oPOSSUM protocols

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chevron_left De novo motif discovery Transcription factor binding site prediction chevron_right
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oPOSSUM specifications

Information


Unique identifier OMICS_00488
Name oPOSSUM
Alternative name oPOSSUM-3
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Maintainers


  • person_outline Wyeth Wasserman <>
  • person_outline pPOSSUM Team <>

Additional information


http://opossum.cisreg.ca/oPOSSUM3/help.html

Information


Unique identifier OMICS_00488
Name oPOSSUM
Alternative name oPOSSUM-3
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

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Versioning


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Maintainers


  • person_outline Wyeth Wasserman <>
  • person_outline pPOSSUM Team <>

Additional information


http://opossum.cisreg.ca/oPOSSUM3/help.html

Publications for oPOSSUM

oPOSSUM in pipelines

 (12)
2018
PMCID: 5766484
PMID: 29330469
DOI: 10.1038/s41598-017-18528-y

[…] (http://www.drive5.com/usearch). no matches above 50% were found., the upstream regions of down- and up-regulated genes were searched for known transcription factor binding sites (tfbs) using the opossum software (http://opossum.cisreg.ca/). upstream regions of the controls were used for background control purposes. no sites were found with better than z-score of 10 or greater and a fisher […]

2017
PMCID: 5209944
PMID: 28049421
DOI: 10.1186/s12864-016-3384-9

[…] gene module were analysed for enrichment of transcription factor (tf)-binding sites (tfbs) against a background gene set of all detectable genes in the placenta dataset (15,861) using the opossum program and the jaspar vertebrate core profiles [, ]. for each gene, we searched for tfbs motifs in the conserved regions of the 10kb upstream/downstream sequences using a conservation […]

2017
PMCID: 5314486
PMID: 28209164
DOI: 10.1186/s13059-017-1159-5

[…] using the genomic regions enrichment of annotations tool (great version 3.0.0) []. sequence-based motif analysis for upregulated genes associated with enhancers in rnf40 –/– mefs was performed using opossum (version 3.0) []. the input file contained the regions (±150 bp) surrounding h3k27ac peak centers on enhancers associated with genes upregulated in rnf40 –/– mefs. the remaining enhancers […]

2016
PMCID: 5062749
PMID: 27790248
DOI: 10.3389/fgene.2016.00183

[…] we used a previous study that lists genes that are targets of erα (jin et al., )., transcription factor (tf) binding sites within 10 kb upstream/downstream of sex-biased genes were analyzed using opossum-3 and the jaspar vertebrate core profiles (kwon et al., ; mathelier et al., ). we chose 10 kb upstream/downstream of genes as this was the largest range the opossum-3 would allow. thus, […]

2016
PMCID: 5389510
PMID: 27980063
DOI: 10.1093/nar/gkw1276

[…] analyses. for chip-seq and rna-seq analyses, q-value (to call peaks) and adjusted p-value of ≤0.05 was considered for statistical significance respectively. motif analyses were performed using opossum 3.0 and z-score and fisher score (negative natural logarithm of p-value) were utilized for showing significant motifs. enrichment score and normalized enrichment score were shown for gsea […]


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oPOSSUM in publications

 (82)
PMCID: 5859033
PMID: 29593668
DOI: 10.3389/fmicb.2018.00380

[…] to better understand the complex mechanisms of cancer-related, differentially expressed genes controlling important biological functions at transcriptional and post-transcriptional levels, opossum web tool (ho sui et al., ) was used to identify the transcription factor (tf) binding sites and over-represented regulatory motif of target matrices (pavesi et al., ) in promoter regions […]

PMCID: 5766484
PMID: 29330469
DOI: 10.1038/s41598-017-18528-y

[…] (http://www.drive5.com/usearch). no matches above 50% were found., the upstream regions of down- and up-regulated genes were searched for known transcription factor binding sites (tfbs) using the opossum software (http://opossum.cisreg.ca/). upstream regions of the controls were used for background control purposes. no sites were found with better than z-score of 10 or greater and a fisher […]

PMCID: 5709375
PMID: 29192143
DOI: 10.1038/s41598-017-16687-6

[…] the data, and location determined relative to the transcription start site (tss)., genes with retinoic acid response elements (rares) were identified from published data (lalevee et al.) or from the opossum database within 10 kb of the tss of the gene of interest. rare sequences were entered into weblogo with default settings. where a gene was identified with more than 1 rare within 10 kb […]

PMCID: 5702388
PMID: 29209359
DOI: 10.3389/fgene.2017.00183

[…] up-regulated genes shown as positive and clusters enriched among down-regulated genes shown as negative., overrepresentation of predicted transcription factor binding sites was determined using opossum 3.0 single site analysis (ssa) (; ). gene lists were loaded into the browser-based software by gene symbol, and putative transcription factor binding sites (tfbs) were scored based […]

PMCID: 5605092
PMID: 28863187
DOI: 10.1371/journal.ppat.1006577

[…] respectively. pathway analysis was performed with innatedb for over-representation analysis []. transcription factor binding site enrichment on differentially expressed genes was performed using opossum []., flow cytometry data was analysed using flowjo v10. statistical analysis of all other experiments was performed with graphpad prism 6 and is indicated where appropriate., we thank […]


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oPOSSUM institution(s)
Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada; Department of Medical Genetics, Genetics Graduate Program, and Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
oPOSSUM funding source(s)
Supported by funding from the National Institutes of Health (USA) grant 1R01GM084875, the Canadian Institutes for Health Research, the National Science and Engineering Research Council (NSERC), GenomeBC (CanEuCre Project), and Genome Canada (Pleiades Promoter Project), a NSERC fellowship, and a fellowship from the Canadian Institutes of Health Research and the Michael Smith Foundation for Health Research.

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