MetaCore protocols

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MetaCore specifications

Information


Unique identifier OMICS_02716
Name MetaCore
Interface Web user interface
Restrictions to use License purchase required
License Commercial
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Jaimie Brown <>

MetaCore in pipelines

 (88)
2018
PMCID: 5743562
PMID: 29290822
DOI: 10.7150/thno.22059

[…] of species conservation) were recovered. these targets were further subjected to pathway enrichment analysis using online david functional annotation tools (https://david.ncifcrf.gov) and genego metacore software (thomson reuters; new york, ny, usa)., for the growth curve assay, oscc cells were seeded in 96-well plates. the cells were then fixed with 3.7% formaldehyde and stained […]

2018
PMCID: 5763955
PMID: 29321057
DOI: 10.1186/s40168-017-0386-z

[…] according to the design model with r/bioconductor edger v. 3.4.2. gene ontology analysis was performed using significantly upregulated mrnas (iav vs. mock, cutoff twofold, p < 0.05) as input for metacore (genego, thomson reuters) pathway analysis tools., 16s rrna gene ngs data were deposited at ncbi bioproject (https://www.ncbi.nlm.nih.gov/bioproject/) under the accession numbers prjna419860 […]

2017
PMCID: 5319192
PMID: 28219365
DOI: 10.1186/s12906-017-1586-6

[…] and displayed using the tigr multiexperiment viewer (http://mev.tm4.org/). an interaction network for genes with fold changes ≤ −2.0 was generated using transcription regulation algorithm in metacore™ analytic suit (genego inc., st. joseph, mi, usa)., the expression level of eukaryotic translation initiation factor 4a isoform 2 (eif4a2) was validated by qpcr. total rna […]

2017
PMCID: 5356255
PMID: 28302135
DOI: 10.1186/s12974-017-0834-5

[…] for each module to obtain a correlation. gene symbols and normalized values were appended, and heatmap visualization of individual modules was obtained within the wgcna package in r. finally the metacore™ platform was used to obtain the described interactions of proteins among the different modules to produce “external knowledge networks”, while visant software was used with the correlation […]

2017
PMCID: 5356255
PMID: 28302135
DOI: 10.1186/s12974-017-0834-5

[…] genotype differences (additional file : figure s1b). module violet contained c/ebpβ as expected (additional file : figure s1c) and additionally a set of genes linked by outer literature databases (metacore™; additional file : figure s1d) and within the distance measures of experiment data (additional file : figure s1e)., finally, we used the genecodis platform [] to obtain deg enrichment […]


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MetaCore in publications

 (1005)
PMCID: 5954162
PMID: 29765130
DOI: 10.1038/s41598-018-25827-5

[…] gene pathways that might assist in understanding potential disease mechanisms underlying scm, pathway analysis of the leading 100 snps in the eqscm versus hvols pairwise comparison was performed in metacore. disease biomarker pathway analysis identified myocardial ischemia as the third most enriched pathway (fdr-adjusted p = 1.3e−2), featuring 11 snp loci on our list out of 886 pathway objects, […]

PMCID: 5946489
PMID: 29747653
DOI: 10.1186/s13046-018-0754-y

[…] methylation (fig. ). to further understand the contribution of the inactivation of these genes toward npc carcinogenesis, we further analyzed them by using gene ontology pathway analysis software metacore (thomson reuters, toronto, canada). the tight junction pathway is a significant pathway involved in cell adhesion (−log p = 3.25; fig. ). the tight junction-related gene cldn11 was selected […]

PMCID: 5943364
PMID: 29743579
DOI: 10.1038/s41598-018-24240-2

[…] component analysis (pca) and plot heatmaps were computed using the entire set of significantly differentially methylated cpgs between different conditions., pathway analysis was performed using metacore software (thomson reuters) version 6.31 using the process networks gene ontologies default analysis in differential methylated cpgs of each comparison., genomic dna was prepared […]

PMCID: 5941680
PMID: 29739336
DOI: 10.1186/s12864-018-4670-5

[…] a high-stringency circrna-mirna-mrna interaction network with four circrnas, 11 mirnas and 49 genes (fig. , table ). our overall workflow is outlined in additional file : figure s3.fig. 3table 1, metacore pathway analysis on the 255 filtered differentially expressed target genes from the previous analysis revealed 112 perturbed pathways (corrected p < 0.01; table , additional file : table […]

PMCID: 5952427
PMID: 29766046
DOI: 10.1523/ENEURO.0436-17.2018

[…] expression determined using deseq2. adjusted p < 0.05 and log2 fold change >0.5 or <-0.5 were used as the cutoff for differential expression. significantly regulated genes were uploaded to metacore for downstream analysis to determine gene ontology (go) processes and molecular functions that were significantly altered in nav-tsc2 mice., rna-seq fastq files were deposited at the ncbi […]


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