Table 1 Examples of predicted TF-target gene pairs generated by the LINK and STAR models to the S. cerevisiae transcriptional regulatory network published by Milo et al. [22]. The table shows the overlap of these links with: a) high confidence ChIP-on-chip data [6] at P ≤ 0.001 and with sequence conservation across at least 3 yeast species, b) moderate confidence ChIP-on-chip data at P ≤ 0.005 but excluding the high confidence binding events in (a), or c) the literature-driven gene regulatory network constructed by Herrgard et al. [21]
From: Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae
Links predicted by the LINK model | |
|---|---|
Overlap with ChIP-on-chip data at P ≤ 0.001 with sequence conservation in at least 3 yeast species | ACE2→CST13, GAT1→DAL2, GCN4→ATR1, GCN4→FOL2, GCN4→IDP1, GCN4→ISU1, GLN3→ARG1, GLN3→UGA3, GLN3→YHR029C, ROX1⊣YLR413W, STE12→FUS2, STE12→GPA1, STE12→INP52, STE12→KAR4, STE12→TEC1, SWI4→OCH1, SWI5→YPL158C, TEC1→GFA1, TEC1→GIC2, TEC1→PCL2, TEC1→STE12, UME6→YOR291W, YAP1→CYT2 |
Overlap with ChIP-on-chip data at P ≤ 0.005 excluding events at P ≤ 0.001 with sequence conservation across at least 3 yeast species | ACE2→SCW11, ASH1→HSP150, ASH1→PIR1, ASH1→PIR3, DAL80→YLR053C, GAT1→PUT1, GCN4→YMC1, GCN4→ALD5, GCN4→YMC2, GCN4→CAF16, GCN4→BAT1, GCN4→ORT1, STE12→ASG7, STE12→YDR249C, STE12→MFA2, TEC1→PRM1, TEC1→PRM6, TEC1→AGA2, TEC1→KAR5, TEC1→PRP39, YAP1→AAD6, YAP1→GTT2, YAP1→YLR460C |
Literature supported | BAS1→HIS7, DAL80→GAP1, MSN4→TPS2, STE12→MFA2, STE12→TEC1, TEC1→STE12 |
Links predicted by the STAR model | |
Overlap with ChIP-on-chip data at P ≤ 0.001 with sequence conservation in at least 3 yeast species | ACE2⊣BUD9, ADR1→PXA1, BAS1→HIS4, BAS1→SHM2, FKH2→ALK1, FKH2→SWI5, GAT1→DAL2, GCN4→ATR1, GCN4→FOL2, GCN4→IDP1, GCN4→ILV3, GCN4→UGA3, GCR1→CDC19, GLN3→CPS1, HAP4→ATP1, HSF1→CPR6, MCM1→YNL058C, MSN2→TSL1, MSN4→TSL1, PHO4→PHO86, RPN4→PUP2, STE12→FUS2, STE12→GPA1, STE12→INP52, STE12→KAR4, STE12→TEC1, SWI5⊣CYK3 |
Overlap with ChIP-on-chip data at P ≤ 0.005 excluding events at P ≤ 0.001 with sequence conservation across at least 3 yeast species | ABF2→RPS28A, ACE2→FAA3, ACE2→PRY3, ACE2→SCW11, DAL80→YLR053C, FKH2→ACE2, FKH2→HOF1, FKH2→YLR190W, FKH2→YOR315W, FKH2→YPL141C, GAT1→DAL3, GAT1→DAL5, GAT1→DAL7, GAT1→MEP2, GAT1→PUT1, GCN4→ALD5, GCN4→BAT1, GCN4→CAF16, GCN4→ORT1, GCN4→YMC1, GCN4→YMC2, GCN4→YNL129W, GLN3→MEP2, GLN3→OPT2, GLN3→YGR125W, GLN3→YMR088C, HAP4→NDI1, HAP4→SDH1, HSF1→HSP10, HSF1→HSP60, HSF1→TSL1, LEU3→BAT1, MCM1→BUD4, MCM1→YOR315W, RAP1⊣GPM1, RAP1⊣PGI1, RCS1→ARN1, RCS1→TAF1, RPN4→RPN12, RPN4→RPN6, SKN7⊣DDR48, SKN7⊣GPX2, STE12→ASG7, STE12→MFA2, SWI5⊣FAA3, SWI5⊣PIR1, SWI5⊣PRY3, SWI5⊣TEC1, YAP1→AAD6 |
Literature supported | BAS1→ADE1, BAS1→ADE13, BAS1→ADE17, BAS1→ADE2, BAS1→ADE5,7, BAS1→HIS1, BAS1→HIS4, BAS1→HIS7, DAL80→GAP1, GCR1→CDC19, HAP4→SDH1, HSF1→SSA4, STE12→MFA2, STE12→TEC1 |