Talk:Dahlquist:Yeast Transcription Factors

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

Back to Dahlquist Lab main page.

To Do

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.
• Need to finish Cin5p target MAPPs for:
  • 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.

• Gasch et al. 2000
• Causton et al. 2001
• Sahara et al. 2002; have complete dataset offline
• Schade et al. 2004; have complete dataset from author
• Kandror et al. 2004; dataset not available
• Murata et al. 2006; dataset not available?
• Tai et al. 2007
• De Nicola et al. 2007; Supplemental Data but not complete dataset
• Pizarro et al. 2008; Supplemental Data
• Check with online compendia, Hughes and Princeton

Bibliography

Cin5 Literature Curation Summary from SGD

1. Agarwal AK, Xu T, Jacob MR, Feng Q, Lorenz MC, Walker LA, and Clark AM. Role of heme in the antifungal activity of the azaoxoaporphine alkaloid sampangine. Eukaryot Cell. 2008 Feb;7(2):387-400. DOI:10.1128/EC.00323-07 |
2. Tan K, Feizi H, Luo C, Fan SH, Ravasi T, and Ideker TG. A systems approach to delineate functions of paralogous transcription factors: role of the Yap family in the DNA damage response. Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):2934-9. DOI:10.1073/pnas.0708670105 |
3. Kresnowati MT, van Winden WA, Almering MJ, ten Pierick A, Ras C, Knijnenburg TA, Daran-Lapujade P, Pronk JT, Heijnen JJ, and Daran JM. When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation. Mol Syst Biol. 2006;2:49. DOI:10.1038/msb4100083 |
4. Lacefield S, Magendantz M, and Solomon F. Consequences of defective tubulin folding on heterodimer levels, mitosis and spindle morphology in Saccharomyces cerevisiae. Genetics. 2006 Jun;173(2):635-46. DOI:10.1534/genetics.105.055160 |
5. Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, and Ideker T. A systems approach to mapping DNA damage response pathways. Science. 2006 May 19;312(5776):1054-9. DOI:10.1126/science.1122088 |
6. Ishikawa T, Unno K, Nonaka G, Nakajima H, and Kitamoto K. Isolation of Saccharomyces cerevisiae RNase T1 hypersensitive (rns) mutants and genetic analysis of the RNS1/DSL1 gene. J Gen Appl Microbiol. 2005 Apr;51(2):73-82. DOI:10.2323/jgam.51.73 |
7. Zakrzewska A, Boorsma A, Brul S, Hellingwerf KJ, and Klis FM. Transcriptional response of Saccharomyces cerevisiae to the plasma membrane-perturbing compound chitosan. Eukaryot Cell. 2005 Apr;4(4):703-15. DOI:10.1128/EC.4.4.703-715.2005 |
8. Nevitt T, Pereira J, Azevedo D, Guerreiro P, and Rodrigues-Pousada C. Expression of YAP4 in Saccharomyces cerevisiae under osmotic stress. Biochem J. 2004 Apr 15;379(Pt 2):367-74. DOI:10.1042/BJ20031127 |
9. Nevitt T, Pereira J, and Rodrigues-Pousada C. YAP4 gene expression is induced in response to several forms of stress in Saccharomyces cerevisiae. Yeast. 2004 Dec;21(16):1365-74. DOI:10.1002/yea.1188 |
10. Dagkessamanskaia A, Martin-Yken H, Basmaji F, Briza P, and Francois J. Interaction of Knr4 protein, a protein involved in cell wall synthesis, with tyrosine tRNA synthetase encoded by TYS1 in Saccharomyces cerevisiae. FEMS Microbiol Lett. 2001 Jun 12;200(1):53-8. DOI:10.1111/j.1574-6968.2001.tb10692.x |
11. Furuchi T, Ishikawa H, Miura N, Ishizuka M, Kajiya K, Kuge S, and Naganuma A. Two nuclear proteins, Cin5 and Ydr259c, confer resistance to cisplatin in Saccharomyces cerevisiae. Mol Pharmacol. 2001 Mar;59(3):470-4. DOI:10.1124/mol.59.3.470 |
12. Jackson T, Kwon E, Chachulska AM, and Hyman LE. Novel roles for elongin C in yeast. Biochim Biophys Acta. 2000 Apr 25;1491(1-3):161-76. DOI:10.1016/s0167-4781(00)00052-x |
13. Delling U, Raymond M, and Schurr E. Identification of Saccharomyces cerevisiae genes conferring resistance to quinoline ring-containing antimalarial drugs. Antimicrob Agents Chemother. 1998 May;42(5):1034-41. DOI:10.1128/AAC.42.5.1034 |

Short explanation of the relevance of each paper to CIN5 can be seen if you click on "Edit."

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)

Completed

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)