Dahlquist:Yeast Transcription Factors

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==Dahlquist Lab Yeast Transcription Factor Resources==
==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.
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.
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===TF Network Data===
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*TF-Target interactions through DNA damage response
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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.
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:*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]
===Web Servers===
===Web Servers===
* [http://cg1.iis.sinica.edu.tw/~mybs/index.php MYBS] Mining Yeast Binding Sites
* [http://cg1.iis.sinica.edu.tw/~mybs/index.php 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.
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.
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:*From Tsai, HK et al. MYBS: A comprehensive web server for mining transcription factor binding sites in yeast. ''Nucleic Acids Research'' 2007. [http://www.ncbi.nlm.nih.gov/pubmed/17537814?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
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:*From Tsai, HK, ''et al.'' MYBS: A comprehensive web server for mining transcription factor binding sites in yeast. ''Nucleic Acids Research'' 2007. [http://www.ncbi.nlm.nih.gov/pubmed/17537814?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
* [http://cagt10.bu.edu/TFSVM/QueryPage.htm TFSVM] Transcription Factor Support Vector Machine
* [http://cagt10.bu.edu/TFSVM/QueryPage.htm 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.
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.
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:*From Holloway, DT et al. Classifying transcription factor targets and discovering relevant biological features. ''Biology Direct'' 2008. 3:22. [http://www.ncbi.nlm.nih.gov/pubmed/18513408?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
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:*From Holloway, DT, ''et al.'' Classifying transcription factor targets and discovering relevant biological features. ''Biology Direct'' 2008. 3:22. [http://www.ncbi.nlm.nih.gov/pubmed/18513408?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
* [http://www.yeastract.com/index.php YEASTRACT] Yeast Search for Transcriptional Regulators and Consensus Tracking
* [http://www.yeastract.com/index.php 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.  
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.  
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:*From Monteiro, PT et al. YEASTRACT-DISCOVERER: new tools to improve analysis of transcriptional regulatory associations in ''Saccharomyces cerevisiae''. ''Nucleic Acids Research'' 2008. [http://www.ncbi.nlm.nih.gov/pubmed/18032429?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
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:*From Monteiro, PT, ''et al.'' YEASTRACT-DISCOVERER: new tools to improve analysis of transcriptional regulatory associations in ''Saccharomyces cerevisiae''. ''Nucleic Acids Research'' 2008. [http://www.ncbi.nlm.nih.gov/pubmed/18032429?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]

Revision as of 17:20, 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

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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