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)

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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. 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

Bibliography

Note to Kevin: if you enclose each reference within its own biblio tags, then your hidden text will reappear, see example below. — Kam D. Dahlquist 18:39, 23 December 2008 (EST)

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 |

• Overexpression of CIN5 confers resistance to sampagine (involved in oxidative stress)

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 |

• Explains how CIN5 is related to other YAP family transcription factors. CIN5 involved in DNA damage response and bound to greatest number of genes in DNA damaging conditions. Along with YAP1, CIN5 is a major regulator of the Yap transcriptional network. Provides CIN5 DNA binding motif.

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 |

• CIN5 involved in downregulation of genes under sudden glucose limitation

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 |

• A tripple mutant, ΔPAC10ΔPLP1ΔCIN5, shows significantly decreased levels of tubulin (~20% of wildtype). The authors were unsure what role CIN5 plays in the tubulin pathway.

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 |

• Same paper used in adding to CIN5 TF targets, found under DNA damaging conditions. Shows CIN5 involved in the DNA damage response pathway.

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 |

• Cin5p interacts with Rns1p, a protein proposed to be inovlved in intracellular protein transport.

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 |

• CIN5 is involved in the response to chitosan, an antimicrobial drug.

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 |

• CIN5 is involved in the response to osmotic stress.

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 |

• CIN5 is involved in the response to heat, oxidative, heavy metal, metalloid stresses. Regulated by phosphorylation.

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 |

• CIN5 interacts with Knr4p to regulate genes in response to salt stress.

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 |

• Overexpression of CIN5 confers resistance to cisplatin as well as DNA-alkylating agents methylmethanesulfonate and mitomycin C. Also found that CIN5 is located in the nucleus.

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 |

• CIN5 interacts with Elc1, which also interacts with other proteins involved in the stress response.

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 |

• Overexpression of CIN5 confers resistance to quinoline-containing antimalarial drugs quinidine, mefloquine and chloroquine.

14. Mendizabal I, Rios G, Mulet JM, Serrano R, and de Larrinoa IF. Yeast putative transcription factors involved in salt tolerance. FEBS Lett. 1998 Mar 27;425(2):323-8. DOI:10.1016/s0014-5793(98)00249-x |

• Overexpression of CIN5 increases sodium and lithium tolerance.

15. Fernandes L, Rodrigues-Pousada C, and Struhl K. Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions. Mol Cell Biol. 1997 Dec;17(12):6982-93. DOI:10.1128/MCB.17.12.6982 |

• Explains Yap family of transcription factors. Also mutations in CIN5 cause chromosome instability and suppress cold sensitivity of yap1 mutants.

</biblio>

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. — 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)
• 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.