T-profiler protocols

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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 in pipelines

 (3)
2016
PMCID: 5056719
PMID: 27723775
DOI: 10.1371/journal.pone.0164513

[…] genes so that the t-test is insignificant and the tfs are not predicted to be active. in general, the two regression-based methods ismara and plsgenomics clearly perform better than drem and t-profiler if the dense ismara network is used., overall, when the ismara network is used fewer unexplained target genes are observed. however, this does not necessarily mean that the predictions […]

2010
PMCID: 2841119
PMID: 20202201
DOI: 10.1186/1471-2164-11-153

[…] with treeview []http://jtreeview.sourceforge.net. significant associations to either go-terms or transcription factors were obtained by go-term finder at sgd http://www.yeastgenome.org and t-profiler http://www.t-profiler.org []. treeview files corresponding to the figures are supplied as additional files , , , , , . values of genes associated with the most significant terms […]

2008
PMCID: 2631581
PMID: 19087243
DOI: 10.1186/1471-2164-9-601

[…] enriched. promoter regions (800 bp upstream of the transcription start site, or until the next orf was reached) were taken from the rsat database []. a list of s. cerevisiae motifs from t-profiler [] were tested for enrichment, along with some additional motifs such as the complete mig1 motif [] and the pds site []. in total, 152 motifs were tested (see additional file : table s4). […]


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T-profiler in publications

 (29)
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 […]

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 […]

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 […]

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 […]

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, […]


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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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