Pscan protocols

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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 in pipelines

 (5)
2017
PMCID: 5261807
PMID: 28068333
DOI: 10.1371/journal.pgen.1006541

[…] < 0.05 and a fold change below -2 or above 2 (). gene ontology analysis was performed using the generic go-term mapper developed by the max planck institute (http://cpdb.molgen.mpg.de/ycpdb)., pscan tool was used to explore the promoter of the genes which are downregulated in bdf1-y187f-y354f 4 and 8h after sporulation induction (http://159.149.160.88/pscan/, []). binding motifs for yeast […]

2017
PMCID: 5526874
PMID: 28743894
DOI: 10.1038/s41598-017-06231-x

[…] value of 0.4) with revigo software to reduce redundancy, and then manually grouped into categories based on go ancestors and gene overlapping between terms., to identify creb target genes we used pscan to predict cre-binding sites of the transfac database in the promoter region (−450/+50) of selected genes, and the database of salk institute. additional software included ‘gplots’ […]

2017
PMCID: 5647435
PMID: 29044196
DOI: 10.1038/s41598-017-14081-w

[…] analysis was performed with david 6.8 beta, and kegg (kyoto encyclopedia of genes and genomes) database (http://www.kegg.jp/kegg/pathway.html)–, respectively, while tfbs analysis was performed with pscan using jaspar 2016 database and a promoter region of −950 to +50 bp. heat maps and hierarchical clustering was performed with gene-e […]

2013
PMCID: 3549877
PMID: 23257959
DOI: 10.4161/epi.23366

[…] project) in the probe sequence or interrogated cpg site. samples were clustered by hierarchical clustering using manhattan distances., transcription factor enrichment analysis was performed using pscan. transcription factor binding annotations were extracted from transfac. the gene promoter region was defined as -1,000 and +0 bp to the transcription start site. z-test p-values were corrected […]

2011
PMCID: 3333890
PMID: 22210892
DOI: 10.1093/nar/gkr1290

[…] with the yy1 proximal peaks. in this way we defined three sets, namely the yy1-bound myc-unbound, the yy1-bound myc-bound and the yy1-unbound myc-bound. for each different class of genes, we used pscan () to detect statistically significant over-represented pwms against a background dataset consisting of the three sets pulled together. in this case, the non-redundant set was used. in case […]


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Pscan in publications

 (100)
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 […]

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 […]

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 […]

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 […]

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 […]


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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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