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Protocols

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


No version available

Maintainers


  • person_outline Nathan Salomonis
  • person_outline Bruce Conklin

Additional information


MAPPFinder is a part of the GenMAPP software.

Publications for GenMAPP

GenMAPP citations

 (153)
library_books

Bioinformatics analysis of microRNAs related to blood stasis syndrome in diabetes mellitus patients

2018
Biosci Rep
PMCID: 5861324
PMID: 29437903
DOI: 10.1042/BSR20171208

[…] on 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) > 5) […]

library_books

Gene master regulators of papillary and anaplastic thyroid cancers

2017
Oncotarget
PMCID: 5788649
PMID: 29416781
DOI: 10.18632/oncotarget.23417

[…] ifferentiation. Sophisticated algorithms using reverse engineering of transcriptional networks have been proposed and validated for use in therapeutic decision making []. KEGG (http://www.genome.jp), GenMapp (http://genmapp.org), IPA (http://ingenuity.com), DAVID (http://david.abcc.ncifcrf.gov) and other popular software have been developed to ensemble the biomarkers and other genes in functional […]

library_books

A Review of Pathway Based Analysis Tools That Visualize Genetic Variants

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

[…] ided 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 […]

library_books

MiRNAs regulate oxidative stress related genes via binding to the 3′ UTR and TATA box regions: a new hypothesis for cataract pathogenesis

2017
PMCID: 5556341
PMID: 28806956
DOI: 10.1186/s12886-017-0537-9

[…] (average fold change >2 or <0.5) (Fig. ). Gene symbols of the top 100 up-regulated genes and top 100 down-regulated genes were uploaded to MAS 3.0 system to generate gene-pathway network graph using GenMAPP database, as it was too complex to generate graph by Graphviz if more than 200 gene symbols were included (Fig. ). It is shown that oxidative stress related pathway was involved in cataract re […]

library_books

Fam64a is a novel cell cycle promoter of hypoxic fetal cardiomyocytes in mice

2017
Sci Rep
PMCID: 5493652
PMID: 28667270
DOI: 10.1038/s41598-017-04823-1

[…] re normalized by global normalization methods. Genes with normalized ratios of > 2.0 and < 0.5 were defined, respectively, as upregulated and downregulated genes. Pathway analyses were performed with GenMAPP software version 2.1 (MAPP Finder at http://www.genmapp.org/, Gladstone Institutes, University of California at San Francisco) with threshold ratios of 2.0 (up)/0.5 (down) in array #1 and 1.5 […]

library_books

Short term application of dexamethasone on stem cells derived from human gingiva reduces the expression of RUNX2 and β catenin

2017
PMCID: 5536397
PMID: 28459354
DOI: 10.1177/0300060517701035

[…] estimate their abundances, and detect differential expressions of genes or isoforms using cufflinks. Gene classification was based on searches performed using the BioCarta (http://www.biocarta.com/), GenMAPP (http://www.genmapp.org/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline databases (http://www.ncbi.nlm.nih.gov/). […]

Citations

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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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