpiperazin-1-yl)carbonyl)-1H-pyrrol-2-yl)methylene)-N-methyl-2-oxo-2,3-dihydro-1H-indole-5-sulfonamide) inhibits the reaction [Berberine inhibits the reaction [Bleomycin results in decreased expression of PTEN mRNA]]; Berberine inhibits the reaction [Bleomycin results in decreased expression of PTEN mRNA]; Berberine inhibits the reaction [Bleomycin results in decreased expression of PTEN protein]
Berberine results in increased expression of PTEN protein		 CTD PMID:29408570 NCBI chr10:87,863,625...87,971,930
Ensembl chr10:87,862,638...87,971,930 		JBrowse link
G PTGS2 prostaglandin-endoperoxide synthase 2 multiple interactions ISO Berberine inhibits the reaction [Carbon Tetrachloride results in increased expression of PTGS2 protein] CTD PMID:21095217 NCBI chr 1:186,671,791...186,680,423
Ensembl chr 1:186,671,791...186,680,922 		JBrowse link
G PYCARD PYD and CARD domain containing multiple interactions ISO Berberine inhibits the reaction [[Water deficiency co-treated with NG-Nitroarginine Methyl Ester co-treated with Indomethacin co-treated with Iohexol] results in increased expression of PYCARD mRNA] CTD PMID:38705399 NCBI chr16:31,201,486...31,202,760
Ensembl chr16:31,201,486...31,203,450 		JBrowse link
G RAC2 Rac family small GTPase 2 multiple interactions EXP Berberine promotes the reaction [CYBB protein binds to NCF1 protein binds to NCF2 protein binds to RAC2 protein]; Berberine promotes the reaction [CYBB protein binds to RAC2 protein]; Berberine results in increased expression of and results in increased activity of RAC2 protein CTD PMID:36070022 NCBI chr22:37,225,270...37,244,269
Ensembl chr22:37,225,270...37,259,594 		JBrowse link
G RBP4 retinol binding protein 4 multiple interactions ISO Berberine inhibits the reaction [[Dietary Fats co-treated with Streptozocin] results in increased secretion of RBP4 protein] CTD PMID:19080170 NCBI chr10:93,591,694...93,601,744
Ensembl chr10:93,591,687...93,601,744 		JBrowse link
G RELA RELA proto-oncogene, NF-kB subunit multiple interactions ISO
EXP		 Berberine inhibits the reaction [Bleomycin affects the localization of and results in increased expression of RELA protein]
Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased phosphorylation of RELA protein]; KPNA4 protein inhibits the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased phosphorylation of RELA protein]]		 CTD PMID:23523906 PMID:34427876 NCBI chr11:65,653,601...65,663,857
Ensembl chr11:65,653,599...65,663,090 		JBrowse link
G RLN1 relaxin 1 affects binding
increases expression
multiple interactions		 ISO Berberine binds to RLN1 promoter
Berberine results in increased expression of RLN1 mRNA
[Berberine binds to RLN1 promoter] which results in increased expression of RLN1 mRNA		 CTD PMID:22363579 NCBI chr 9:5,334,930...5,340,916
Ensembl chr 9:5,334,930...5,339,876 		JBrowse link
G RPS6 ribosomal protein S6 decreases phosphorylation EXP Berberine results in decreased phosphorylation of RPS6 protein CTD PMID:23363784 NCBI chr 9:19,375,715...19,380,236
Ensembl chr 9:19,375,715...19,380,236 		JBrowse link
G RUNX2 RUNX family transcription factor 2 multiple interactions
increases expression		 EXP CTNNB1 mutant form inhibits the reaction [Berberine results in increased expression of RUNX2 mRNA]; DKK1 protein inhibits the reaction [Berberine results in increased expression of RUNX2 mRNA] CTD PMID:26478571 NCBI chr 6:45,328,330...45,551,082
Ensembl chr 6:45,328,157...45,664,349 		JBrowse link
G SETD1B SET domain containing 1B, histone lysine methyltransferase increases expression EXP Berberine results in increased expression of SETD1B mRNA CTD PMID:27311644 NCBI chr12:121,790,155...121,832,656
