Metascape protocols

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Associated diseases

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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

 (9)
2018
PMCID: 5915415
PMID: 29691479
DOI: 10.1038/s41598-018-24683-7

[…] 3′utr, 5′utr, tss (transcription start site, by default defined from −1kb to +100 bp) and intergenic regions. the protein coding genes associated with the de-apss were then used as input in the metascape program and pathways were enriched using “go biological processes”. protein-protein interaction networks were identified using the string database (https://string-db.org/) and visualized […]

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 (). 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 expression. quantitative […]

2017
PMCID: 5423031
PMID: 28529766
DOI: 10.1038/celldisc.2017.13

[…] analysis and the final data set was ready to be analyzed., the gene ontology database david was used for pathway analysis (search performed on 3 june 2016; https://david.ncifcrf.gov []), as well as metascape (search performed on 3 june 2016; http://metascape.org [])., enrichment analysis was performed with gprofiler, an r-package derived from the web-based gprofile toolset []. gprofiler was run […]

2017
PMCID: 5515408
PMID: 28719624
DOI: 10.1371/journal.pone.0180147

[…] extended by 250bp on either side (total region +/-350bp)., for the gene ontology analyses, the genes associated with myc peaks or summits containing only cme or ne motifs were analyzed by using metascape (http://metascape.org) []. the annotation field “biological process” was used in the analyses., in order to identify in an unbiased manner the dna sequences preferentially bound by myc/max […]


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Metascape in publications

 (44)
PMCID: 5945735
PMID: 29760954
DOI: 10.1038/s41420-018-0059-0

[…] analyses using a dna chip. from these analyses, common genes altered by both of the alk inhibitors, crizotinib and alectinib, were identified and subjected to a gene ontology analysis using metascape (fig. ; supplementary table , see also the methods section). the data showed that many cell cycle-related genes, as well as e2f1-target genes, were downregulated by alk inhibition. […]

PMCID: 5915415
PMID: 29691479
DOI: 10.1038/s41598-018-24683-7

[…] development, synapse organization, regulation of ion transport, learning, neurotransmitter transport, and regulation of vesicle-mediated transport as top ten summary pathways revealed by the metascape program. importantly, independent validation indicated that apss altered transcriptome expression of plasticity related genes in the hypothalamus. these findings suggest that differentially […]

PMCID: 5874256
PMID: 29619268
DOI: 10.1038/s41413-018-0011-1

[…] fig. ) from these six groups. annotation of the genes associated with these loci was done by nearest neighbor analysis and subsequent functional enrichment was performed using metascape. functional enrichment analysis of the runx2-enh-bmd-snp genes revealed ob differentiation and negative regulation of cell migration as the top ranking biological processes as well […]

PMCID: 5853091
PMID: 29540203
DOI: 10.1186/s13059-018-1416-2

[…] and mesenchymal cells (fig. ; additional file : figure s2a). the top organ-specific tfs also supported their identities (additional file : figure s2b). then, we used the meta-analysis workflow in metascape [] to combine these organ-specific degs of epithelial and mesenchymal cells to identify the shared pathways in which they participated. both cell type-specific and shared terms […]

PMCID: 5845222
PMID: 29523209
DOI: 10.1186/s13287-018-0793-5

[…] finally, back-spliced junction reads were combined and scaled to rpb (reads per billion mapped reads, including tophat mapping and tophat-fusion mapping) to quantify every back-spliced event., metascape (http://metascape.org) was applied for gene ontology (go) term detection and clustering., three types of sirnas targeting the human qki gene were designed and synthesized by guangzhou […]


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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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