Dahlquist:Yeast Transcription Factors

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Revision as of 10:39, 18 June 2010 by Kam D. Dahlquist (talk | contribs) (TF Network Data: fixed formatting of biblio tagged papers)

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Dahlquist Lab Yeast Transcription Factor Resources

This page displays a compiled list of yeast transcription factor resources. Included are data on transcription factor target genes and transcription factor regulatory networks in yeast, links to web servers providing easy-to-use TF searches and other potentially helpful resources. I also added notes about what data I have gotten from each dataset for the Cin5p targets list.

TF Network Data

  1. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, and Young RA. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 2002 Oct 25;298(5594):799-804. DOI:10.1126/science.1075090 | PubMed ID:12399584 | HubMed [Paper1]
  2. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, and Young RA. Transcriptional regulatory code of a eukaryotic genome. Nature. 2004 Sep 2;431(7004):99-104. DOI:10.1038/nature02800 | PubMed ID:15343339 | HubMed [Paper2]
  3. MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, and Fraenkel E. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics. 2006 Mar 7;7:113. DOI:10.1186/1471-2105-7-113 | PubMed ID:16522208 | HubMed [Paper3]
  4. 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 | PubMed ID:16709784 | HubMed [Paper4]
  5. Hu Z, Killion PJ, and Iyer VR. Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet. 2007 May;39(5):683-7. DOI:10.1038/ng2012 | PubMed ID:17417638 | HubMed [Paper5]
  6. Jothi R, Balaji S, Wuster A, Grochow JA, Gsponer J, Przytycka TM, Aravind L, and Babu MM. Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol. 2009;5:294. DOI:10.1038/msb.2009.52 | PubMed ID:19690563 | HubMed [Paper6]
  7. Balaji S, Babu MM, Iyer LM, Luscombe NM, and Aravind L. Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J Mol Biol. 2006 Jun 30;360(1):213-27. DOI:10.1016/j.jmb.2006.04.029 | PubMed ID:16762362 | HubMed [Paper7]

All Medline abstracts: PubMed | HubMed

  • TF-target interactions through DNA damage response
    • Measured binding locations(ChIP-chip) of damage-related transcription factors (including Cin5) after exposure to MMS. Validated by checking against binding in knock-out strains for TFs.
    • Downloaded the MMS and Untreated ChIP datasets to be filtered for Cin5p targets, Excel spreadsheet of p values for binding.
    • This was a paper mentioned in the Yeastract database along with Lee, Harbison, Tan.
    • From Workman, Christopher T., et al. A systems approach to mapping DNA damage response pathways. Science 2006. 1054-1059. PubMed
  • TF network though systematic deletions
    • Performed microarray analysis of knockout strains for many transcription factors and compared expression profiles to determine regulatory relationships. Allows distinguishing between activated and repressed transcription factor targets
    • Downloaded the filtered and unfiltered network in X-score format. Gene-gene-value triples.
    • From Hu, Zhanzhi, et al. Genetic reconstruction of a functional transcriptional regulatory network. Nature Genetics 2007. 39:5. 683-687. PubMed
  • Updated TF network to determine new relationships
    • Used improved algorithms to detect new regulatory relationships in the transcription factor network
    • Fig. 3 Shows that the effect on Cin5 was to gain approximately 10 new interactions and lose approximately two as compared to the older model.
    • A figure of the new network was downloaded. PDF format
    • From MacIsaac, Kenzie D., et al. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 2006, 7:113. PubMed
  • Kam D. Dahlquist 12:08, 13 October 2008 (EDT) NEW Balaji et al. (2006) Comprehensive Analysis of Combinatorial Regulation using the Transcriptional Regulatory Network of Yeast. Journal of Molecular Biology 360: 213-227. Full text from ScienceDirect

Web Servers

  • MYBS Mining Yeast Binding Sites
    • The search regulatory associations function allows the user to input a list of genes of interest and search for candidate transcription factors that regulate the list of genes. Allows filtering according to multiple criteria.
    • From Tsai, HK, et al. MYBS: A comprehensive web server for mining transcription factor binding sites in yeast. Nucleic Acids Research 2007. PubMed
  • TFSVM Transcription Factor Support Vector Machine
    • Allows user to input either a single transcription factor to get a list of regulated target genes or a single gene to get a list of transcription factors that regulate that gene. Can also filter according to a threshold value
    • Downloaded the list of Cin5p targets with a threshold value >0.997.
    • From Holloway, DT, et al. Classifying transcription factor targets and discovering relevant biological features. Biology Direct 2008. 3:22. PubMed
  • YEASTRACT Yeast Search for Transcriptional Regulators and Consensus Tracking
    • Multiple tools are provided on this server. Those of interest include a search for regulatory relationships either by transcription factor or by target gene. Applies a different algorithm to find new regulatory relationships in previously published data from Lee, Harbison, Tan and Workman
    • Downloaded list of documented Cin5p targets.
    • From Monteiro, PT, et al. YEASTRACT-DISCOVERER: new tools to improve analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Research 2008. PubMed
  • ChIPCodis Mining of Regulatory Transcription Factor Data in Yeast
    • Allows the user to input a list of genes and provides list of candidate transcription factors that regulate. References either Harbison or MacIsaac data.
    • From Abascal, F et al. ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data. Bioinformatics 2008. PubMed


  • 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.

Other Papers of Interest

  • Cold Shock Temporal Network Data

Used new algoithm to construct temporal networks of yeast's response to various stresses, including cold shock. For cold shock data, the paper analyzes data from the Gasch, et al. (2000) paper. Supplementary data has cold shock temporal response, but does not show any interactions between transcription factors and targets. (Note: the Gasch et al. paper does not have a true "cold shock" response. They only measure the effect of a temperature downshift from 37°C to 25°C. Cold shock is defined in the range of 10°C to 18°CKam D. Dahlquist 16:59, 22 September 2008 (EDT))

  • From Ernst, J; Vainas, O; Harbison, CT; Simon, I; Bar-Joseph, Z. Reconstructing dynamic regulatory maps. Molecular Systems Biology 2007. PubMed