Ensembl chr12:121,804,009...121,832,656 		JBrowse link
G SETD2 SET domain containing 2, histone lysine methyltransferase increases expression EXP Berberine results in increased expression of SETD2 mRNA CTD PMID:27311644 NCBI chr 3:47,016,436...47,164,840
Ensembl chr 3:47,016,428...47,164,113 		JBrowse link
G SETD3 SET domain containing 3, actin N3(tau)-histidine methyltransferase increases expression EXP Berberine results in increased expression of SETD3 mRNA CTD PMID:27311644 NCBI chr14:99,397,748...99,486,458
Ensembl chr14:99,397,748...99,480,889 		JBrowse link
G SETD5 SET domain containing 5 increases expression EXP Berberine results in increased expression of SETD5 mRNA CTD PMID:27311644 NCBI chr 3:9,397,615...9,478,154
Ensembl chr 3:9,397,615...9,479,240 		JBrowse link
G SETD6 SET domain containing 6, protein lysine methyltransferase increases expression EXP Berberine results in increased expression of SETD6 mRNA CTD PMID:27311644 NCBI chr16:58,515,479...58,523,842
Ensembl chr16:58,515,479...58,523,842 		JBrowse link
G SETD7 SET domain containing 7, histone lysine methyltransferase increases expression EXP Berberine results in increased expression of SETD7 mRNA CTD PMID:27311644 NCBI chr 4:139,492,974...139,556,219
Ensembl chr 4:139,495,941...139,606,699 		JBrowse link
G SETDB1 SET domain bifurcated histone lysine methyltransferase 1 increases expression EXP Berberine results in increased expression of SETDB1 mRNA CTD PMID:27311644 NCBI chr 1:150,926,263...150,964,737
Ensembl chr 1:150,926,263...150,964,744 		JBrowse link
G SETDB2 SET domain bifurcated histone lysine methyltransferase 2 increases expression EXP Berberine results in increased expression of SETDB2 mRNA CTD PMID:27311644 NCBI chr13:49,444,274...49,495,003
Ensembl chr13:49,444,274...49,495,003 		JBrowse link
G SI sucrase-isomaltase decreases expression
multiple interactions		 EXP
ISO		 Berberine results in decreased expression of SI mRNA
N-(2-(4-bromocinnamylamino)ethyl)-5-isoquinolinesulfonamide inhibits the reaction [Berberine results in decreased expression of SI mRNA]		 CTD PMID:20229011 NCBI chr 3:164,978,898...165,157,921
Ensembl chr 3:164,978,898...165,078,496 		JBrowse link
G SIRT1 sirtuin 1 decreases expression
multiple interactions		 EXP
ISO		 Berberine results in decreased expression of SIRT1 mRNA; Berberine results in decreased expression of SIRT1 protein
Berberine inhibits the reaction [Bortezomib results in decreased expression of SIRT1 protein]
[Berberine co-treated with Niacinamide] results in decreased expression of SIRT1 protein; SRT1720 inhibits the reaction [Berberine results in decreased expression of SIRT1 protein]		 CTD PMID:26712469 PMID:35121005 NCBI chr10:67,884,656...67,918,390
Ensembl chr10:67,884,656...67,918,390 		JBrowse link
G SIRT2 sirtuin 2 multiple interactions EXP [Berberine co-treated with Niacinamide] results in decreased expression of SIRT2 protein CTD PMID:26712469 NCBI chr19:38,878,555...38,899,618
Ensembl chr19:38,878,555...38,899,862 		JBrowse link
G SIRT3 sirtuin 3 multiple interactions
increases expression
decreases expression		 EXP [Berberine co-treated with Niacinamide] results in decreased expression of SIRT3 protein
Berberine results in increased expression of SIRT3 mRNA
Berberine results in decreased expression of SIRT3 mRNA; Berberine results in decreased expression of SIRT3 protein		 CTD PMID:26712469 PMID:27311644 NCBI chr11:215,030...236,931
Ensembl chr11:215,030...236,931 		JBrowse link
G SLC27A5 solute carrier family 27 member 5 decreases expression EXP Berberine results in decreased expression of SLC27A5 mRNA CTD PMID:28038998 NCBI chr19:58,498,333...58,511,992
