Dahlquist:Yeast Transcription Factors: Difference between revisions
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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. | ||
===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. [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. | ||
:*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] | :*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. | ||
:*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] | :*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. | ||
:*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] | :*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 14:20, 9 September 2008
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
