Transcription factors with DNA binding sites over-represented in downregulated genes
| TF . | Description . | # of genes & (P value) . | Reference . |
|---|---|---|---|
| Fkh1 | Forkhead family transcription factor with a minor role in the expression of G2/M phase genes; negatively regulates transcriptional elongation; positive role in chromatin silencing at HML and HMR; regulates donor preference during switching | 80 (0) | (Pondugula et al., 2009; Knott et al., 2012; Ostrow et al., 2014; Reimand et al., 2010; Workman et al., 2006; Harbison et al., 2004; Lee et al., 2002) |
| Ifh1 | Coactivator that regulates transcription of ribosomal protein (RP) genes; recruited to RP gene promoters during optimal growth conditions via Fhl1p; subunit of CURI, a complex that coordinates RP production and pre-rRNA processing | 42 (0) | (Rudra et al., 2005; Schawalder et al., 2004; Lavoie et al., 2010; Cai et al., 2013; Venters and Pugh, 2009; Wade et al., 2004; Reja et al., 2015) |
| Spt23 | ER membrane protein involved in regulation of OLE1 transcription; inactive ER form dimerizes and one subunit is then activated by ubiquitin/proteasome-dependent processing followed by nuclear targeting; SPT23 has a paralog, MGA2, that arose from the whole genome duplication | 62 (6.6E-14) | (Auld et al., 2006; Reimand et al., 2010) |
| Fhl1 | Regulator of ribosomal protein transcription; has forkhead associated domain that binds phosphorylated proteins; also has forkhead DNA-binding domain but does not bind DNA in vitro; suppresses RNA pol III and splicing factor prp4 mutants | 53 (1.11E-07) | (Rudra et al., 2005; Lee et al., 2002; Tai et al., 2017; Harbison et al., 2004; Kasahara et al., 2007; Lavoie et al., 2010) |
| Yap6 | Basic leucine zipper (bZIP) transcription factor; physically interacts with the Tup1-Cyc8 complex and recruits Tup1p to its targets; overexpression increases sodium and lithium tolerance; computational analysis suggests a role in regulation of expression of genes involved in carbohydrate metabolism; YAP6 has a paralog, CIN5, that arose from the whole genome duplication | 33 (6.0E-07) | (Lee et al., 2002; Harbison et al., 2004; Ni et al., 2009; Reimand et al., 2010) |
| Fkh2 | Forkhead family transcription factor with a major role in the expression of G2/M phase genes; positively regulates transcriptional elongation; negative role in chromatin silencing at HML and HMR; substrate of the Cdc28p/Clb5p kinase | 53 (7.82E-07) | (Zhu et al., 2000; Simon et al., 2001; Harbison et al., 2004; Shapira et al., 2004; Workman et al., 2006; Pondugula et al., 2009; Reimand et al., 2010; Ostrow et al., 2014; Linke et al., 2017; Ghavidel et al., 2018) |
| Rap1 | DNA-binding protein involved in either activation or repression of transcription, depending on binding site context; also binds telomere sequences and plays a role in telomeric position effect (silencing) and telomere structure | 59 (9.6E-05) | (Chua et al., 2006; Reimand et al., 2010; Lavoie et al., 2010; Workman et al., 2006; Kasahara et al., 2007; Venters and Pugh, 2009; Lieb et al., 2001; De Sanctis et al., 2002; Buchman et al., 1988b; Yarragudi et al., 2007; Lee et al., 2002; Harbison et al., 2004; Hall et al., 2006; Reja et al., 2015) |
| Ndt80 | Meiosis-specific transcription factor required for exit from pachytene and for full meiotic recombination; activates middle sporulation genes; competes with Sum1p for binding to promoters containing middle sporulation elements (MSE) | 49 (1.4E-04) | (Nocedal et al., 2017; Reimand et al., 2010; Chu and Herskowitz, 1998) |
| TF . | Description . | # of genes & (P value) . | Reference . |
