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PscanChIP specifications


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 citations


Decoding the dynamic DNA methylation and hydroxymethylation landscapes in endodermal lineage intermediates during pancreatic differentiation of hESC

Nucleic Acids Res
PMCID: 5888657
PMID: 29394393
DOI: 10.1093/nar/gky063

[…] ifferentiation, 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 wit […]


Transcriptional interference by small transcripts in proximal promoter regions

Nucleic Acids Res
PMCID: 5815073
PMID: 29309647
DOI: 10.1093/nar/gkx1242

[…] mputed 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/ (). Resulting motifs were converted into PWMs as described above and utilized for further analysis via STAP tools.TRAP graphical repres […]


The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading

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

[…] on, 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. […]


Loss of liver specific and sexually dimorphic gene expression by aryl hydrocarbon receptor activation in C57BL/6 mice

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

[…] nge| ≥ 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 []. […]


YAP regulates cell mechanics by controlling focal adhesion assembly

Nat Commun
PMCID: 5440673
PMID: 28504269
DOI: 10.1038/ncomms15321

[…]  bp to +1 kb)CDS exons5′ UTR exons3′ UTR exons**CpG islands**RepeatsIntronsIntergenicOver-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 2016Organism: Homo SapiensAssembly: hg19Background: MixedDescriptors: Jaspar 201 […]


Genome Wide Identification of Target Genes for the Key B Cell Transcription Factor Ets1

Front Immunol
PMCID: 5383717
PMID: 28439269
DOI: 10.3389/fimmu.2017.00383
call_split See protocol

[…] were visualized in GenomeBrowser ( 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 from the GE […]


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

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