Ensembl chr19:58,479,512...58,512,413 		JBrowse link
G SLC2A4 solute carrier family 2 member 4 multiple interactions ISO Berberine inhibits the reaction [[Dietary Fats co-treated with Streptozocin] results in decreased expression of SLC2A4 protein] CTD PMID:19080170 NCBI chr17:7,281,718...7,288,257
Ensembl chr17:7,281,718...7,288,257 		JBrowse link
G SLC6A19 solute carrier family 6 member 19 multiple interactions ISO Berberine affects the reaction [Lipopolysaccharides affects the expression of SLC6A19 mRNA]; Berberine affects the reaction [Lipopolysaccharides affects the expression of SLC6A19 protein] CTD PMID:21073932 NCBI chr 5:1,201,595...1,225,111
Ensembl chr 5:1,201,595...1,225,111 		JBrowse link
G SMYD3 SET and MYND domain containing 3 affects expression EXP Berberine affects the expression of SMYD3 mRNA CTD PMID:27311644 NCBI chr 1:245,749,347...246,507,279
Ensembl chr 1:245,749,342...246,507,312 		JBrowse link
G SOCS3 suppressor of cytokine signaling 3 multiple interactions ISO Berberine inhibits the reaction [Particulate Matter results in decreased expression of SOCS3 mRNA]; Berberine inhibits the reaction [Particulate Matter results in decreased expression of SOCS3 protein] CTD PMID:37839514 NCBI chr17:78,356,778...78,360,925
Ensembl chr17:78,356,778...78,360,077 		JBrowse link
G SOD1 superoxide dismutase 1 multiple interactions ISO Berberine inhibits the reaction [Carbon Tetrachloride results in decreased activity of SOD1 protein]; Berberine inhibits the reaction [Particulate Matter results in decreased expression of SOD1 protein]; Berberine inhibits the reaction [Streptozocin affects the expression of SOD1 mRNA]
Berberine inhibits the reaction [Chlorpyrifos results in decreased activity of SOD1 protein]		 CTD PMID:21095217 PMID:22775417 PMID:35439518 PMID:37839514 NCBI chr21:31,659,693...31,668,931
Ensembl chr21:31,659,666...31,668,931 		JBrowse link
G SOD2 superoxide dismutase 2 multiple interactions ISO Berberine inhibits the reaction [Streptozocin affects the expression of SOD2 mRNA]
Berberine inhibits the reaction [acetamiprid results in decreased expression of SOD2 mRNA]; Berberine inhibits the reaction [Mercuric Chloride results in decreased expression of SOD2 mRNA]		 CTD PMID:22775417 PMID:24751971 PMID:33460233 PMID:37350525 NCBI chr 6:159,669,069...159,762,281
Ensembl chr 6:159,669,069...159,762,529 		JBrowse link
G SOX9 SRY-box transcription factor 9 decreases expression EXP Berberine results in decreased expression of SOX9 mRNA CTD PMID:26478571 NCBI chr17:72,121,020...72,126,416
Ensembl chr17:72,121,020...72,126,416 		JBrowse link
G SP7 Sp7 transcription factor increases expression EXP Berberine results in increased expression of SP7 mRNA CTD PMID:26478571 NCBI chr12:53,326,575...53,344,793
Ensembl chr12:53,326,575...53,345,315 		JBrowse link
G SPARC secreted protein acidic and cysteine rich increases expression EXP Berberine results in increased expression of SPARC mRNA CTD PMID:26478571 NCBI chr 5:151,661,096...151,686,915
Ensembl chr 5:151,661,096...151,686,975 		JBrowse link
G SPP1 secreted phosphoprotein 1 increases expression
multiple interactions		 EXP Berberine results in increased expression of SPP1 mRNA; Berberine results in increased expression of SPP1 protein
CTNNB1 mutant form inhibits the reaction [Berberine results in increased expression of SPP1 protein]; DKK1 protein inhibits the reaction [Berberine results in increased expression of SPP1 protein]		 CTD PMID:26478571 NCBI chr 4:87,975,714...87,983,411
Ensembl chr 4:87,975,667...87,983,532 		JBrowse link
G SQSTM1 sequestosome 1 increases expression
multiple interactions		 EXP
