GenMAPP protocols

View GenMAPP computational protocol

GenMAPP statistics

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Associated diseases

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GenMAPP specifications

Information


Unique identifier OMICS_02697
Name GenMAPP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/GenMAPP

Subtool


  • MAPPFinder

Versioning


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Maintainers


  • person_outline Nathan Salomonis <>
  • person_outline Bruce Conklin <>

Additional information


MAPPFinder is a part of the GenMAPP software.

Publications for GenMAPP

GenMAPP in pipelines

 (20)
2018
PMCID: 5802208
PMID: 29328449
DOI: 10.3892/mmr.2018.8385

[…] the toppgene database (https://toppgene.cchmc.org/) () integrates pathway information in biosystems [including biocyc, kyoto encyclopedia of genes and genomes (kegg), reactome, wikipathways], genmapp, msigdb c2 (including biocarta, sigmaaldrich and signaling gateway), pantherdb, pathway ontology and small molecule pathway database databases, and can be used for functional and pathway […]

2017
PMCID: 5453167
PMID: 28599476
DOI: 10.3892/ol.2017.6084

[…] 5 non-metastatic ccrcc samples. differentially expressed genes (degs) were screened using the limma package. then, pheatmap package was used to conduct two-way clustering for the degs. subsequently, mappfinder and genmapp were employed separately to perform functional and pathway enrichment analysis for the degs. additionally, a protein-protein interaction (ppi) network was constructed using […]

2017
PMCID: 5681904
PMID: 29163640
DOI: 10.3389/fgene.2017.00174

[…] as input. metacore employs a hyper-geometric model to determine the significance of the enrichments. pathvisio also uses an over-representation analysis and it is based on methods adopted in the mappfinder tool () with settings designed for gene expression data. finally, ipa utilizes a method for combining p-values. in the over-representation test, an association for each gene in the dataset […]

2016
PMCID: 5028088
PMID: 27695320
DOI: 10.2147/IJN.S110332

[…] genes with greater than twofold and less than 0.5-fold change in expression level were selected as up- or downregulated genes, respectively. gene-ontology information on each deg was obtained from genmapp, david,, and medline databases., functional analysis of degs in the context of the molecular networks and biological pathways was conducted using the ingenuity pathways analysis (ipa; qiagen, […]

2016
PMCID: 5342096
PMID: 27683030
DOI: 10.18632/oncotarget.12229

[…] predicted the functions of mirnas based on the functional enrichment analysis of their target genes. mirgator and diana-mirpath provided the statistically enriched gene ontology functions and kegg/genmapp/biocarta pathways [, ]. another comprehensive analysis established a dictionary on mirnas and their putative target pathways and uncovered that differentially expressed genes in cancers […]


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GenMAPP in publications

 (314)
PMCID: 5861324
PMID: 29437903
DOI: 10.1042/BSR20171208

[…] to extract and analyze biological molecule relationships from the public knowledgebase of biological molecules and signification, including genbank, embl, swissprot, gene ontology, kegg, biocarta, genmapp, mirbase, epd, hprd, mind, bind, intact, transfac, unigene, dbsnp, omim, interpro, hugo, mgi, rgd, etc. in addition, the significantly enriched go annotations were chosen (−log10(p-value) […]

PMCID: 5802208
PMID: 29328449
DOI: 10.3892/mmr.2018.8385

[…] the toppgene database (https://toppgene.cchmc.org/) () integrates pathway information in biosystems [including biocyc, kyoto encyclopedia of genes and genomes (kegg), reactome, wikipathways], genmapp, msigdb c2 (including biocarta, sigmaaldrich and signaling gateway), pantherdb, pathway ontology and small molecule pathway database databases, and can be used for functional and pathway […]

PMCID: 5753510
PMID: 29298665
DOI: 10.1186/s12885-017-3941-x

[…] of differently expressed genes in hcc and classified the related genes into three major groups: biological processes, cellular component and molecular functions. pathway analysis was applied in genmapp v2.1 for kyoto encyclopedia of genes and genomes (kegg) pathway enrichment and the value of p was calculated to select the significantly enriched pathway. we also combined three different […]

PMCID: 5792724
PMID: 29286585
DOI: 10.1111/1759-7714.12572

[…] databases with the mas core database. the information required for pathway analysis was obtained from three pathway databases, the kyoto encyclopedia of genes and genomes (kegg), biocarta, and genmapp, which are the major authoritative pathway databases. , total rna was extracted and then reverse transcribed into complementary dna (cdna) using a primescript rt reagent kit (takara […]

PMCID: 5945262
PMID: 29271183
DOI: 10.5009/gnl17277

[…] (anova) analysis., for identification of involved specific signaling or metabolic pathways in human hepato- or cholangiocarcinogenesis, data of significantly expressed genes were transferred in genmapp, a public domain software program 2.0 beta© (gladstone institutes, san francisco, ca, usa). genmapp allows the graphic representation of various pathways and the expression levels of involved […]


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GenMAPP institution(s)
Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA, USA; Cardiovascular Research Institute, University of California, San Francisco, CA, USA; Departments of Medicine and Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA; Functional Genomics Lab, University of California, Berkeley, CA, USA
GenMAPP funding source(s)
Supported by the J. David Gladstone Institutes, the San Francisco General Hospital General Clinical Research Center, the National Heart, Lung, and Blood Institute, San Francisco General Hospital General Clinical Research Center MO1RR00083 and the NHLBI Programs for Genomic Applications (BayGenomics).

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