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T-profiler specifications


Unique identifier OMICS_18763
Name T-profiler
Interface Web user interface
Restrictions to use None
Input data A microarray data.
Input format TSV
Computer skills Basic
Stability Stable
Maintained Yes


  • Plants and Fungi
    • Candida albicans
    • Saccharomyces cerevisiae


  • person_outline Harmen J. Bussemaker <>

Publication for T-profiler

T-profiler citations


Deconvolution of Transcriptional Networks in Post Traumatic Stress Disorder Uncovers Master Regulators Driving Innate Immune System Function

PMCID: 5670244
PMID: 29101382
DOI: 10.1038/s41598-017-15221-y

[…] (pleiotropy) for computing the enrichment of a protein regulon in differentially expressed genes. the main advantage of viper compared to the other gene enrichment analysis methods such as t-profiler, fisher’s exact test, and gene set enrichment analysis (gsea) is that it uses a fully probabilistic enrichment analysis framework, supporting seamless integration of genes with different […]


Evaluating Transcription Factor Activity Changes by Scoring Unexplained Target Genes in Expression Data

PMCID: 5056719
PMID: 27723775
DOI: 10.1371/journal.pone.0164513

[…] all regulations of the tf from f. the difference between the normal and the knockout model is used to calculate a z-score that indicates how important the respective tf is for the experiments., t-profiler [] performs a t-test between the fold changes of the genes that are targets of a tf and all other genes. to account for overlaps in the target sets of the tfs, the method iteratively […]


Comparative Transcriptome Analysis Reveals That Lactose Acts as an Inducer and Provides Proper Carbon Sources for Enhancing Exopolysaccharide Yield in the Deep Sea Bacterium Zunongwangia profunda SM A87

PMCID: 4332637
PMID: 25679965
DOI: 10.1371/journal.pone.0115998

[…] absolute fold-change ratio and displayed an fdr-adjusted p value <0.01. the changes in the expression of overall lipopolysaccharide (lps) and of the eps gene clusters were tested using the t-profiler method []., the dna binding sites of the laci transcriptional regulator on the sm-a87 genome were predicted by the pepper webserver using the motif mining method […]


Functional Study of the Hap4 Like Genes Suggests That the Key Regulators of Carbon Metabolism HAP4 and Oxidative Stress Response YAP1 in Yeast Diverged from a Common Ancestor

PMCID: 4257542
PMID: 25479159
DOI: 10.1371/journal.pone.0112263

[…] correlations between mutants . this method was applied to the same data (normalized log2 ratios) than those treated with the heat map clustering method., gene ontology categorization was done with t-profiler tool. this tool uses the t-test to score changes in the average activity of pre-defined groups ., total rna was extracted from h. polymorpha wild-type strain (ncyc495 leu1-1) and hpδhap4-a […]


Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast

PMCID: 4124144
PMID: 24947676
DOI: 10.1186/1471-2164-15-494

[…] intensities were quantile normalized using matlab bioinformatics toolbox., functional enrichment of probes by gene ontology (go) categories [] was determined using a matlab implementation of the t-profiler algorithm []. the go annotation was downloaded from sgd (gene ontology consortium validation date: 01/25/2014)., condition specificity was calculated as follows: for each ypd experiment, […]


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

PMCID: 4057180
PMID: 24926786
DOI: 10.1371/journal.pone.0099627

[…] for genes and/or proteins., to identify changes in the overall expression of a predefined set of genes or proteins due to temperature downshift, the t-test based method of boorsma et al. , known as t-profiler, was performed on the normalized log2 expression ratios. the predefined sets of genes and proteins used in the t-profiler analysis were based on the selected functional role categories […]

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T-profiler institution(s)
Swammerdam Institute for Life Sciences–Microbiology, University of Amsterdam, Biocentrum Amsterdam, Amsterdam, Netherlands; Department of Biological Sciences, Columbia University, New York, NY, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
T-profiler funding source(s)
Supported by grants from the Netherlands Foundation for Technical Research (STW) (APB.5504) and from the National Institutes of Health to (R01HG003008).

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