Discriminative motif finding using ChIP-chip data

In this research, we combined WordSpy with ChIP-chip data on S. cerevisiae for finding TF binding motifs. The ChIP-chip data are from the Science paper of Young Lab. In this set of data, 113 transcription factors (TFs) are tested. For each of these TFs, we selected as positive data those promoters that the TF could bind to with p-value <0.01 in ChIP-chip experiments and selected the promoters with p-value >0.99 as negative data. For convienence, we give each TF an ID number (transcription factor IDs). Then the gene names of the positive and negative data for each TF are available below.

• positive gene names
• negative gene names

The promoter sequences are gotten with RSA tools. By filtered out some dubious genes, we have 5864 promoter sequences as a whole set. The fasta file is available here (5864 yeast promoters). The corresponding promoter sequences (fasta files) of the positive and negative data for each TF are available below.

• positive promoter sequences
• negative promoter sequences

Among 113 TFs, we carefully select some putative binding motifs for 12 cell-cycle related transcription factors.

• putative discriminative binding motifs for 12 cell-cycle related TFs
• MEME results for comparison
• AlignACE results for comparison

The complete list of putative binding motifs for 113 transcription factors is also available.

• putative discrimiative binding motifs for 113 TFs

The complete outputs for all the TFs are available below.

• dictionaries for 113 transcrition factors