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T-profiler specifications

Information


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

Taxon


  • Plants and Fungi
    • Candida albicans
    • Saccharomyces cerevisiae

Maintainer


  • person_outline Harmen J. Bussemaker <>

Publication for T-profiler

T-profiler citations

 (29)
library_books

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

2017
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 […]

library_books

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

2016
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 […]

library_books

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

2015
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 […]

library_books

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

2014
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 […]

library_books

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

2014
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, […]

library_books

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

2014
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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