TFBS Model Estimation ===================== Organism: yeast, Saccharomyces cerevisiae Factor Accession Number: T00487 Factor Name: MATalpha2 Short Functional Description: Repressor of a-specific genes in alpha cells; with a1: repressor of haploid-specific genes in diploid cells alpha2 causes stable nucleosome binding adjacent to the operator; together with MCM1: specific recognition of STE6 promoter; cooperation with Ssn6-Tup1 required for alpha2/MCM1 action and, probably, also for that of alpha2/a1; >M00031 NCATGTNAWN Subsequences for Estimating PSSM Model CAATGTAGAA AGATGTCACA GCTTGTTAAT TCATGTACTT GCGTTTAGAA TCATGTCCAC TCATGTTATT TCGTGTATTT ACATGTCTTC TCATGTATTC TAGAGTGAAA GCCTGCGATG TTATGTTAAA CCGCGTTAAA Factor Accession Number: T00500 Factor Name: MCM1 Short Functional Description: activator by its own or, for alpha-specific genes, in cooperation with MATalpha1; repressor of a-specific genes in cooperation with MATalpha2; activator of replication of DNA; presumably regulates genes involved in cell cycle control, in synthesis of cell wall/membrane structures, cell metabolism, and an heat-shock-inducible secreted glycoprotein; interacts with Arg80p T00043 and is stabilised by Arg82p T01259; >M00125 WTTCCYAAWNNGGTAA Subsequences for Estimating PSSM Model CATCCTAAAAAGGAAA ATGCCTAAACAGGTAG CGTCCTAAACAGGACA TCGCCTAAATAAGTAA ACTCCTAAATAGGCTA TTGCCTAAAGCGGTAA TTTCCTAATCGGTTGT TATCCTAATGTGGTAT ACTCCTATATAAATCG TTTCCTAGACCGGTCA ATGCCTTAACGGGTAA ATACCTTATGTGGTAT TTACCTCATCCAGCCT TTGCCCAAAAGGGACA ATACCCAAAGTAGAAA GTTCCCAATCAGGAGA CCACCCAATCCAGTAA AGTCCCAATCGGGTCA TGACCCAATATGGTAT TATCCCATTAAGGTAA AGTCCCATTAGGGTAA GTTCCCTATCGGGTAA TTACCCGATTTGGAAT 5 TFBS for Cis-Regulatory Element Prediction ============================================ These given here are frequency/count PSSM tables. You would have to normalize them, possibly adding pseudocounts to smooth the normalization. Accession Number: T00056 Factor Name: ABF1 Short Functional Description: functionally similar to RAP1 T00715; C-terminal region CS1 is responsible for transcriptional silencing and/or repression in context-dependent manner, CS2 is required for all functions of Abf1p, namely transcriptional activation, stimulation of DNA replication, and gene silencing.; >M00197 NRTCAYTNNNNACGW A C G T 3.2000 4.0300 3.0200 4.9900 9.9700 0.0000 5.2600 0.0000 0.0000 0.0000 0.0000 15.2400 0.0000 15.2400 0.0000 0.0000 10.5400 0.6500 2.3400 1.7000 0.0000 8.1300 0.0000 7.1000 1.4500 1.6300 2.9500 9.2000 6.1100 3.5600 2.4000 3.1700 2.5200 2.9900 2.2800 7.4500 6.9400 4.0200 1.8700 2.4200 5.8500 1.9200 3.9300 3.5300 15.2400 0.0000 0.0000 0.0000 0.0000 15.2400 0.0000 0.0000 0.0000 0.0000 15.2400 0.0000 5.8300 0.0000 3.2100 5.3600 Accession Number: T03717 Factor Name: ZAP1 Short Functional Description: Zap1p plays a central role in zinc ion homeostasis by regulating transcription of the zinc uptake system genes (ZRT1, ZRT2) in response to zinc; Zap1p regulates transcription of its own promoter in response to zinc through a positive autoregulatory mechanism.; >M00754 ACCCTAAAGGT A C G T 7.0000 0.0000 0.0000 0.0000 0.0000 7.0000 0.0000 0.0000 0.0000 7.0000 0.0000 0.0000 0.0000 6.0000 0.0000 1.0000 0.0000 1.0000 0.0000 6.0000 4.0000 2.0000 0.0000 1.0000 7.0000 0.0000 0.0000 0.0000 7.0000 0.0000 0.0000 0.0000 0.0000 0.0000 7.0000 0.0000 0.0000 0.0000 7.0000 0.0000 0.0000 0.0000 0.0000 7.0000