ISO		 Berberine results in increased expression of SQSTM1 protein
[Berberine co-treated with Water deficiency co-treated with NG-Nitroarginine Methyl Ester co-treated with Indomethacin co-treated with Iohexol] results in increased expression of SQSTM1 protein		 CTD PMID:36070022 PMID:38705399 NCBI chr 5:179,806,393...179,838,078
Ensembl chr 5:179,806,398...179,838,078 		JBrowse link
G SREBF1 sterol regulatory element binding transcription factor 1 multiple interactions
decreases expression		 ISO
EXP		 Berberine inhibits the reaction [Clozapine results in increased expression of SREBF1 mRNA]; Berberine inhibits the reaction [Clozapine results in increased expression of SREBF1 protein]; Berberine inhibits the reaction [Risperidone results in increased expression of SREBF1 mRNA]; Berberine inhibits the reaction [Risperidone results in increased expression of SREBF1 protein]
Berberine results in decreased expression of SREBF1 mRNA		 CTD PMID:20564506 PMID:26478571 NCBI chr17:17,811,334...17,836,986
Ensembl chr17:17,810,399...17,837,002 		JBrowse link
G STAT3 signal transducer and activator of transcription 3 multiple interactions ISO Berberine inhibits the reaction [Bortezomib results in increased expression of STAT3 mRNA]
Berberine inhibits the reaction [Particulate Matter results in increased expression of STAT3 mRNA]		 CTD PMID:35121005 PMID:37839514 NCBI chr17:42,313,324...42,388,442
Ensembl chr17:42,313,324...42,388,568 		JBrowse link
G TERT telomerase reverse transcriptase decreases activity EXP Berberine results in decreased activity of TERT protein CTD PMID:25265580 NCBI chr 5:1,253,167...1,295,068
Ensembl chr 5:1,253,147...1,295,068 		JBrowse link
G TGFB1 transforming growth factor beta 1 decreases expression
multiple interactions		 ISO Berberine results in decreased expression of TGFB1 protein
Berberine inhibits the reaction [Particulate Matter results in increased expression of TGFB1 mRNA]
Berberine inhibits the reaction [Bleomycin results in increased expression of TGFB1 protein]; Berberine inhibits the reaction [Thioacetamide results in increased expression of TGFB1 mRNA]		 CTD PMID:17973934 PMID:23523906 PMID:30138605 PMID:37839514 NCBI chr19:41,330,323...41,353,922
Ensembl chr19:41,301,587...41,353,922 		JBrowse link
G TLR4 toll like receptor 4 multiple interactions ISO Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased expression of TLR4 mRNA]; Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased secretion of TLR4 protein]; Berberine inhibits the reaction [Lipopolysaccharides results in increased expression of TLR4 mRNA]
Berberine inhibits the reaction [Bortezomib results in increased expression of TLR4 protein]		 CTD PMID:21963898 PMID:30240693 PMID:35121005 NCBI chr 9:117,704,403...117,724,735
Ensembl chr 9:117,704,175...117,724,735 		JBrowse link
G TNF tumor necrosis factor multiple interactions
increases secretion
increases expression		 EXP
ISO		 Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of TNF protein]; Berberine inhibits the reaction [TNF protein results in increased expression of CCL2 mRNA]; Berberine inhibits the reaction [TNF protein results in increased expression of CXCL8 mRNA]; Berberine inhibits the reaction [TNF protein results in increased secretion of CCL2 protein]; Berberine inhibits the reaction [TNF protein results in increased secretion of CXCL8 protein]; KPNA4 protein inhibits the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of TNF protein]]; LINC00943 inhibits the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of TNF protein]]; MIR142 affects the reaction [Berberine inhibits the reaction [1-Methyl-4-phenylpyridinium results in increased expression of TNF protein]]
