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T-profiler: scoring the activity of predefined groups of genes using gene expression data

A. Boorsma, B. C. Foat, D. Vis, F. Klis, H. J. Bussemaker
2005 Nucleic Acids Research  
Here we describe T-profiler, a tool that uses the t-test to score changes in the average activity of predefined groups of genes.  ...  One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state.  ...  ACKNOWLEDGEMENTS We would like to thank Merijn Schuurmans and Ania Zakrzewska for helpful discussions and for testing T-profiler, Reka Letso for a critical reading of the manuscript, and Xiang-Jun Lu for  ... 
doi:10.1093/nar/gki484 pmid:15980543 pmcid:PMC1160244 fatcat:fi6pagky2nd3phszstkpjdtlcm

Comparative Analysis of Transcriptome and Fitness Profiles Reveals General and Condition-Specific Cellular Functions Involved in Adaptation to Environmental Change in Saccharomyces cerevisiae

Anna Zakrzewska, Andre Boorsma, Alex Ter Beek, Jos A. Hageman, Johan A. Westerhuis, Klaas J. Hellingwerf, Stanley Brul, Frans M. Klis, Gertien J. Smits
2010 Omics  
Comparative analysis of transcriptome and fitness profiles reveals general and condition-specific cellular functions involved in adaptation to environmental change in Saccharomyces cerevisiae Zakrzewska  ...  Acknowledgments The authors thank Drs. Parsons and Boone for generous sharing of data prior to publication, and Dr. Bussemaker for useful discussions.  ...  This research was financially supported by grant APB.5504 from The Netherlands Technology Foundation (STW) (to F.M.K.), and by the BioRange program of The Netherlands Bioinformatics Centre (NBIC), which  ... 
doi:10.1089/omi.2010.0049 pmid:20695823 fatcat:copbitg325crthomaeg2rhvxui

Genomic analysis suggests higher susceptibility of children to air pollution

Danitsja M. van Leeuwen, Marie Pedersen, Peter J.M. Hendriksen, André Boorsma, Marcel H.M. van Herwijnen, Ralph W.H. Gottschalk, Micheline Kirsch-Volders, Lisbeth E. Knudsen, Radim J. Šrám, Edyta Bajak, Joost H.M. van Delft, Jos C.S. Kleinjans
2008 Carcinogenesis  
Acknowledgements The authors gratefully acknowledge Dr D.Horakova, Dr J.Ruzickova and Dr M.Weigartova for administration of questionnaires and blood sampling and the Laboratory of Genetic Toxicology, National  ...  Institute of Public Health, Prague, for processing of MN cultures.  ...  T-profiler uses the unpaired t-test to score changes in average transcriptomic activity of predefined groups of genes within a single expression profile and expresses the significance of the change as  ... 
doi:10.1093/carcin/bgn065 pmid:18332047 fatcat:5qz4neddxzgk5iuqvfupcudl4u

Inferring Condition-Specific Modulation of Transcription Factor Activity in Yeast through Regulon-Based Analysis of Genomewide Expression

André Boorsma, Xiang-Jun Lu, Anna Zakrzewska, Frans M. Klis, Harmen J. Bussemaker, Guillaume Bourque
2008 PLoS ONE  
Methodology/Principal Findings: We first validate experimentally that by scoring differential expression at the level of gene sets or "regulons" comprised of the putative targets of a TF, we can accurately  ...  Conclusions/Significance: We analyze the degree to which the mRNA expression level of each TF is predictive of its regulatory activity.  ...  Results Creating a database of inferred TF activities We used T-profiler [22] to populate a database of t-values that quantify the change in mean expression for a large number of predefined gene sets  ... 
doi:10.1371/journal.pone.0003112 pmid:18769540 pmcid:PMC2518834 fatcat:3fzmkivvcjdjbp4625ragkd3aa

Time Series Analysis of Benzo[A]Pyrene-Induced Transcriptome Changes Suggests That a Network of Transcription Factors Regulates the Effects on Functional Gene Sets

Joost H. M. van Delft, Karen Mathijs, Yvonne C. M. Staal, Marcel H. M. van Herwijnen, Karen J. J. Brauers, André Boorsma, Jos C. S. Kleinjans
2010 Toxicological Sciences  
The time series analysis tool Short Time-series Expression Miner (STEM) was used to identify time-dependent correlation of pathways, gene sets, TF networks, and biological parameters.  ...  Chemical carcinogens may cause a multitude of effects inside cells, thereby affecting transcript levels of genes by direct activation of transcription factors (TF) or indirectly through the formation of  ...  T-profiler uses the unpaired t-test to score the difference between the mean expression level of predefined sets of genes and that of all other genes within the complete data set (Boorsma et al., 2005  ... 
doi:10.1093/toxsci/kfq214 pmid:20624995 fatcat:dsxejfukmncd7nd5coy5iv6mqm

