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TFM-Explorer specifications

Information


Unique identifier OMICS_09259
Name TFM-Explorer
Alternative name Transcription Factor Matrix Explorer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Hélène Touzet

Information


Unique identifier OMICS_09259
Name TFM-Explorer
Alternative name Transcription Factor Matrix Explorer
Interface Web user interface
Restrictions to use None
Programming languages Python
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Hélène Touzet

Publications for Transcription Factor Matrix Explorer

TFM-Explorer citations

 (18)
library_books

Screening of Tumor Suppressor Genes in Metastatic Colorectal Cancer

2017
Biomed Res Int
PMCID: 5394352
PMID: 28473981
DOI: 10.1155/2017/2769140

[…] essor genes (ALOX15B, TP53, and GABARAP). In order to clarify the potential mechanism of the 8 tumor suppressor genes, enrichment analysis of transcription factor binding sites was performed by using TFM-Explorer [] in 22 genes in 17P13.3 zone and 27 genes in 17P13.1 zone. A total of 29 proteins interacted with MBD1 after being verified by BioGRID [] database search. Intersection was obtained base […]

library_books

Whole genome association analysis of pork meat pH revealed three significant regions and several potential genes in Finnish Yorkshire pigs

2017
BMC Genet
PMCID: 5307873
PMID: 28193157
DOI: 10.1186/s12863-017-0482-x

[…] .nih.gov/gene/). The two-sided hypergeometric test of the ClueGO plug-in of Cytoscape [] was used to construct a gene network highlighting the pathways and relations across the four sets of genes.The TFM-Explorer program (http://bioinfo.lifl.fr/TFM/TFME/) was used to identify the TF related to significant SNPs and regions. The TFM-Explorer takes a set of gene sequences and searches for locally ove […]

library_books

ITGA6 is directly regulated by hypoxia inducible factors and enriches for cancer stem cell activity and invasion in metastatic breast cancer models

2016
Mol Cancer
PMCID: 4802728
PMID: 27001172
DOI: 10.1186/s12943-016-0510-x

[…] The Itga6 and ITGA6 proximal promoters (−2000 to +500 bp) were scanned for the presence of putative functional hypoxia response elements (HREs) using the Transcription Factor Matrix (TFM) Explorer algorithm applying weight matrices available from JASPAR and TRANSFAC. Primers were designed to three independent HREs in the ITGA6 promoter, or the one HRE site in the Itga6 (murine) pr […]

library_books

Revealing new candidate genes for reproductive traits in pigs: combining Bayesian GWAS and functional pathways

2016
PMCID: 4736284
PMID: 26830357
DOI: 10.1186/s12711-016-0189-x

[…] ctional gene ontology (GO) terms and pathways with GeneCards (http://www.genecards.org/) and TOPPCLUSTER (http://toppcluster.cchmc.org/).TF enriched in the identified set of genes were found with the TFM-Explorer program (http://bioinfo.lifl.fr/TFM/TFME/). This program uses weight matrices from the JASPAR database [] to detect all potential TF binding sites (TFBS) from a set of gene sequences and […]

library_books

Mechanism of Wnt signaling induced down regulation of mrhl long non coding RNA in mouse spermatogonial cells

2015
Nucleic Acids Res
PMCID: 4705645
PMID: 26446991
DOI: 10.1093/nar/gkv1023

[…] c RNA polymerase II promoter elements like the TATA box and the CAAT box. We also observe a consensus TCF4 binding site (A/T-A/T-C-A-A-A-G) at −175 bp position. Also, by bioinformatics analysis using TFM explorer we could find putative binding sites for many transcription factors like FoxA1, FoxA2, FoxQ1 and Nkx3-2. In order to validate whether the 1 kb upstream region can function as a promoter e […]

library_books

The Human Blood Metabolome Transcriptome Interface

2015
PLoS Genet
PMCID: 4473262
PMID: 26086077
DOI: 10.1371/journal.pgen.1005274

[…] n-specific weight matrices of the transcription factor binding motifs were taken from the vertebrate collection of the Jaspar database version 5.0 alpha []. Enrichment analysis was performed with the TFM-Explorer command line tool []. The p-value threshold to determine significance of the motifs in all input sets was set to 1.0 × 10−7 which lies in the recommended optimal range given the numbers o […]

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TFM-Explorer institution(s)
LIFL, UMR CNRS 8022, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq, France

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