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Table 4 Eleven extracted relations with disconnected gene nodes from GeneMANIA

From: Building a glaucoma interaction network using a text mining approach

Gene1 Gene2 Confidence Disconnected node PMC Excerpt PMCID/Year Remark
DCDC1 PAX6 0.96 DCDC1 ELP4 and DCDC1 are located downstream of PAX6. PMC2375324/2008  
ALB ELP4 0.93 ELP4 ALB was used to normalize ELP4 and PAX6 values for the detection of the relative copy number of the deletion region. PMC3859656/2013  
ATOH7 FBN1 0.88 ATOH7 We found 10 candidate POAG genes that were highly expressed in both the CPE and NPE (AKAP13, C1QBP, CHSY1, COL8A2, CYP1B1, FBN1, IBTK, MFN2, TMCO1, and TMEM248), three genes that were expressed significantly higher in the CPE (CDH1, CDKN2B, and SIX1), and six genes that were expressed significantly higher in the NPE (ATOH7, CYP1B1, FBN1, MYOC, PAX6, and SIX6). PMC3909915/2014  
FBN1 TMEM248 0.88 TMEM248 We found 10 candidate POAG genes that were highly expressed in both the CPE and NPE (AKAP13, C1QBP, CHSY1, COL8A2, CYP1B1, FBN1, IBTK, MFN2, TMCO1, and TMEM248), three genes that were expressed significantly higher in the CPE (CDH1, CDKN2B, and SIX1), and six genes that were expressed significantly higher in the NPE (ATOH7, CYP1B1, FBN1, MYOC, PAX6, and SIX6). PMC3909915/2014  
GSK3B MTHFR 0.85 MTHFR For example, GSK3B has a direct connection with IL4 and a secondary connection with MTHFR. PMC2653647/2009  
GAPDH VSX1 0.85 VSX1 Each bar represents the relative expression of VSX1 normalized to GAPDH in a different tissue/age; mean ± SD (Sc: sclera, Co: cornea, Ir: iris, CB: ciliary body, Len: lens, Cho: PMC2267740/2008  
GLS2 HMGB1 0.80 GLS2 the HMGB1 inhibitor GA attenuated diabetes-induced upregulation of HMGB1 and downregulation of BDNF PMC3671668/2013 GLS2 is a synonym of GA
SHH ATOH7 0.78 ATOH7 Thus the SHH and GDF11 regulate ATOH7, which in turn regulates Brn3b. PMC2883590/2010  
LMX1B COL3A1 0.45 LMX1B Recent immunohistological studies in NPS patients with severe glomerular disease suggest a possible regulation of type III collagen by LMX1B, while the homozygous PMC2669506/2007 COL3A1 is a synonym of Type_III_collagen
NPS PAX6 0.05 NPS Research has demonstrated that retinal neurons and RGCs are mainly comprised of anteriorized NPS that express PAX6 and OTX2. PMC3747054/2013  
NPS OTX2 0.05 NPS Research has demonstrated that retinal neurons and RGCs are mainly comprised of anteriorized NPS that express PAX6 and OTX2 PMC3747054/2013  
  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 disconnected node in the relation is listed under the “Disconnected 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