|---|---|---|---|
| Fkh1 | Forkhead family transcription factor with a minor role in the expression of G2/M phase genes; negatively regulates transcriptional elongation; positive role in chromatin silencing at HML and HMR; regulates donor preference during switching | 80 (0) | (Pondugula et al., 2009; Knott et al., 2012; Ostrow et al., 2014; Reimand et al., 2010; Workman et al., 2006; Harbison et al., 2004; Lee et al., 2002) |
| Ifh1 | Coactivator that regulates transcription of ribosomal protein (RP) genes; recruited to RP gene promoters during optimal growth conditions via Fhl1p; subunit of CURI, a complex that coordinates RP production and pre-rRNA processing | 42 (0) | (Rudra et al., 2005; Schawalder et al., 2004; Lavoie et al., 2010; Cai et al., 2013; Venters and Pugh, 2009; Wade et al., 2004; Reja et al., 2015) |
| Spt23 | ER membrane protein involved in regulation of OLE1 transcription; inactive ER form dimerizes and one subunit is then activated by ubiquitin/proteasome-dependent processing followed by nuclear targeting; SPT23 has a paralog, MGA2, that arose from the whole genome duplication | 62 (6.6E-14) | (Auld et al., 2006; Reimand et al., 2010) |
| Fhl1 | Regulator of ribosomal protein transcription; has forkhead associated domain that binds phosphorylated proteins; also has forkhead DNA-binding domain but does not bind DNA in vitro; suppresses RNA pol III and splicing factor prp4 mutants | 53 (1.11E-07) | (Rudra et al., 2005; Lee et al., 2002; Tai et al., 2017; Harbison et al., 2004; Kasahara et al., 2007; Lavoie et al., 2010) |
| Yap6 | Basic leucine zipper (bZIP) transcription factor; physically interacts with the Tup1-Cyc8 complex and recruits Tup1p to its targets; overexpression increases sodium and lithium tolerance; computational analysis suggests a role in regulation of expression of genes involved in carbohydrate metabolism; YAP6 has a paralog, CIN5, that arose from the whole genome duplication | 33 (6.0E-07) | (Lee et al., 2002; Harbison et al., 2004; Ni et al., 2009; Reimand et al., 2010) |
| Fkh2 | Forkhead family transcription factor with a major role in the expression of G2/M phase genes; positively regulates transcriptional elongation; negative role in chromatin silencing at HML and HMR; substrate of the Cdc28p/Clb5p kinase | 53 (7.82E-07) | (Zhu et al., 2000; Simon et al., 2001; Harbison et al., 2004; Shapira et al., 2004; Workman et al., 2006; Pondugula et al., 2009; Reimand et al., 2010; Ostrow et al., 2014; Linke et al., 2017; Ghavidel et al., 2018) |
| Rap1 | DNA-binding protein involved in either activation or repression of transcription, depending on binding site context; also binds telomere sequences and plays a role in telomeric position effect (silencing) and telomere structure | 59 (9.6E-05) | (Chua et al., 2006; Reimand et al., 2010; Lavoie et al., 2010; Workman et al., 2006; Kasahara et al., 2007; Venters and Pugh, 2009; Lieb et al., 2001; De Sanctis et al., 2002; Buchman et al., 1988b; Yarragudi et al., 2007; Lee et al., 2002; Harbison et al., 2004; Hall et al., 2006; Reja et al., 2015) |
| Ndt80 | Meiosis-specific transcription factor required for exit from pachytene and for full meiotic recombination; activates middle sporulation genes; competes with Sum1p for binding to promoters containing middle sporulation elements (MSE) | 49 (1.4E-04) | (Nocedal et al., 2017; Reimand et al., 2010; Chu and Herskowitz, 1998) |
Analysis of genes with >twofold decrease in response to edelfosine (115 genes) as determined by Yeastract (Monteiro et al., 2020) using DNA binding evidence only. P values calculated using the hypergeometric test.