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Pscan specifications

Information


Unique identifier OMICS_09256
Name Pscan
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.3
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Giulio Pavesi

Information


Unique identifier OMICS_09256
Name Pscan
Interface Web user interface
Restrictions to use None
Programming languages C++
Computer skills Basic
Version 1.3
Stability Stable
Maintained Yes

Maintainer


  • person_outline Giulio Pavesi

Publication for Pscan

Pscan citations

 (101)
library_books

Environmental Enrichment Prevents Transcriptional Disturbances Induced by Alpha Synuclein Overexpression

2018
PMCID: 5932345
PMID: 29755323
DOI: 10.3389/fncel.2018.00112

[…] their interconnections) were selected. grouping and coloring based on manually determined gene ontology categories of the genes. transcription factor binding site (tfbs) analyses were carried out in pscan (v1.4) (zambelli et al., ) on the mus musculus genome, considering −450 to +50 bp of promoter regions for motifs against the jaspar 2016 database. all gene id conversions were done using […]

library_books

T197. A DRD2 CO EXPRESSION GENE SET ENRICHED FOR SCHIZOPHRENIA RISK GENES IS CHARACTERIZED BY A COMMON TRANSCRIPTIONAL REGULATION INVOLVING NURR1 TRANSCRIPTION FACTOR

2018
Schizophr Bull
PMCID: 5887402
DOI: 10.1093/schbul/sby016.473

[…] factors (tfs)., in order to identify tf binding sites (tfbss) in the promoter region of the 85 genes belonging to the drd2 co-expression network, we performed a motif enrichment analysis using pscan and genomatix matinspector tools. biological validation experiments were performed in primary mouse cortical neurons. by real-time pcr analysis we measured the mrna transcript levels of a group […]

library_books

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

2018
Nucleic Acids Res
PMCID: 5888657
PMID: 29394393
DOI: 10.1093/nar/gky063

[…] 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 within hergs (figure ). cux1 and onecut1 are also reported as key tfs for normal pancreas […]

library_books

High Resolution Mapping and Dynamics of the Transcriptome, Transcription Factors, and Transcription Co Factor Networks in Classically and Alternatively Activated Macrophages

2018
Front Immunol
PMCID: 5778122
PMID: 29403501
DOI: 10.3389/fimmu.2018.00022

[…] were displayed using shapes to represent functional classes of gene products., ncbi reference sequence mrna accession numbers were subjected to tf binding motif analysis using the web-based software pscan (). the jaspar () database of tf binding sequences were analyzed using enriched groups of −950 base pair (bp) sequences to +50 bp of the 5′ upstream promoters. the range −950 to +50 […]

library_books

Global mapping of transcription factor motifs in human aging

2018
PLoS One
PMCID: 5749797
PMID: 29293662
DOI: 10.1371/journal.pone.0190457

[…] remain highly correlated (r > 0.93) when the number of transcripts is trimmed down from 250 to 150, but correlations drop below 0.9 when less than 100 transcripts are included (). we used pscan, 2016 build, to scan promoter regions between -450 bp upstream to 50 bp downstream of the transcription start site in the direction of transcription []. the motivating choice of this search […]

library_books

ChIP Seq analysis identifies p27(Kip1) target genes involved in cell adhesion and cell signalling in mouse embryonic fibroblasts

2017
PLoS One
PMCID: 5695801
PMID: 29155860
DOI: 10.1371/journal.pone.0187891

[…] from transfac database (professional version release 2009.4)., possible occurrence of tf motifs in peak regions (150bp around peak summit) and overrepresentation of these tfs is based on the tool pscan [] with parameter: mixed background mm9, transfac matrix. pscan evaluates local enrichment, comparing with a t-test mean and standard deviation of the score of the best matching […]


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Pscan institution(s)
Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milan, Milan; Dipartimento di Biochimica e Biologia Molecolare ‘E Quagliariello’, University of Bari; Istituto Tecnologie Biomediche—Consiglio Nazionale delle Ricerche, Bari, Italy
Pscan funding source(s)
Italian Ministry of Education and Scienfic Research (MIUR) within the FIRB project ‘Laboratorio Internazionale di Bioinformatica’ (LIBI)

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