PscanChIP protocols

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PscanChIP specifications

Information


Unique identifier OMICS_00490
Name PscanChIP
Alternative name pscan-chip
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for PscanChIP

PscanChIP in pipeline

2017
PMCID: 5602546
PMID: 28922406
DOI: 10.1371/journal.pone.0184842

[…] ≥ 2.0 and p1(t) ≥ 0.8 difference between male and female transcriptomic data sets (). identification of over-represented transcription factor binding sites for chip-seq peaks was performed using pscan-chip []., gene set enrichment analysis (gsea) [] of sexually dimorphic and liver-specific genes was performed using a pre-ranked gene list based on the magnitude of the fold-change (largest […]


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PscanChIP in publications

 (13)
PMCID: 5888657
PMID: 29394393
DOI: 10.1093/nar/gky063

[…] we analyze 5hmc enrichment at pdx1 enriched regions at the pe stage () and observed a significant enrichment of 5hmc signals at pdx1 binding sites (figure ). furthermore, we performed pscan-chip () motif analysis on hergs at the pe stage. in addition to the foxa1 binding motif, pscan analysis revealed the overrepresentation of binding motifs for cux1 and onecut1, atf1 and gmeb1 […]

PMCID: 5815073
PMID: 29309647
DOI: 10.1093/nar/gkx1242

[…] cell line specific background files representing jund, c-jun and c-myc chip-seq binding signals in k562 and hela cell lines were used to calculate binding motifs in tfbitr and non-tfbitr loci (pscan_chip -r input.bed -g hg19 -m -bg bg/k562/hela.transfac.bg) (). resulting motifs were converted into pwms as described above and utilized for further analysis via stap tools.trap graphical […]

PMCID: 5634881
PMID: 29017520
DOI: 10.1186/s13059-017-1321-0

[…] and quantification were performed using seqminer []. over-represented sequence motifs for known transcription factors, according to motif descriptors in the jaspar database, were determined using pscan-chip []. only over-represented motifs with p value ≤ 1e-10 were considered., the predicted sequences of erβ and ago2 binding sites were extracted and used for de novo motif discovery using […]

PMCID: 5440673
PMID: 28504269
DOI: 10.1038/ncomms15321

[…] exons, 5′ utr exons, 3′ utr exons, **cpg islands, **repeats, introns, intergenic, over-represented sequence motifs were defined according to motif descriptors of jaspar database and computed using pscan-chip. the following parameters were set: organism: homo sapiensassembly: hg19background: mixeddescriptors: jaspar 2016, organism: homo sapiens, assembly: hg19, background: mixed, descriptors: […]

PMCID: 5383717
PMID: 28439269
DOI: 10.3389/fimmu.2017.00383

[…] visualized in genomebrowser (https://genome.ucsc.edu/cgi-bin/hggateway)., ets1 consensus binding sites and other transcription factor-binding sites in the ets1-bound regions were identified using pscanchip (). the regions were then aligned centered on the ets1 consensus motif. chip-seq data for acetylated and methylated lysine variants of histone h3 in primary b cells were obtained […]


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PscanChIP institution(s)
Dipartimento di Bioscienze, Università di Milano, Milano, Italy

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