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ConTra specifications

Information


Unique identifier OMICS_09258
Name ConTra
Alternative name conserved TFBSs
Interface Web user interface
Restrictions to use None
Output data A list of PWMs for the exploration part and alignment blocks for the visualization part.
Programming languages Perl, R
Database management system MySQL
Computer skills Basic
Version 3
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Mammals
    • Bos taurus
  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
  • Vertebrates
    • Danio rerio
    • Gallus gallus
    • Xenopus tropicalis

Documentation


Maintainer


  • person_outline Pieter De Bleser

Additional information


http://bioit2.irc.ugent.be/contra/v3/#/help

Publications for conserved TFBSs

ConTra citations

 (6)
library_books

Increased immunization coverage addresses the equity gap in Nepal

2017
Bull World Health Organ
PMCID: 5407251
PMID: 28479621
DOI: 10.2471/BLT.16.178327

[…] todas las vacunas a la edad de 12 meses aumentó de un 68,8% (intervalo de confianza, IC, del 95%: 67,5–70,1) a un 82,4% (IC del 95%: 80,7–84,0). Estadísticamente, si bien la cobertura de inmunización contra BGC, DPT y sarampión aumentó durante el periodo de estudio, el porcentaje de niños que recibieron la tercera dosis de la vacuna antipoliomielítica descendió de un 93,3% (IC del 95%: 92,7–93,9) […]

library_books

Noncanonical SQSTM1/p62 Nrf2 pathway activation mediates proteasome inhibitor resistance in multiple myeloma cells via redox, metabolic and translational reprogramming

2016
Oncotarget
PMCID: 5340085
PMID: 27626179
DOI: 10.18632/oncotarget.11960

[…] -1/Cfz and KMS-11/Cfz cells, we performed ChIP-qPCR analysis on the promoter region of the GABARAPL1 gene.An evolutionarily conserved Nrf2 motif was identified in the GABARAPL1 promoter region by the ConTra v2 transcription factor binding site motif discovery program using position weight matrices from both the JASPAR CORE and TRANSFAC database libraries [] (). Of note, this motif coincided with a […]

library_books

The transcription factor Zeb2 regulates development of conventional and plasmacytoid DCs by repressing Id2

2016
PMCID: 4886362
PMID: 27185854
DOI: 10.1084/jem.20151715

[…] As Zeb2 is itself a TF, we next examined whether this effect was through direct binding of Zeb2 to the Id2 promoter region or through an indirect mechanism. In silico analysis using PhysBinder () or ConTra () identified several conserved Zeb binding sites () in Id2 and the surrounding regions in mice and humans (Fig. S8). Thus, we next designed two sets of primers to amplify two overlapping regio […]

library_books

Vitamin D receptor agonist calcitriol reduces calcification in vitro through selective upregulation of SLC20A2 but not SLC20A1 or XPR1

2016
Sci Rep
PMCID: 4868979
PMID: 27184385
DOI: 10.1038/srep25802

[…] and cellular process, as well as confirming its gene-selective effects. We performed in silico analysis of the respective promoters of these genes for potential vitamin D response elements using the Contra version 2 website (data not shown, http://bioit.dmbr.ugent.be contrav2/index.php). Consistent with the expression data, we found possible binding sites within 500 bp upstream of the transcripti […]

library_books

Transcriptome characterization of immune suppression from battlefield like stress

2012
Genes Immun
PMCID: 3564018
PMID: 23096155
DOI: 10.1038/gene.2012.49

[…] t prediction and repository databases: DBD (www.transcriptionfactor.org), JASPAR (http://jaspar.cgb.ki.se), TRANSFAC 7.0 - Public (http://www.gene-regulation.com/pub/databases.html) using ChipMAPPER, ConTra v2, Pscan and IPA (Ingenuity Systems Inc.). Expression data-based prediction Z-scores and regulatory targets were analyzed using IPA. Regulator–target interaction networks and pathways were gen […]

library_books

Yes Associated Protein 65 (YAP) Expands Neural Progenitors and Regulates Pax3 Expression in the Neural Plate Border Zone

2011
PLoS One
PMCID: 3110623
PMID: 21687713
DOI: 10.1371/journal.pone.0020309

[…] o find conservation of this previously described TEAD-binding site in the Xenopus tropicalis genome (). Using the genomic alignment and conserved transcription factor binding site prediction program, ConTra , a predicted TEAD-binding site that was highly conserved in 15 different vertebrates was identified 58 base pairs upstream of the previously described mouse neural crest enhancer TEAD2-binding […]

Citations

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ConTra institution(s)
VIB Bioinformatics Core, Zwijnaarde-Ghent, Belgium; VIB-UGent Center for Inflammation Research, Zwijnaarde-Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Zwijnaarde-Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium

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