Dahlquist:Yeast Transcription Factors

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==Dahlquist Lab Yeast Transcription Factor Resources==
==Dahlquist Lab Yeast Transcription Factor Resources==
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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.
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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 Network Data ===
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*[http://www.sciencemag.org/content/298/5594/799.long Lee 2002]
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<biblio>
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**Pub med reference = 12399584
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#Paper1 pmid=12399584
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*[http://www.nature.com/nature/journal/v431/n7004/full/nature02800.html  Harbison 2004]
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#Paper2 pmid=15343339
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**Pub med reference = 15343339
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#Paper3 pmid=16522208
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*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1435934/pdf/1471-2105-7-113.pdf  MacIsaac 2006]
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**Pub med reference = 16522208
//Updated TF network to determine new relationships
//Updated TF network to determine new relationships
Used improved algorithms to detect new regulatory relationships in the transcription factor network
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.
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
A figure of the new network was downloaded. PDF format
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#Paper4 pmid=16709784
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[http://fraenkel.mit.edu/improved_map/ Supplementary Data Web Site]
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[[Media:MacIsaac_BMCBioinformatics_06_SuppData_orfs_by_factor.zip | Supplementary Data in zipped .xls file]]
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*[http://www.sciencemag.org/content/312/5776/1054.full.pdf  Workman 2006]
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**Pub med reference = 16709784
//TF-target interactions in DNA damage response
//TF-target interactions in 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.  
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.
Downloaded the MMS and Untreated ChIP datasets to be filtered for Cin5p targets, Excel spreadsheet of p values for binding.
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#Paper5 pmid=17417638
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*[http://www.nature.com/ng/journal/v39/n5/full/ng2012.html  Hu 2007]
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**Pub med reference = 17417638
//TF network discovered through systematic deletions
//TF network discovered through 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
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.
Downloaded the filtered and unfiltered network in X-score format.  Gene-gene-value triples.
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#Paper6 pmid=19690563
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*[http://www.nature.com/msb/journal/v5/n1/full/msb200952.html  Jothi 2009]
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#Paper7 pmid=16762362
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**Pub med reference = 19690563
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*[http://www.sciencedirect.com/science/article/pii/S0022283606004931  Balaji 2006]
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**Pub med reference = 16762362
//[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4JW10XT-1&_user=945462&_coverDate=06%2F30%2F2006&_rdoc=22&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236899%232006%23996399998%23626365%23FLA%23display%23Volume)&_cdi=6899&_sort=d&_docanchor=&_ct=23&_acct=C000048964&_version=1&_urlVersion=0&_userid=945462&md5=b67d2bfd6d27c7704eece1bbc163f1e6 Full text from ScienceDirect]
//[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4JW10XT-1&_user=945462&_coverDate=06%2F30%2F2006&_rdoc=22&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236899%232006%23996399998%23626365%23FLA%23display%23Volume)&_cdi=6899&_sort=d&_docanchor=&_ct=23&_acct=C000048964&_version=1&_urlVersion=0&_userid=945462&md5=b67d2bfd6d27c7704eece1bbc163f1e6 Full text from ScienceDirect]
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</biblio>
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*Bar-Joseph 2003
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**Pub med reference = 14555958
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//[http://www.nature.com/nbt/journal/v21/n11/abs/nbt890.html Abstract and Supplemental Data]
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*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800355/?tool=pubmed  Ernst 2007]
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* ''&mdash; [[User:Kam D. Dahlquist|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.  
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**Pub med reference = 17224918
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//Cold Shock Temporal Network Data
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* ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 17:04, 13 October 2008 (EDT) NEW'' Bar-Joseph et al. (2003) Computational discovery of gene modules and regulatory networks. ''Nature Biotechnology'' 21: 1337-1342. [http://www.nature.com/nbt/journal/v21/n11/abs/nbt890.html Abstract and Supplemental Data]
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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°C
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*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665775/?tool=pubmed  Zhu 2009]
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**Pub med reference = 19158363
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*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1488875/?tool=pubmed  Kim 2006]
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**Pub med reference = 16551355
===Web Servers===
===Web Servers===
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** 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]
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* [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 a threshold 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 a threshold value
** Downloaded the list of Cin5p targets with a threshold value >0.997.
** 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. [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]
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* [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
** Downloaded list of documented Cin5p targets.  
** 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. [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]
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* [http://chipcodis.dacya.ucm.es/ ChIPCodis] Mining of Regulatory Transcription Factor Data in Yeast
* [http://chipcodis.dacya.ucm.es/ 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.  
** 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. [http://www.ncbi.nlm.nih.gov/pubmed/18339638?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
** From Abascal, F ''et al.'' ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data. ''Bioinformatics'' 2008. [http://www.ncbi.nlm.nih.gov/pubmed/18339638?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
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* [http://biochemie.web.med.uni-muenchen.de/YTFD/ List of Yeast Transcription Factors] (don't know when this web page was updated)
* [http://biochemie.web.med.uni-muenchen.de/YTFD/ List of Yeast Transcription Factors] (don't know when this web page was updated)
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* [http://jaspar.genereg.net/ Jaspar] TF binding site motif database
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=== Summary ===
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* Have downloaded Cin5p targets from the following sources:
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** Lee et al.
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** Harbison et al.
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** Tan et al.
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*** One consolidated MAPP with Lee, Harbison, and Tan has been completed.
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** Workman et al.
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** Hu et al.
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** TVSM
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** Yeastract
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*** MAPPs for each of the above have been created as well.
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* 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.
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===Other Papers of Interest===
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*Cold Shock Temporal Network Data
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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°C''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 16:59, 22 September 2008 (EDT)'')
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:*From Ernst, J; Vainas, O; Harbison, CT; Simon, I; Bar-Joseph, Z. Reconstructing dynamic regulatory maps. ''Molecular Systems Biology'' 2007. [http://www.ncbi.nlm.nih.gov/pubmed/17224918?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor PubMed]
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Current revision

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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

//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

Supplementary Data Web Site

Supplementary Data in zipped .xls file

//TF-target interactions in 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.

  • Hu 2007
    • Pub med reference = 17417638

//TF network discovered through 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.

//Full text from ScienceDirect

  • Bar-Joseph 2003
    • Pub med reference = 14555958

//Abstract and Supplemental Data

//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°C

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
  • List of Yeast Transcription Factors (don't know when this web page was updated)
  • Jaspar TF binding site motif database
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