Discovering Transcription Factor Binding Sites in Co-expressed Genes
(A) Choose a group of co-expressed genes from the Yeast Cell Cycle Database by first entering a single gene of interest to you and then clicking on select all co-expressed genes:
(B) Collect all the names of the genes and enter them in Go Term Finder to discover common biological processes, common molecular mechanisms and common cellular components in the Saccharomyces Genome Database. Be sure to include the graphical network figure for each and zoom in on important areas:
(C) Using the Batch download link (located at: http://www.yeastgenome.org/cgi-bin/batchDownload ), collect all the gene sequences plus 1 KB upstream and enter the 1 KB upstream sequence from all the genes into MDScan and search for motifs 8, 10 and 12 bases long:
(D) You may have to remove simple sequences such as (tatatatata or tttttttttt or cacacacaca) by globally replacing them with an X
character in order to ignore simple sequence repeats from the list of motifs found.
(E) Enter your list of co-expressed gene names in YeasTract web site and see if MDScan has discovered any known transcription binding sites:
(F) Be sure to include sequence logos of all the Transcription factor binding sites
Please submit your homework to bioc218-spr1314-staff@lists.stanford.edu. Please include sufficient output from your analyses (including sequence logos of all the Transcription factor binding sites) to support each of your answers/conclusions.