Berberine inhibits the reaction [[Cadmium co-treated with Aluminum co-treated with Fluorides] results in increased expression of TNF mRNA]; Berberine inhibits the reaction [[Cadmium co-treated with Aluminum co-treated with Fluorides] results in increased expression of TNF protein]; Berberine inhibits the reaction [Bleomycin results in increased expression of TNF protein]; Berberine inhibits the reaction [Bortezomib results in increased expression of TNF mRNA]; Berberine inhibits the reaction [Mercuric Chloride results in increased expression of TNF protein]
Berberine results in increased secretion of TNF protein
Berberine results in increased expression of TNF mRNA
Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in decreased expression of and results in increased phosphorylation of MAP3K5 protein]; Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased expression of IL23A mRNA]; Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased expression of IL6 mRNA]; Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased expression of TLR4 mRNA]; Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased expression of TRAF2 mRNA]; Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased secretion of IL23A protein]; Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased secretion of IL6 protein]; Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased secretion of TLR4 protein]; Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased secretion of TRAF2 protein]; Berberine inhibits the reaction [[Lipopolysaccharides co-treated with Galactosamine] results in increased expression of TNF mRNA]; Berberine inhibits the reaction [[Lipopolysaccharides co-treated with Galactosamine] results in increased expression of TNF protein]; Berberine inhibits the reaction [[Water deficiency co-treated with NG-Nitroarginine Methyl Ester co-treated with Indomethacin co-treated with Iohexol] results in increased expression of TNF mRNA]; Berberine inhibits the reaction [Benzo(a)pyrene results in increased expression of TNF mRNA]; Berberine inhibits the reaction [Carbon Tetrachloride results in increased expression of TNF protein]; Berberine inhibits the reaction [Dietary Fats results in increased secretion of TNF protein]; Berberine inhibits the reaction [Lipopolysaccharides results in increased expression of TNF mRNA]; Berberine inhibits the reaction [Particulate Matter results in increased expression of TNF protein]		 CTD PMID:16391493 PMID:20656010 PMID:21095217 PMID:21867779 PMID:23523906 More... NCBI chr 6:31,575,565...31,578,336
Ensembl chr 6:31,575,565...31,578,336 		JBrowse link
G TOP1 DNA topoisomerase I decreases activity EXP Berberine results in decreased activity of TOP1 protein CTD PMID:23747414 NCBI chr20:41,028,822...41,124,487
Ensembl chr20:41,028,822...41,124,487 		JBrowse link
G TOP2A DNA topoisomerase II alpha multiple interactions
affects response to substance		 EXP TOP2A protein affects the reaction [Berberine results in increased expression of H2AX protein modified form]
TOP2A protein affects the susceptibility to Berberine		 CTD PMID:23747414 NCBI chr17:40,388,525...40,417,896
Ensembl chr17:40,388,525...40,417,896 		JBrowse link
G TP53 tumor protein p53 increases expression
multiple interactions		 EXP Berberine results in increased expression of TP53 mRNA; Berberine results in increased expression of TP53 protein
[Berberine co-treated with Niacinamide] results in increased expression of and results in increased acetylation of TP53 protein; Berberine results in increased phosphorylation of and results in increased acetylation of TP53 protein		 CTD PMID:20656010 PMID:26712469 NCBI chr17:7,668,421...7,687,490
