Literature DB >> 20739311

TFInfer: a tool for probabilistic inference of transcription factor activities.

H M Shahzad Asif1, Matthew D Rolfe, Jeff Green, Neil D Lawrence, Magnus Rattray, Guido Sanguinetti.   

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 SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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Year:  2010        PMID： 20739311     DOI： 10.1093/bioinformatics/btq469

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  13 in total

1.  Analysis of the bacterial response to Ru(CO)3Cl(Glycinate) (CORM-3) and the inactivated compound identifies the role played by the ruthenium compound and reveals sulfur-containing species as a major target of CORM-3 action.

Authors:  Samantha McLean; Ronald Begg; Helen E Jesse; Brian E Mann; Guido Sanguinetti; Robert K Poole
Journal:  Antioxid Redox Signal       Date:  2013-04-16       Impact factor: 8.401

2.  Transcript profiling and inference of Escherichia coli K-12 ArcA activity across the range of physiologically relevant oxygen concentrations.

Authors:  Matthew D Rolfe; Alex Ter Beek; Alison I Graham; Eleanor W Trotter; H M Shahzad Asif; Guido Sanguinetti; Joost Teixeira de Mattos; Robert K Poole; Jeffrey Green
Journal:  J Biol Chem       Date:  2011-01-20       Impact factor: 5.157

3.  Reprogramming of Escherichia coli K-12 metabolism during the initial phase of transition from an anaerobic to a micro-aerobic environment.

Authors:  Eleanor W Trotter; Matthew D Rolfe; Andrea M Hounslow; C Jeremy Craven; Michael P Williamson; Guido Sanguinetti; Robert K Poole; Jeffrey Green
Journal:  PLoS One       Date:  2011-09-27       Impact factor: 3.240

4.  CO-Releasing Molecules Have Nonheme Targets in Bacteria: Transcriptomic, Mathematical Modeling and Biochemical Analyses of CORM-3 [Ru(CO)3Cl(glycinate)] Actions on a Heme-Deficient Mutant of Escherichia coli.

Authors:  Jayne Louise Wilson; Lauren K Wareham; Samantha McLean; Ronald Begg; Sarah Greaves; Brian E Mann; Guido Sanguinetti; Robert K Poole
Journal:  Antioxid Redox Signal       Date:  2015-04-28       Impact factor: 8.401

5.  Adaptation of anaerobic cultures of Escherichia coli K-12 in response to environmental trimethylamine-N-oxide.

Authors:  Katie J Denby; Matthew D Rolfe; Ellen Crick; Guido Sanguinetti; Robert K Poole; Jeffrey Green
Journal:  Environ Microbiol       Date:  2015-02-03       Impact factor: 5.491

6.  The Broad-Spectrum Antimicrobial Potential of [Mn(CO)4(S2CNMe(CH2CO2H))], a Water-Soluble CO-Releasing Molecule (CORM-401): Intracellular Accumulation, Transcriptomic and Statistical Analyses, and Membrane Polarization.

Authors:  Lauren K Wareham; Samantha McLean; Ronald Begg; Namrata Rana; Salar Ali; John J Kendall; Guido Sanguinetti; Brian E Mann; Robert K Poole
Journal:  Antioxid Redox Signal       Date:  2017-09-28       Impact factor: 8.401

7.  Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations.

Authors:  Matthew D Rolfe; Andrea Ocone; Melanie R Stapleton; Simon Hall; Eleanor W Trotter; Robert K Poole; Guido Sanguinetti; Jeffrey Green
Journal:  Open Biol       Date:  2012-07       Impact factor: 6.411

8.  Analysis of transcript changes in a heme-deficient mutant of Escherichia coli in response to CORM-3 [Ru(CO)3Cl(glycinate)].

Authors:  Jayne Louise Wilson; Samantha McLean; Ronald Begg; Guido Sanguinetti; Robert K Poole
Journal:  Genom Data       Date:  2015-06-13

9.  Carbon Monoxide Gas Is Not Inert, but Global, in Its Consequences for Bacterial Gene Expression, Iron Acquisition, and Antibiotic Resistance.

Authors:  Lauren K Wareham; Ronald Begg; Helen E Jesse; Johan W A Van Beilen; Salar Ali; Dimitri Svistunenko; Samantha McLean; Klaas J Hellingwerf; Guido Sanguinetti; Robert K Poole
Journal:  Antioxid Redox Signal       Date:  2016-03-30       Impact factor: 8.401

10.  Transcriptome and proteome dynamics in chemostat culture reveal how Campylobacter jejuni modulates metabolism, stress responses and virulence factors upon changes in oxygen availability.

Authors:  Edward J Guccione; John J Kendall; Andrew Hitchcock; Nitanshu Garg; Michael A White; Francis Mulholland; Robert K Poole; David J Kelly
Journal:  Environ Microbiol       Date:  2017-10-02       Impact factor: 5.491
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