ArticleNucleic acids research2013
PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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56 citing papers in PubMed.
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- B lymphocytes in treatment-naive paediatric patients with lupus are epigenetically distinct from healthy children.Lupus science & medicine · 2023Article
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- Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection.Cell host & microbe · 2021Article
- DROSHA is recruited to DNA damage sites by the MRN complex to promote non-homologous end joining.Journal of cell science · 2021Article
- On the NF-Y regulome as in ENCODE (2019).PLoS computational biology · 2020Article
- MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates.BMC bioinformatics · 2020Article
- TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions.Nucleic acids research · 2020Article
- Enhancer occlusion transcripts regulate the activity of human enhancer domains via transcriptional interference: a computational perspective.Nucleic acids research · 2020Article
- A molecular network regulating the proinflammatory phenotype of human memory T lymphocytes.Nature immunology · 2020Article
- Genome-wide plasma DNA methylation features of metastatic prostate cancer.The Journal of clinical investigation · 2020Article
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3 authors.
Funding
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Abstract
Chromatin immunoprecipitation followed by sequencing with next-generation technologies (ChIP-Seq) has become the de facto standard for building genome-wide maps of regions bound by a given transcription factor (TF). The regions identified, however, have to be further analyzed to determine the actual DNA-binding sites for the TF, as well as sites for other TFs belonging to the same TF complex or in general co-operating or interacting with it in transcription regulation. PscanChIP is a web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria. PscanChIP can successfully identify not only the actual binding sites for the TF investigated by a ChIP-Seq experiment but also secondary motifs corresponding to other TFs that tend to bind the same regions, and, if present, precise positional correlations among their respective sites. The web interface is free for use, and there is no login requirement. It is available at http://www.beaconlab.it/pscan_chip_dev.
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