Molecular Signatures of N-nitroso Compounds in Caco-2 Cells: Implications for Colon Carcinogenesis

Dennie G. A. J. Hebels, Danyel G. J. Jennen, Jos C. S. Kleinjans, Theo M. C. M. de Kok
2009 Toxicological Sciences  
Gene Ontology gene group, consensus motif gene group and biological pathway analysis revealed that nitrosamides had little effect on gene expression after 24 h of exposure, whereas nitrosamines had a strong  ...  Many of these pathways and gene groups are implicated in the carcinogenic process and their modulation by nitrosamine exposure may therefore influence the development of colon cancer.  ...  T-profiler uses the unpaired t-test to score changes in average transcriptomic activity of predefined groups of genes within a single expression profile and expresses the significance of the change as  ... 
doi:10.1093/toxsci/kfp035 pmid:19221148 fatcat:j5w7eahzsrf6rirkakmuusf6ma

Integrated Transcriptomic and Proteomic Analysis of the Physiological Response ofEscherichia coliO157:H7 Sakai to Steady-state Conditions of Cold and Water Activity Stress

Chawalit Kocharunchitt, Thea King, Kari Gobius, John P. Bowman, Tom Ross
2011 Molecular & Cellular Proteomics  
Predefined group enrichment analysis revealed that a universal response of E. coli to all test conditions included activation of the master stress response regulator RpoS and the Rcs phosphorelay system  ...  Gene and protein expression profiles of E. coli were more strongly affected by low water activity (a w 0.967) than by low temperature (14°C).  ...  Acknowledgments-Their support, in particular that of Ian Jenson, Manager of the Food Safety and Strategic Science program, is gratefully acknowledged.  ... 
doi:10.1074/mcp.m111.009019 pmid:22008207 pmcid:PMC3270098 fatcat:fc5tqsmquzddpjchguxebzkica

Impact of Acute Metal Stress in Saccharomyces cerevisiae

Dagmar Hosiner, Susanne Gerber, Hella Lichtenberg-Fraté, Walter Glaser, Christoph Schüller, Edda Klipp, Jörg Langowski
2014 PLoS ONE  
Hierarchical clustering, transcription factor analyses, and gene ontology data further revealed activation of genes involved in metal-specific protein catabolism along with repression of growth-related  ...  Metal ion group specific differences in the expression responses with shared transcriptional regulators for both, up-regulation and repression were also observed.  ...  Performed the experiments: DH SG WG. Analyzed the data: DH SG HLF WG CS EK. Wrote the paper: DH SG HLF CS EK.  ... 
doi:10.1371/journal.pone.0083330 pmid:24416162 pmcid:PMC3886979 fatcat:gg7hsqotkvaaphuxashd6tayzi

Transcriptome Analysis of Sorbic Acid-Stressed Bacillus subtilis Reveals a Nutrient Limitation Response and Indicates Plasma Membrane Remodeling

A. T. Beek, B. J. F. Keijser, A. Boorsma, A. Zakrzewska, R. Orij, G. J. Smits, S. Brul
2007 Journal of Bacteriology  
We have used genome-wide transcriptional profiling of Bacillus subtilis cells during mild sorbic acid stress to reveal the growth-inhibitory activity of this preservative and to identify potential resistance  ...  This is indicated by the strong derepression of the CcpA, CodY, and Fur regulon and the induction of tricarboxylic acid cycle genes, SigL-and SigH-mediated genes, and the stringent response.  ...  We acknowledge Jurgo Verkooijen and Tessa Dillerop-van der Hoeven of the Microarray Department of Amsterdam for the hybridization and scanning of the microarray slides, Muus de Haan for assistance with  ... 
doi:10.1128/jb.01516-07 pmid:18156260 pmcid:PMC2258692 fatcat:oy77w7obonfihozvb3mrdhylga

Transcriptional activity around bacterial cell death reveals molecular biomarkers for cell viability

Remco Kort, Bart J Keijser, Martien PM Caspers, Frank H Schuren, Roy Montijn
2008 BMC Genomics  
In bacteriology, the ability to grow in selective media and to form colonies on nutrient agar plates is routinely used as a retrospective criterion for the detection of living bacteria.  ...  Therefore, we investigated the correlation between transcriptional activity, membrane integrity and cultivation-based viability in the Grampositive model bacterium Bacillus subtilis.  ...  We thank the 4 anonymous referees for reviewing the manuscript.  ... 
doi:10.1186/1471-2164-9-590 pmid:19061518 pmcid:PMC2648990 fatcat:jawophor5fcnvox67nqivk4gs4

Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data

Kristina M Hettne, André Boorsma, Dorien A M van Dartel, Jelle J Goeman, Esther de Jong, Aldert H Piersma, Rob H Stierum, Jos C Kleinjans, Jan A Kors
2013 BMC Medical Genomics  
We tested for significant differential expression (SDE) (false discovery rate -corrected p-values < 0.05) of the next-gen TM-derived gene sets and the CTD-derived gene sets in gene expression (GE) data  ...  None of the fibrate signatures in cMap scored significant against the PPARA GE signature. 33 environmental toxicant gene sets were significantly altered in the triazole GE data sets. 21 of these toxicants  ...  We would like to acknowledge Herman van Haagen and Erik Schultes for advice on the cut-off for the number of concepts in a concept profile used for matching.  ... 
doi:10.1186/1755-8794-6-2 pmid:23356878 pmcid:PMC3572439 fatcat:r6evkgbtpzgrhjbbxqxmr6d44m

Comparative Transcriptome Analysis of Bacillus subtilis Responding to Dissolved Oxygen in Adenosine Fermentation

Wen-Bang Yu, Shu-Hong Gao, Chun-Yun Yin, Ying Zhou, Bang-Ce Ye, Eshel Ben-Jacob
2011 PLoS ONE  
Expression of genes involved in energy, cell type differentiation, protein synthesis was also influenced by oxygen supply.  ...  The microarrays representing 4,106 genes were used to study temporal transcript profiles of B. subtilis fermentation in response to high oxygen supply (agitation 700 r/min) and low oxygen supply (agitation  ...  T-profiler is a computational tool that uses the t-test to score changes in the average activity of predefined groups of genes based on Gene Ontology categorization, upstream matches to a consensus transcription  ... 
doi:10.1371/journal.pone.0020092 pmid:21625606 pmcid:PMC3097244 fatcat:6fyo6lcs6bcmzcgsrfxe5mzwx4

Global Genome Response of Escherichia coli O157∶H7 Sakai during Dynamic Changes in Growth Kinetics Induced by an Abrupt Downshift in Water Activity

Chawalit Kocharunchitt, Thea King, Kari Gobius, John P. Bowman, Tom Ross, Dipankar Chatterji
2014 PLoS ONE  
The present study was undertaken to investigate growth kinetics and time-dependent change in global expression of Escherichia coli O157:H7 Sakai upon an abrupt downshift in water activity (a w ).  ...  Finally, we highlighted the ability of E. coli to activate multiple stress responses by transiently inducing the RpoE and RpoH regulons to control protein misfolding, while simultaneously activating the  ...  Acknowledgments We would like to thank Ian Jenson, Manager of the Food Safety and Strategic Science program from Meat and Livestock Australia for his support and guidance on the project.  ... 
doi:10.1371/journal.pone.0090422 pmid:24594867 pmcid:PMC3940904 fatcat:boku6fjmofbvjlfhr7nnqg3uti

Time-Resolved Transcriptome Analysis of Bacillus subtilis Responding to Valine, Glutamate, and Glutamine

Bang-Ce Ye, Yan Zhang, Hui Yu, Wen-Bang Yu, Bao-Hong Liu, Bin-Cheng Yin, Chun-Yun Yin, Yuan-Yuan Li, Ju Chu, Si-Liang Zhang, Paul Cobine
2009 PLoS ONE  
The highlighted genes were analyzed based on diverse sources of gene functions using a variety of computational tools, including T-profiler analysis, and hierarchical clustering.  ...  A total of 673, 835, and 1135 amino-acid-regulated genes were identified having significantly changed expression at one or more time points in response to valine, glutamate, and glutamine, respectively  ...  T-profiler is a computational tool that uses the t-test to score changes in the average activity of predefined groups of genes based on Gene Ontology categorization, upstream matches to a consensus transcription  ... 
doi:10.1371/journal.pone.0007073 pmid:19763274 pmcid:PMC2743287 fatcat:wdrbkuea6vdctbt74xdj6iekw4

Molecular Characterization of Trimellitic Anhydride–induced Respiratory Allergy in Brown Norway Rats

C. Frieke kuper, Wilbert H. M. Heijne, Marinus Dansen, Kitty C. M. Verhoeckx, Andre Boorsma, Marijana Radonjic, Joost Bruijntjes, Rob Stierum, Hans Muijser, Josje H. E. Arts
2008 Toxicologic pathology (Print)  
Whole genome analysis of lung, sampled 24 hours after challenge, showed expression changes of not only genes belonging to several Gene Ontology groups with up-regulation of inflammatory-associated genes  ...  Unsensitized animals challenged with TMA exhibited also an increased number of macrophages in BAL, but gene expression in the above-mentioned gene pathways was unchanged or down-regulated.  ...  ACKNOWLEDGMENTS The authors gratefully acknowledge CEFIC-LRI Brussels, Belgium, and the Dutch Ministry of Social Affairs and Employment for financial support. They also thank Dr. R. A.  ... 
doi:10.1177/0192623308327410 pmid:19126793 fatcat:o72bwdgj6fe3nfw6lscvuap5jy
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