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Protocols

i-cisTarget specifications

Information


Unique identifier OMICS_08301
Name i-cisTarget
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Maintainer


  • person_outline Stein Aerts

Publications for i-cisTarget

i-cisTarget citations

 (14)
library_books

Comparative transcriptomics reveals CrebA as a novel regulator of infection tolerance in D. melanogaster

2018
PLoS Pathog
PMCID: 5812652
PMID: 29394281
DOI: 10.1371/journal.ppat.1006847

[…] ues from these analyses were corrected using the Benjamini and Hochberg procedure [] with the FDR threshold set to 0.05. The search for putative transcription factor binding sites was performed using i-cisTarget under the default parameter values [,]. […]

library_books

Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood brain barrier integrity

2018
PLoS Genet
PMCID: 5796731
PMID: 29360820
DOI: 10.1371/journal.pgen.1007180

[…] d motifs for classical retinal determination genes such as So, Ey or Glass (Gl) in any of the 13 clusters, due to the fact that respective ChIP-seq data is either not available or not included in the i-cisTarget database. Therefore, our analysis is biased towards those transcription factors for which ChIP-seq data is publicly available. We performed a preliminary power analysis to evaluate the pot […]

call_split

Defining the molecular basis of oncogenic cooperation between TAL1 expression and Pten deletion in T ALL using a novel pro T cell model system

2018
Leukemia
PMCID: 5886055
PMID: 29151585
DOI: 10.1038/leu.2017.328
call_split See protocol

[…] K-means clustering was performed using Multiple Experiment Viewer (http://mev.tm4.org). For the prediction of cis-regulatory features and cis-regulatory modules ‘i-cisTarget’ was used and for gene ontology enrichment analysis, Gorilla. […]

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

[…] richment for Gene Ontology (GO) terms were realized using Flymine database [http://www.flymine.org/]. Benjamini-Hochberg corrected P values of less than 0.05 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 represen […]

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

[…] 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 computationally predict transcription factors and gene […]

library_books

Nuclear receptors connect progenitor transcription factors to cell cycle control

2017
Sci Rep
PMCID: 5501803
PMID: 28687780
DOI: 10.1038/s41598-017-04936-7

[…] ppl. Fig. ).To identify transcription factors (TFs) that may control directly these DE genes we looked for TF binding site motif enrichment in the vicinity of the differentially expressed genes using i-cisTarget, (See Materials and Methods). Down-regulated and up-regulated genes showed different motif enrichment: potential binding sites for E-box (top-enriched motif with a NES score of 4.73) and […]

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i-cisTarget institution(s)
Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, Leuven, Belgium

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