Table 4.
Eleven extracted relations with disconnected gene nodes from GeneMANIA
| 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 |
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