Table 2 Examples of top network links or in degree of genes
From: Characterizing disease states from topological properties of transcriptional regulatory networks
Dataset | Network Links | Genes with Differential In Degrees |
|---|---|---|
Leukemia | ||
ALL/AML | RUNX1→RAG1 CBFB→RAG1 RARA→ELA2 RARA→SERPING1 RARA→PFC RARA→MSH2 RARA→MPO | MGST1 HOXA9 DF PYGL CD33 CTSC PFC PTX3 VPREB1 POU2AF1 MLC1SA RAG1 CSTA LAMP2 MPO BLK ELA2 UPP1 MAN2B1 CXCL2 ACTA2 ANXA1 CD24 ZYX BAT1 PLEK GATA3 |
Myeloid Leukemia | NFKB1→F3 EGR1→F3 CEBPA→PPARG FOXO3A→RUNX1T1 MYC→LTC4S MAX→LTC4S MYC→HLA-DM | CDH7 NFKB1 ZNF516 BNIP2 STAT3 PLEKHM1 CPS1 CDC2 CD2 MT1DP HNF4A BLOC1S1 CRISP2 ARR3 EZH1 IGHGP EZH2 |
Breast Cancer | ||
Duke | NFKB1→BTRC FOXO3A→PLS1 BHLHB2→HGFBP6 POU2F1→TRAF3IP1 FOXJ2→MEP1A MEF2D→MEP1A | DRD2 RPA3 NDUFA6 NRF1 HBB CLCNKB PDE3A FKBP4 MFAP1 SURF1 PIM1 SLIT1 TAF1 DUSP4 CRYBB2 TNP2 MAPK7 LTBP1 TCEB2 SOX15 HIP2 |
Dutch | PAX8→FEN1 PAX8→E2F1 TCF2→KLHL5 FOXM1→TAD3 TCF2→ZBTB4 ELK1→UBE2C TCF2→UBE2C E2F1→CELSR2 PAX8→TK1 FOXM1→DPF2 FOXM1→CD160 FOXM1→CCL3 E2F1→UBE2Q USF1→MYBL2 FOXM1→ABCB1 E2F1→TK2 PBX1→TROAP | PSMB10 TCP10 BAK1 DPP6 PDGFRL ADCY7 SEC13L1 ALDH3A2 RAB5A HDAC3 PCTK1 PGC IFNA7 IHH ABCD3 PFKFB3 |
Paired Cell Types | ||
Renal Carcinoma vs. Normal Kidney | BHLHB3→IL15RA FOXO3A→PLK2 BHLHB3→HLX1 NR1H3→CDCA7L PAX2→KCNK10 | ABCA4 AP2A2 ALDH3B2 AGXT AGRP ADCY2 ACOX1 ACP2 ABCA1 ABAT NAT1 ADCY8 AHSG ADCY3 PARP4 ACVR2 ADRA2A ACY1 AIM1 |
Monocytes vs. Granulocytes | PAX8→MARCO NR1H2→MARCO PAX8→MARCO CEBPA→MARCO CEBPG→MARCO RXRB→MARCO RARA→MARCO HIF1A→PRSS15 EGR2→RIS1 RARA→SLC30A6 | MRPS16 CYP4F12 ARL4A GSS TPST1 PMPCA CTAGE5 HEY1 KIF20A PKN2 SLC30A6 DNAJD1 PRSS15 HBEGF MARCO NDUFA7 |