RGD Reference Report - Integrated microarray analysis provided novel insights to the pathogenesis of glaucoma. - Rat Genome Database

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Integrated microarray analysis provided novel insights to the pathogenesis of glaucoma.

Authors: Wang, Jinhui  Qu, Daofei  An, Jinghong  Yuan, Guoming  Liu, Yufu 
Citation: Wang J, etal., Mol Med Rep. 2017 Dec;16(6):8735-8746. doi: 10.3892/mmr.2017.7711. Epub 2017 Oct 4.
RGD ID: 155630605
Pubmed: PMID:28990066   (View Abstract at PubMed)
PMCID: PMC5779953   (View Article at PubMed Central)
DOI: DOI:10.3892/mmr.2017.7711   (Journal Full-text)

Glaucoma is characterized as a visual field defect, which is the second most common cause of blindness. The present study performed an integrated analysis of microarray studies of glaucoma derived from Gene Expression Omnibus (GEO). Following the identification of the differentially expressed genes (DEGs) in glaucoma compared with normal control (NC) tissues, the functional annotation, glaucoma‑specific protein‑protein interaction (PPI) network and transcriptional regulatory network constructions were performed. The acute intraocular pressure (IOP) elevation rat models were established and reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) was performed for DEGs expression confirmation. Three datasets were downloaded from GEO. A total of 97 DEGs, 82 upregulated and 15 downregulated were identified in glaucoma compared with NC groups with false discovery rate <0.05. Response to virus and immune response were two significantly enriched GO terms in glaucoma. Valine, leucine and isoleucine degradation was a significantly enriched pathway of DEGs in glaucoma. According to the PPI network, HDAC1, HBN, UBR4 and PDK1 were hub proteins in glaucoma. FOXD3, HNF‑4 and AP‑1 were the three transcription factors (TFs) derived from top 10 TFs which covered the majority of downstream DEGs in glaucoma. Based on the RT‑qPCR results, the expression levels of 3 DEGs, raftlin, lipid raft linker 1 (RFTN1), PBX homeobox 1 (PBX1), HDAC1 were significantly upregulated and the expression of GEM was significantly downregulated in acute IOP elevation rat model at the first and fifth day. These four DEGs had the same expression pattern with our integrated analysis. Therefore, the current study concluded that 6 DEGs, including HEPH, SELENBP1, RFTN1, ID1, HDAC‑1 and PBX1 and three TFs, including FOXD3, HNF‑4 and AP‑1 may be involved with the pathogenesis of glaucoma. The findings of the current study may improve diagnosis and drug design for glaucoma.

RGD Manual Disease Annotations    Click to see Annotation Detail View
TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
glaucoma  IEP 155630605; 155630605; 155630605; 155630605; 155630605; 155630605; 155630605; 155630605; 155630605mRNA:increased expression:optic nerve head (human)RGD 
glaucoma  ISOFOXD3 (Homo sapiens)155630605; 155630605mRNA:increased expression:optic nerve head (human)RGD 
glaucoma  ISOGem (Rattus norvegicus)155630605; 155630605mRNA:decreased expression:optic nerve head (rat)RGD 
glaucoma  IEP 155630605mRNA:decreased expression:optic nerve head (rat)RGD 
glaucoma  ISOHdac1 (Rattus norvegicus)155630605; 155630605mRNA:increased expression:optic nerve head (rat)RGD 
glaucoma  ISOHDAC1 (Homo sapiens)155630605; 155630605mRNA:increased expression:optic nerve head (human)RGD 
glaucoma  IEP 155630605; 155630605; 155630605mRNA:increased expression:optic nerve head (rat)RGD 
glaucoma  ISOHEPH (Homo sapiens)155630605; 155630605mRNA:increased expression:optic nerve head (human)RGD 
glaucoma  ISOHNF4A (Homo sapiens)155630605; 155630605mRNA:increased expression:optic nerve head (human)RGD 
glaucoma  ISOID1 (Homo sapiens)155630605; 155630605mRNA:increased expression:optic nerve head (human)RGD 
glaucoma  ISOJUN (Homo sapiens)155630605; 155630605mRNA:increased expression:optic nerve head (human)RGD 
glaucoma  ISOPbx1 (Rattus norvegicus)155630605; 155630605mRNA:increased expression:optic nerve head (rat)RGD 
glaucoma  ISOPBX1 (Homo sapiens)155630605; 155630605mRNA:increased expression:optic nerve head (human)RGD 
glaucoma  ISORftn1 (Rattus norvegicus)155630605; 155630605mRNA:increased expression:optic nerve head (rat)RGD 
glaucoma  ISORFTN1 (Homo sapiens)155630605; 155630605mRNA:increased expression:optic nerve head (human)RGD 
glaucoma  ISOSELENBP1 (Homo sapiens)155630605; 155630605mRNA:increased expression:optic nerve head (human)RGD 

Objects Annotated

Genes (Rattus norvegicus)
Foxd3  (forkhead box D3)
Gem  (GTP binding protein overexpressed in skeletal muscle)
Hdac1  (histone deacetylase 1)
Heph  (hephaestin)
Hnf4a  (hepatocyte nuclear factor 4, alpha)
Id1  (inhibitor of DNA binding 1)
Jun  (Jun proto-oncogene, AP-1 transcription factor subunit)
Pbx1  (PBX homeobox 1)
Rftn1  (raftlin lipid raft linker 1)
Selenbp1  (selenium binding protein 1)

Genes (Mus musculus)
Foxd3  (forkhead box D3)
Gem  (GTP binding protein overexpressed in skeletal muscle)
Hdac1  (histone deacetylase 1)
Heph  (hephaestin)
Hnf4a  (hepatic nuclear factor 4, alpha)
Id1  (inhibitor of DNA binding 1, HLH protein)
Jun  (jun proto-oncogene)
Pbx1  (pre B cell leukemia homeobox 1)
Rftn1  (raftlin lipid raft linker 1)
Selenbp1  (selenium binding protein 1)

Genes (Homo sapiens)
FOXD3  (forkhead box D3)
GEM  (GTP binding protein overexpressed in skeletal muscle)
HDAC1  (histone deacetylase 1)
HEPH  (hephaestin)
HNF4A  (hepatocyte nuclear factor 4 alpha)
ID1  (inhibitor of DNA binding 1)
JUN  (Jun proto-oncogene, AP-1 transcription factor subunit)
PBX1  (PBX homeobox 1)
RFTN1  (raftlin, lipid raft linker 1)
SELENBP1  (selenium binding protein 1)


Additional Information