Ensembl chr17:7,661,779...7,687,546 		JBrowse link
G TRAF1 TNF receptor associated factor 1 increases expression EXP Berberine results in increased expression of TRAF1 protein CTD PMID:20656010 NCBI chr 9:120,902,393...120,929,171
Ensembl chr 9:120,902,393...120,929,173 		JBrowse link
G TRAF2 TNF receptor associated factor 2 multiple interactions ISO Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased expression of TRAF2 mRNA]; Berberine inhibits the reaction [[lipopolysaccharide, Escherichia coli O111 B4 co-treated with TNF protein] results in increased secretion of TRAF2 protein] CTD PMID:30240693 NCBI chr 9:136,881,958...136,926,607
Ensembl chr 9:136,881,912...136,926,607 		JBrowse link
G TRIM21 tripartite motif containing 21 multiple interactions EXP Berberine promotes the reaction [IGF2BP3 protein binds to TRIM21 protein] CTD PMID:36822301 NCBI chr11:4,384,897...4,393,702
Ensembl chr11:4,384,897...4,393,702 		JBrowse link
G TSTD1 thiosulfate sulfurtransferase like domain containing 1 increases expression EXP Berberine results in increased expression of TSTD1 mRNA CTD PMID:27311644 NCBI chr 1:161,037,631...161,038,964
Ensembl chr 1:161,037,631...161,038,977 		JBrowse link
G UBE2A ubiquitin conjugating enzyme E2 A decreases expression EXP Berberine results in decreased expression of UBE2A mRNA CTD PMID:27311644 NCBI chr  X:119,574,563...119,584,423
Ensembl chr  X:119,474,802...119,591,083 		JBrowse link
G UBE2B ubiquitin conjugating enzyme E2 B decreases expression EXP Berberine results in decreased expression of UBE2B mRNA CTD PMID:27311644 NCBI chr 5:134,371,569...134,392,108
Ensembl chr 5:134,371,184...134,392,108 		JBrowse link
G UCP2 uncoupling protein 2 multiple interactions
increases expression		 ISO Berberine inhibits the reaction [Benzo(a)pyrene results in increased expression of UCP2 mRNA]
Berberine results in increased expression of UCP2 mRNA		 CTD PMID:28533128 PMID:37511356 NCBI chr11:73,974,672...73,983,202
Ensembl chr11:73,974,672...73,982,843 		JBrowse link
G VEGFA vascular endothelial growth factor A decreases expression EXP Berberine results in decreased expression of VEGFA protein CTD PMID:33325633 NCBI chr 6:43,770,211...43,786,487
Ensembl chr 6:43,770,184...43,786,487 		JBrowse link
G VEGFC vascular endothelial growth factor C increases expression EXP Berberine results in increased expression of VEGFC mRNA CTD PMID:26478571 NCBI chr 4:176,683,538...176,792,922
Ensembl chr 4:176,683,538...176,792,922 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  CHEBI ontology 26092
    role 26008
      chemical role 24299
        antioxidant 17508
          berberine 276
Path 2
Term Annotations click to browse term
  CHEBI ontology 26092
    subatomic particle 26067
      composite particle 26067
        hadron 26067
          baryon 26067
            nucleon 26067
              atomic nucleus 26067
                atom 26067
                  main group element atom 25894
                    p-block element atom 25894
                      carbon group element atom 25481
                        carbon atom 25440
                          organic molecular entity 25440
                            organic molecule 25253
                              organic cyclic compound 24300
                                organic heterocyclic compound 22339
                                  organonitrogen heterocyclic compound 20355
                                    dibenzoquinolizine 436
                                      berberine alkaloid 436
                                        berberine 276
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