Table 3 Twenty one extracted relations with unverified links from GeneMANIA
From: Building a glaucoma interaction network using a text mining approach
Gene1 | Gene2 | Confidence | Unverified node | PMC Excerpt | PMCID/Year | Remark |
|---|---|---|---|---|---|---|
CDKN2B-AS1 | CDKN2B | 0.93 | CDKN2B-AS1 | CDKN2B-AS1 has been shown to be involved in the regulation of CDKN2B, CDKN2A and ARF expression. | PMC4132588/2014 | CDKN2B-AS1 is a CDKN2B antisense. GeneMANIA does not recognize gene anti-sense. |
CDKN2B-AS1 | CDKN2A | 0.93 | CDKN2B-AS1 | CDKN2B-AS1 has been shown to be involved in the regulation of CDKN2B, CDKN2A and ARF expression. | PMC4132588/2014 | CDKN2B-AS1 is CDKN2B antisense. GeneMANIA does not recognize gene anti-sense |
CDKN2B-AS1 | ARF | 0.93 | CDKN2B-AS1 | CDKN2B-AS1 has been shown to be involved in the regulation of CDKN2B, CDKN2A and ARF expression. | PMC4132588/2014 | CDKN2B-AS1 is CDKN2B antisense. GeneMANIA does not recognize gene anti-sense |
CDKN2BAS | CDKN2A | 0.92 | CDKN2BAS | CDKN2BAS also regulates the expression of CDKN2A, a gene previously shown to be down-regulated in other neurodegenerative disorders, including Alzheimer’s disease, suggesting that regulation of CDKN2A expression by CDKN2BAS could also contribute to degeneration of the optic nerve in glaucoma. | PMC3343074/2012 | CDKN2BAS is CDKN2B antisense. GeneMANIA does not recognize gene anti-sense |
CNTF | LIFRß | 0.90 | LIFRß | In mouse, human OSM activates the heterodimer of LIF receptor ß (LIFRß and gp130, like CNTF. | PMC4171539/2014 | LIFRB is a mouse gene that GeneMANIA did not recognize |
miR410 | VEGFA | 0.9 | miR410 | Protein levels of VEGFA were also down-regulated with miR410 overexpression and up-regulated with miR-410 interference. | PMC400246/2014 | GeneMANIA does not recognize microRNAs. |
STAT1 | ANRIL | 0.89 | STAT1 | The binding of STAT1 induces the expression of ANRIL, and represses CDKN2B in endothelial cells. | PMC3565320/2013 | GeneMANIA does not recognize locus ANRIL |
siPITX2 | DKK1 | 0.83 | siPITX2 | DKK1 and KCNJ2 which were shown to be affected by PITX2 siRNAs by real time PCR experiments were each previously reported in one study. | PMC2654047/2009 | siPITX2 is short interfering PITX2. GeneMANIA does not recognize short interfering RNAs. |
siPITX2 | KCNJ2 | 0.83 | siPITX2 | DKK1 and KCNJ2 which were shown to be affected by PITX2 siRNAs by real time PCR experiments were each previously reported in one study. | PMC2654047/2009 | siPITX2 is short interfering PITX2. GeneMANIA does not recognize short interfering RNAs. |
XCPE1 | LTBP2 | 0.82 | XCPE1 | LTBP2 was predicted to be regulated by KLF4 (at 10 promoters), SP1 (at eight promoters), GATA4 and TEAD (at five promoters) and XCPE1 (at four promoters) was associated with LTBP2. | PMC4019825/2014 | XCPE1 is X gene core promoter element 1 (DNA element). GeneMANIA does not recognize XCPE1 |
GLC3A | GLC3B | 0.78 | GLC3B | To narrow down the potential candidate CNVs (genes) and match the identified CNVs to target regions and/or genes, we first focused on known chromosomal loci for PCG, namely GLC3A (2p2-p21), which harbors CYP1B1, GLC3B (1p36.2-p36.1), and GLC3C (14q23). | PMC3250374/2011 | GeneMANIA does not recognize gene locus |
GLC3A | GLC3C | 0.78 | GLC3C | To narrow down the potential candidate CNVs (genes) and match the identified CNVs to target regions and/or genes, we first focused on known chromosomal loci for PCG, namely GLC3A (2p2-p21), which harbors CYP1B1, GLC3B (1p36.2-p36.1), and GLC3C (14q23). | PMC3250374/2011 | GeneMANIA does not recognize gene locus |
E50K | TBK1 | 0.74 | E50K | Recently, it was found that E50K mutant strongly interacted with TBK1, which evoked intracellular insolubility of OPTN, leading to improper OPTN transition from the endoplasmic reticulum to the Golgi body. | PMC4077773/2014 | GeneMANIA recognizes OPTN not its mutated form. E50K is a mutation in the OPTN gene |
DCDC4 | PAX6 | 0.74 | DCDC4 | The 3′ deletion identified in family 86 contained ELP4 and DCD4, which are located downstream of PAX6. | PMC3044699/2011 | DCD4 (double cortin domain containing 4) is not found in HUGO |
MTMR2 | NEFL | 0.60 | NEFL | However, catalytically inactive CMT disease-related MTMR2 mutants lead to NEFL assembly defects and to pathologies similar to the one caused by NEFL mutations, suggesting that MTMR2 and NEFL may function in a common pathway in the development and maintenance of peripheral axons. | PMC3514635/2012 | GeneMANIA does not recognize NEFL. |
TTRV30M | EPO | 0.50 | TTRV30M | It has been suggested that inhibition of EPO production could be caused by the toxicity of prefibrillar aggregates of TTR V30M. | PMC4087117/2014 | GeneMANIA recognizes TTR not its mutated form V30M. V30M is a point mutation within TTR |
BDNF-AS | EZH2 | 0.40 | BDNF-AS | Further characterization of BDNF-AS indicates that BDNF-AS recruits EZH2 and the PRC2 complex to the BDNF promoter to repress BDNF transcription through H3K27me3 histone modifications. | PMC4047558/2014 | BDNF-AS is BDNF antisense. GeneMANIA does not recognize anti-sense |
BDNF-AS | PRC2 | 0.40 | BDNF-AS | Further characterization of BDNF-AS indicates that BDNF-AS recruits EZH2 and the PRC2 complex to the BDNF promoter to repress BDNF transcription through H3K27me3 histone modifications. | PMC4047558/2014 | BDNF-AS is BDNF antisense. GeneMANIA does not recognize anti-sense |
BDNF-AS | BDNF | 0.40 | BDNF-AS | Further characterization of BDNF-AS indicates that BDNF-AS recruits EZH2 and the PRC2 complex to the BDNF promoter to repress BDNF transcription through H3K27me3 histone modifications. | PMC4047558/2014 | BDNF-AS is BDNF antisense. GeneMANIA does not recognize anti-sense |
siCSTA | MYOC | 0.35 | siCSTA | It would be interesting to investigate whether the application of an inhibitor to CSTA, such as its siRNA, could restore the normal MYOC processing and affect the outcome of the disease. | PMC3352898/2012 | siCSTA is short interfering CSTA. GenMANIA does not cover short interfering RNAs. |
Glu50Lys | OPTN | 0.3 | Glu50Lys | More, recently, Minegishi and coworkers reported that the over-expression of a glaucoma causing-mutation in OPTN, Glu50Lys, produces an accumulation of insoluble OPTN protein that can be blocked with chemical inhibition of TBK1 activity in HEK293 cells. | PMC4038935/2014 | Glu50Lys is a mutation in the OPTN gene |