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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
  1. The genes in each extracted relation are listed under the “Gene1” and the “Gene2” columns respectively. A measure of confidence, reported by ReVerb, is listed under the “Confidence” column, and relations with low confidence (<0.5) are bolded. The unverified node is listed under the “Unverified node” column. The associated text that relates the two genes is listed under the “PMC Excerpt” column. Some genes were identified by their synonyms found in either GeneCards or GeneMANIA. The PMCID of the original article coupled with the year of publication is given under”PMCID/Year” column. Important remarks and gene synonyms may be listed under the “Remark” column