Talk:Dahlquist:Yeast Transcription Factors

Kevin, let's use this page to communicate a To Do list. &mdash; Kam D. Dahlquist 18:21, 22 September 2008 (EDT)

Back to Dahlquist Lab main page.

Wild type

 * Run MAPPFinder for all timepoints, increased and decreased
 * Edit GO results lists for redundancy and group related GO terms
 * STEM clustering (might be done; Kam needs to check)
 * EDGE statistics
 * Re-run clusters/groups of genes through TF finding databases

cin5Δ

 * Run MAPPFinder for all timepoints, increased and decreased
 * Edit GO results lists for redundancy and group related GO terms
 * STEM clustering (might be done; Kam needs to check)
 * EDGE statistics
 * Re-run clusters/groups of genes through TF finding databases

MAPPs
See also MAPP Archive page.


 * One humongous consolidated MAPP (also Excel spreadsheet), then individual MAPPs for each data source. DONE
 * Need to finish Cin5p target MAPPs for: DONE
 * Workman et al.
 * Hu et al.
 * TVSM
 * Yeastract

Comparator Expression Datasets

 * We need to download data from comparator studies, load it into GenMAPP, so that we can analyze them side-by-side with our study.
 * List of comparator datasets has been moved to a new Yeast Cold Shock page

MIAME Compliance

 * We need to fill out the "Minimal Information about a Microarray Experiment" information so that when we publish, we can upload the data to a database.
 * MAGE-TAB is one way to do it, but I'm having trouble actually finding a downloadable form that we can fill out. I've e-mailed the MGED "Contact Us" e-mail address asking about it. I guess we can download the paper from that page and try to figure it out ourselves.  &mdash; Kam D. Dahlquist 16:53, 29 October 2008 (EDT)

Wild type

 * Excel-based statistics
 * multtest

cin5Δ

 * Excel-based statistics
 * multtest

MAPPs

 * consolidated Cin5p target MAPP for Lee, Harbison, Tan. (redundant, gene appears more than once if in multiple papers)
 * individual Cin5p target MAPPs for all sources, as well as one huge Cin5p target MAPP containing genes from Lee, Harbison, Tan, Workman, Hu, YEASTRACT, TVSM
 * Have downloaded Cin5p targets from the following sources:
 * Lee et al.
 * Harbison et al.
 * Tan et al.
 * One consolidated MAPP with Lee, Harbison, and Tan has been completed.
 * Workman et al.
 * Hu et al.
 * TVSM
 * Yeastract
 * MAPPs for each of the above have been created as well.
 * Total compiled Cin5p target MAPP has also been created including all of the data above, saved on desktop in "Database and Reference TF Search" as Cin5Targets_Total_Compiled.mapp. Four total MAPPs were created because the max number of genes was exceeded.