Table 3b.
Transcription factor analysis using TRANSFAC database (http://genexplain.com/transfac/) through the access of the GATHER database (https://changlab.uth.tmc.edu/gather/) showed that top 10 transcription factors filtered by P value were involved in each of the four groups of SGs such as CKD upregulated SGs, CKD-downregulated SGs, ESRD-upregulated SGs and ESRD-downregulated SGs. Of note, five out of ten transcription factors that are involved in ESRD downregulated SGs are isoforms of E2F1.
| Annotation | -ln (p value)* | main function/effect | PMID | |
|---|---|---|---|---|
| up SGs in CKD | E2F1(V$E2F1_Q6_01) | 5.94 | control cell-cycle progression from G1 to S phase | 7969176 |
| fork head box J 2(V$FOXJ2_01) | 5.94 | suporession of migration and invasion | 25873280 | |
| NF-kappaB (p65) (V$NFKAPPAB65_01) | 5.13 | proinflammation to disease progression | 30135182 | |
| E2F1(V$E2F1_Q6) | 5.08 | control cell-cycle progression from G1 to S phase | 7969176 | |
| KROX (V$KROX_Q6) | 5.01 | tooth development | 12489153 | |
| DP-1 heterodimer (V$E2F1DP1_01: E2F-1) | 4.31 | cell cycle | 8405995 | |
| E2A (V$E2A_Q2) | 4.31 | pathogenesis of lymphocytic leukemia. | 26301816 | |
| LEF1(V$LEF1TCF1_Q4) | 3.89 | cell proliferation | 31623618 | |
| upstream stimulating factor (V$USF_Q6) | 3.84 | lipid metabolism and atherosclerosis | 19910639 | |
| activator protein 1(V$AP1_Q4) |
3.84 |
cell growth, differentiation, and apoptosis |
15564374 |
|
| down SGs in CKD | nuclear respiratory factor 2(V$NRF2_01) | 5.56 | oxidative stress | 27646262 |
| SREBP(V$SREBP_Q3) | 5.51 | glucose metabolism | 28920951 | |
| NFKB(V$NFKB_Q6_01) | 5.24 | proinflammatory response | 31101940 | |
| c-ETS-1 binding site (V$ETS1_B) | 4.9 | cell differentiation | 30566881 | |
| AP-1 binding site (V$AP1_C) | 4.84 | cell growth, differentiation, and apoptosis | 15564374 | |
| c-Ets-2 binding sites (V$ETS2_B) | 4.84 | osteogenesis | 11175361 | |
| ZTA (V$ZTA_Q2) | 4.78 | Epstein-Barr Virus Reactivation | 27708396 | |
| c-Rel (V$CREL_01) | 4.61 | tumorigenesis | 26757421 | |
| DEAF1(V$DEAF1_01) | 4.61 | intellectual disability | 24726472 | |
| TEL2(V$TEL2_Q6) |
4.49 |
hematopoiesis |
28693791 |
|
| up SGs in ESRD | Egr-1(V$EGR1_01) | 8.42 | inflammation and fibrosis | 21511034 |
| Egr-2(V$EGR2_01) | 7.4 | maintenance of peripheral nerve myelin | 15836632 | |
| CEBPGAMMA (V$CEBPGAMMA_Q6) | 6.61 | antioxidant regulator | 26667036 | |
| PIT1(V$PIT1_Q6) | 6 | obesity and insulin resistance | 27568561 | |
| Ikaros 3(V$IK3_01) | 5.94 | T helper cell 2 transcription factor | 21469117 | |
| Hepatic nuclear factor 1(V$HNF1_C) | 5.79 | transcription inducer for proinflammatory molecules such as C-reactive protein, IL-6, HNF1a and HNF4a in CKD | 29330688 | |
| early growth response gene 3 product (V$EGR3_01) | 5.18 | IL-1b co-expressed inflammatory gene | 31612215 | |
| POU1F1(V$POU1F1_Q6) | 5.13 | inflammation/immunity and hormone regulator | 27709372 | |
| E4BP4(V$E4BP4_01) | 4.96 | obesity and insulin resistance | 27050305 | |
| cell division control protein 5(V$CDC5_01) |
4.72 |
unguarded cellular proliferation |
18583928 |
|
| down SGs in ESRD | E2F1(V$E2F1_Q6) | 12.62 | control cell-cycle progression from G1 to S phase | 7969176 |
| nuclear respiratory factor 2(V$NRF2_01) | 12.62 | oxidative stress | 27646262 | |
| E2F1(V$E2F1_Q6_01) | 12.62 | control cell-cycle progression from G1 to S phase | 7969176 | |
| E2F1(V$E2F1_Q3_01) | 12.62 | control cell-cycle progression from G1 to S phase | 7969176 | |
| E2F(V$E2F_Q6) | 12.62 | control cell-cycle progression from G1 to S phase | 7969176 | |
| E2F(V$E2F_Q3_01) | 12.62 | control cell-cycle progression from G1 to S phase | 7969176 | |
| KROX (V$KROX_Q6) | 12.62 | tooth development | 12489153 | |
| CREB(V$CREBATF_Q6) | 12.62 | formation of long-lasting memories | 20223527 | |
| CREB(V$CREB_Q4_01) | 12.62 | formation of long-lasting memories | 20223527 | |
| NRF1(V$NRF1_Q6) | 12.62 | Cholesterol Homeostasis | 29149604 |
*P value were calculated based on the probability of seeing a Bayes factor of a particular magnitude in a query.