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Information


Unique identifier OMICS_18785
Name cisTargetX
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

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Publication for cisTargetX

cisTargetX citations

 (7)
library_books

Interplay between trauma and Pseudomonas entomophila infection in flies: a central role of the JNK pathway and of CrebA

2017
Sci Rep
PMCID: 5701226
PMID: 29176735
DOI: 10.1038/s41598-017-14969-7

[…] 05 were considered significant. We also used i-cisTarget tool to look for enrichment in TF (TF) position weight matrices and potential binding sites in the regulatory regions of co-expressed genes. i-cisTargetX computes statistical over representation of DNA motifs and ChIP-seq peaks in the non-coding DNA around sets of genes. The enrichment was considered significant when the Normalized Enrichmen […]

library_books

Conserved Transcription Factors Steer Growth Related Genomic Programs in Daphnia

2017
Genome Biol Evol
PMCID: 5569996
PMID: 28854641
DOI: 10.1093/gbe/evx127

[…] pulex, we developed the method Daphnia-cisTarget that identifies overrepresented cis-regulatory motifs and candidate regulators in a set of coexpressed genes. The approach and algorithm are based on cisTargetX. cisTargetX and its follow-up methods i-cisTarget and evo-cisTarget are successfully applied for motif discovery in fruit fly, human, and mouse (; ; ; ; ). We use Daphnia-cisTarget to compu […]

library_books

Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co localization within regulatory modules

2016
BMC Bioinformatics
PMCID: 5117513
PMID: 27871221
DOI: 10.1186/s12859-016-1354-5

[…] newer programs combine phylogeny and possibly other information with TFBS patterns, either with consistent positioning (Stubb []; EMMA []; TWINE []) or without it ([]; PhyloCon []; CisPlusFinder []; cisTargetX [, ]). Programs searching a single genome for the consistent positional preferences within RMs are therefore surprisingly rare [].Notably, all our significant clusters occurred within about […]

library_books

Genome wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization

2013
Genome Biol
PMCID: 4053989
PMID: 23972280
DOI: 10.1186/gb-2013-14-8-r86

[…] Detection of motifs enriched in Svb-dependent and Svb-independent epidermal genes was performed using cisTargetX []. For de novo motif discovery, genomic sequences of enhancer and negative regions were processed through a C++ program and statistical operations performed within the R software, as descr […]

library_books

Transcriptional and epigenetic signatures of zygotic genome activation during early drosophila embryogenesis

2013
BMC Genomics
PMCID: 3706223
PMID: 23560912
DOI: 10.1186/1471-2164-14-226

[…] The analysis of regulatory sequences relied on the Regulatory Sequence Analysis Tools (RSAT, http:// rsat.ulb.ac.be/rsat/) [,] and CisTargetX (http://med. kuleuven.be/cme-mg/lng/cisTargetX/) []. […]

library_books

dJun and Vri/dNFIL3 Are Major Regulators of Cardiac Aging in Drosophila

2012
PLoS Genet
PMCID: 3510041
PMID: 23209438
DOI: 10.1371/journal.pgen.1003081

[…] age-regulated genes, we performed in silico predictions of TF-binding motifs potentially involved in the regulation of genes up- and down-regulated in the aging heart. We used the recently published cisTargetX method , . cisTargetX uses identification of clusters of TF-binding motifs across the entire genomes of 12 Drosophila species and ranking statistics, to determine significant associations b […]

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cisTargetX institution(s)
Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium; Laboratory of Computational Biology, Katholieke Universiteit (K.U.) Leuven, Leuven, Belgium; Center for Human Genetics, K.U. Leuven, Leuven, Belgium; Doctoral Program in Molecular and Developmental Genetics, K.U. Leuven Group Biomedicine, Leuven, Belgium
cisTargetX funding source(s)
Supported by VIB and Impuls, CREA, and Geconcerteerd Onderzoeksacties (GOA) grants from K.U. Leuven, FWO project 3M070090, and FWO postdoctoral fellowship.

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