Dahlquist:Yeast Transcription Factors

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(TF Network Data)
(TF Network Data)
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===TF Network Data===
===TF Network Data===
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*TF-Target interactions through DNA damage response
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*TF-target interactions through DNA damage response
Measured binding locations of damage-related transcription factors (including Cin5) after exposure to MMS. Validated by checking against binding in knock-out strains for TFs. Paper has a map of the network, and the supplemental material is downloaded but needs to be sifted through.  
Measured binding locations of damage-related transcription factors (including Cin5) after exposure to MMS. Validated by checking against binding in knock-out strains for TFs. Paper has a map of the network, and the supplemental material is downloaded but needs to be sifted through.  
:*From Workman, Christopher T., ''et al.'' A systems approach to mapping DNA damage response pathways. ''Science'' 2006. 1054-1059. [http://www.ncbi.nlm.nih.gov/pubmed/16709784?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
:*From Workman, Christopher T., ''et al.'' A systems approach to mapping DNA damage response pathways. ''Science'' 2006. 1054-1059. [http://www.ncbi.nlm.nih.gov/pubmed/16709784?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
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*TF Network though systematic deletions
+
*TF network though systematic deletions
Performed microarray analysis of knockout strains for many transcription factors and compared expression profiles to determine regulatory relationships. Have a link to supplementary data, need to search through to find information.
Performed microarray analysis of knockout strains for many transcription factors and compared expression profiles to determine regulatory relationships. Have a link to supplementary data, need to search through to find information.
:*From Hu, Zhanzhi, ''et al.'' Genetic reconstruction of a functional transcriptional regulatory network. ''Nature Genetics'' 2007. 39:5. 683-687. [http://www.ncbi.nlm.nih.gov/pubmed/17417638?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
:*From Hu, Zhanzhi, ''et al.'' Genetic reconstruction of a functional transcriptional regulatory network. ''Nature Genetics'' 2007. 39:5. 683-687. [http://www.ncbi.nlm.nih.gov/pubmed/17417638?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
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*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 on the desktop.
 +
:*From  MacIsaac, Kenzie D., ''et al.'' An improved map of conserved regulatory sites for ''Saccharomyces cerevisiae''. ''BMC Bioinformatics'' 2006, 7:113. [http://www.ncbi.nlm.nih.gov/pubmed/16522208?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
===Web Servers===
===Web Servers===

Revision as of 16:28, 9 September 2008

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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.

TF Network Data

  • TF-target interactions through DNA damage response

Measured binding locations of damage-related transcription factors (including Cin5) after exposure to MMS. Validated by checking against binding in knock-out strains for TFs. Paper has a map of the network, and the supplemental material is downloaded but needs to be sifted through.

  • 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. Have a link to supplementary data, need to search through to find information.

  • 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 on the desktop.

  • From MacIsaac, Kenzie D., et al. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 2006, 7:113. PubMed

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 p-value.

  • 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.

  • From Monteiro, PT, et al. YEASTRACT-DISCOVERER: new tools to improve analysis of transcriptional regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Research 2008. PubMed
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