TFInfer: a tool for probabilistic inference of transcription factor activities

[edit]

H. M. Shahzad Asif
Matthew D. Rolfe
Jeff Green
Neil D. Lawrence, University of Sheffield
Magnus Rattray, University of Manchester
Guido Sanguinetti, University of Edinburgh

Bioinformatics 26, pp 2635-2636

Related Material

Abstract

Summary: TFInfer is a novel open access, standalone tool for genome-wide inference of transcription factor activities from gene expression data. Based on an earlier MATLAB version, the software has now been extended in a number of ways. It has been significantly optimised in terms of performance, and it was given novel functionality, by allowing the user to model both time series and data from multiple independent conditions. With a full documentation and intuitive graphical user interface, together with an in-built data base of yeast and Escherichia coli transcription factors, the software does not require any mathematical or computational expertise to be used effectively.\ Availability: http://homepages.inf.ed.ac.uk/gsanguin/TFInfer.html Contact: gsanguin@staffmail.ed.ac.uk


@Article{asif-tfinfer10,
  title = 	 {TFInfer: a tool for probabilistic inference of transcription factor activities},
  journal =  	 {Bioinformatics},
  author = 	 {H. M. Shahzad Asif and Matthew D. Rolfe and Jeff Green and Neil D. Lawrence and Magnus Rattray and Guido Sanguinetti},
  pages = 	 {2635},
  year = 	 {2010},
  volume = 	 {26},
  month = 	 {00},
  edit = 	 {https://github.com/lawrennd//publications/edit/gh-pages/_posts/2010-01-01-asif-tfinfer10.md},
  url =  	 {http://inverseprobability.com/publications/asif-tfinfer10.html},
  abstract = 	 {**Summary**: TFInfer is a novel open access, standalone tool for genome-wide inference of transcription factor activities from gene expression data. Based on an earlier MATLAB version, the software has now been extended in a number of ways. It has been significantly optimised in terms of performance, and it was given novel functionality, by allowing the user to model both time series and data from multiple independent conditions. With a full documentation and intuitive graphical user interface, together with an in-built data base of yeast and Escherichia coli transcription factors, the software does not require any mathematical or computational expertise to be used effectively.\
**Availability**:  **Contact**: [gsanguin@staffmail.ed.ac.uk](gsanguin@staffmail.ed.ac.uk)},
  key = 	 {Asif-tfinfer10},
  linkpdf = 	 {http://bioinformatics.oxfordjournals.org/content/26/20/2635.full.pdf+html},
  OPTgroup = 	 {}
 

}
%T TFInfer: a tool for probabilistic inference of transcription factor activities
%A H. M. Shahzad Asif and Matthew D. Rolfe and Jeff Green and Neil D. Lawrence and Magnus Rattray and Guido Sanguinetti
%B 
%C Bioinformatics
%D 
%F asif-tfinfer10
%J Bioinformatics	
%P 2635--2636
%R 
%U http://inverseprobability.com/publications/asif-tfinfer10.html
%V 26
%X **Summary**: TFInfer is a novel open access, standalone tool for genome-wide inference of transcription factor activities from gene expression data. Based on an earlier MATLAB version, the software has now been extended in a number of ways. It has been significantly optimised in terms of performance, and it was given novel functionality, by allowing the user to model both time series and data from multiple independent conditions. With a full documentation and intuitive graphical user interface, together with an in-built data base of yeast and Escherichia coli transcription factors, the software does not require any mathematical or computational expertise to be used effectively.\
**Availability**:  **Contact**: [gsanguin@staffmail.ed.ac.uk](gsanguin@staffmail.ed.ac.uk)
TY  - CPAPER
TI  - TFInfer: a tool for probabilistic inference of transcription factor activities
AU  - H. M. Shahzad Asif
AU  - Matthew D. Rolfe
AU  - Jeff Green
AU  - Neil D. Lawrence
AU  - Magnus Rattray
AU  - Guido Sanguinetti
PY  - 2010/01/01
DA  - 2010/01/01	
ID  - asif-tfinfer10	
SP  - 2635
EP  - 2636
L1  - http://bioinformatics.oxfordjournals.org/content/26/20/2635.full.pdf+html
UR  - http://inverseprobability.com/publications/asif-tfinfer10.html
AB  - **Summary**: TFInfer is a novel open access, standalone tool for genome-wide inference of transcription factor activities from gene expression data. Based on an earlier MATLAB version, the software has now been extended in a number of ways. It has been significantly optimised in terms of performance, and it was given novel functionality, by allowing the user to model both time series and data from multiple independent conditions. With a full documentation and intuitive graphical user interface, together with an in-built data base of yeast and Escherichia coli transcription factors, the software does not require any mathematical or computational expertise to be used effectively.\
**Availability**:  **Contact**: [gsanguin@staffmail.ed.ac.uk](gsanguin@staffmail.ed.ac.uk)
ER  -

Asif, H.M.S., Rolfe, M.D., Green, J., Lawrence, N.D., Rattray, M. & Sanguinetti, G.. (2010). TFInfer: a tool for probabilistic inference of transcription factor activities. Bioinformatics 26:2635-2636