oPOSSUM statistics

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Protocols

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

Download


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Versioning


No version available

Maintainers


  • person_outline Wyeth Wasserman
  • person_outline pPOSSUM Team

Additional information


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

Publications for oPOSSUM

oPOSSUM citations

 (58)
library_books

Differential contribution of cis and trans gene transcription regulatory mechanisms in amygdala and prefrontal cortex and modulation by social stress

2018
Sci Rep
PMCID: 5910421
PMID: 29679052
DOI: 10.1038/s41598-018-24544-3

[…] hanisms include transcription factors, we considered that particular gene transcription binding sites may be enriched amongst the genes that are regulated in trans specifically in the amygdala. Using Opossum tool, we tested for transcription factor site enrichment in our sets of genes. We find that transcription factor binding sites upstream of 23 trans expressed genes in the amygdala were likely […]

library_books

How asbestos drives the tissue towards tumors: YAP activation, macrophage and mesothelial precursor recruitment, RNA editing, and somatic mutations

2018
Oncogene
PMCID: 5955862
PMID: 29507420
DOI: 10.1038/s41388-018-0153-z

[…] , was upregulated in crocidolite-exposed tissues and tumors (Fig. ), supporting the hypothesis of environment-driven stimulation of pluripotency potential. This observation was reinforced by unbiased oPOSSUM analysis (http://opossum.cisreg.ca/cgi-bin/oPOSSUM3/opossum_mouse_tca) indicating that Klf4 ranked first among the transcription factors with over-represented binding sites in genes that were […]

library_books

Treatment associated TP53 DNA binding domain missense mutations in the pathogenesis of secondary gliosarcoma

2017
Oncotarget
PMCID: 5788663
PMID: 29416795
DOI: 10.18632/oncotarget.23517

[…] ures, while the IC50 of ruxolitinib was modestly higher than TMZ in GBM1 (Figure ). Significantly downregulated transcription factors common to both gliosarcomas were HOXA5, FOXO1, and CEBPA. We used oPOSSUM [] to identify transcription factor binding sites common to the promoter regions of genes in the secondary gliosarcoma that were significantly upregulated greater than 4-fold. We found that co […]

library_books

Profiling of the transcriptional response to all trans retinoic acid in breast cancer cells reveals RARE independent mechanisms of gene expression

2017
Sci Rep
PMCID: 5709375
PMID: 29192143
DOI: 10.1038/s41598-017-16687-6

[…] 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 of the […]

call_split

Wnt/β catenin Signaling Pathway Regulates Specific lncRNAs That Impact Dermal Fibroblasts and Skin Fibrosis

2017
Front Genet
PMCID: 5702388
PMID: 29209359
DOI: 10.3389/fgene.2017.00183
call_split See protocol

[…] d among 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 on their ov […]

library_books

Evolution of UCP1 Transcriptional Regulatory Elements Across the Mammalian Phylogeny

2017
Front Physiol
PMCID: 5611445
PMID: 28979209
DOI: 10.3389/fphys.2017.00670

[…] 0.1%) in other tissues (Brand and Esteves, ). Interestingly, an enhancer box has been well documented to play a major role in eutherian UCP1 gene transcription, but is absent in the gray short-tailed opossum (Monodelphis domestica; Jastroch et al., ), suggesting that it originated with the advent of eutherian UCP1-mediated NST, thus highlighting the importance that gene regulation likely played in […]

Citations

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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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