Metascape protocols

Metascape specifications

Information


Unique identifier OMICS_13553
Name Metascape
Interface Web user interface
Restrictions to use None
Input data A multiple gene list.
Input format TXT, XLS, CSV
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
    • Plasmodium falciparum
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio

Documentation


Publication for Metascape

Metascape IN pipelines

 (6)
2018
PMCID: 5943334
PMID: 29743643
DOI: 10.1038/s41598-018-25308-9

[…] were performed using cufflinks/cutdiff., functional interpretation of differentially expressed genes and their association to the host cell pathways for each of the mvs treatments were done using metascape software. for each treatment, the affected genes were analyzed separately for up- and downregulated genes. we identified canonical pathways that were enriched or overrepresented, […]

2017
PMCID: 5400508
PMID: 28394251
DOI: 10.7554/eLife.24570.023

[…] called with edger (v3.14.0) with the following criteria: adjusted p-value<0.05 and fold change (fc) >1.5 or <0.67. the gene ontology (go) enrichment analysis of degs was performed using metascape (tripathi et al., 2015). the top six go terms with p-value<0.001 in the ‘biological process’ category were used., real-time pcr was used to measure relative chip enrichment or gene […]

2017
PMCID: 5622043
PMID: 28963538
DOI: 10.1038/s41467-017-01117-y

[…] were counted per gene model (not counting differentiated splices) and differential expression across samples were determined using edger35. gene ontology enrichment (go) analysis was performed using metascape36., p53, rnapii, and histone chromatin immunoprecipitation (chip) assays were performed using sw480, mda-mb-231, or hct116 cells that were (i) untreated or treated with 12.5 ng ml−1 tnf-α […]

2017
PMCID: 5727902
PMID: 29131158
DOI: 10.1038/nm.4429

[…] reads were converted to fpkm (fragments per kilobase of exon per million fragments mapped) by running cuffdiff 2.1.1 to determine gene expression. biological pathway analysis was performed using metascape24. the sequencing data were deposited in arrayexpress (http://www.ebi.ac.uk/arrayexpress/) under accession number e-mtab-4085., concentrations of all the charged metabolites were measured […]

2017
PMCID: 5774495
PMID: 29434723
DOI: 10.3892/etm.2017.5556

[…] pheatmap package in r version 3.1.3 (www.r-project.org/)., gene ontology (go) enrichment analysis and kyoto encyclopedia of genes and genomes (kegg) pathway enrichment analysis were performed using metascape (metascape.org/gp/index.html#/main/step1) to further investigate the biological function of each deg. p<0.01 was considered to indicate a significantly enriched deg., using […]

Metascape institution(s)
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Institute of Medical Virology, University of Zurich, Zurich, Switzerland; Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA; Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA; Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA; Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA; Department of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; University of Texas Southwestern Medical Center, Dallas, TX, USA; Columbia University, Department of Systems Biology and Department of Microbiology and Immunology, New York, NY, USA; Massachusetts General Hospital, Charlestown, MA, USA; Max Planck Institute for Infection Biology, Berlin, Germany; University of California, San Francisco, San Francisco, CA, USA; Host-Pathogen Interactions, Paul-Ehrlich-Institut, Germany; German Center for Infection Research, Langen, Germany; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Metascape funding source(s)
Supported by NIAID research grant U19 AI106754 and supported by a grant from the Swiss National Science Foundation (31003A_135278), a doctoral grant from the AXA Research Fund and the NIH P50 GM085764 and by a grant (1R01AI091786) from the National Institute of Allergy and Infectious Diseases of the NIH, the Burroughs Wellcome Fund, and the Bill and Melinda Gates Foundation.

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