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Number of citations per year for the bioinformatics software tool MADGene
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This map represents all the scientific publications referring to MADGene per scientific context
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MADGene specifications

Information


Unique identifier OMICS_15629
Name MADGene
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publication for MADGene

MADGene citations

 (6)
library_books

Exploiting human and mouse transcriptomic data: Identification of circadian genes and pathways influencing health

2015
BioEssays
PMCID: 5031210
PMID: 25772847
DOI: 10.1002/bies.201400193

[…] Mapping gene names through the tool MadGene , we found that 15 (65%, not including genes with no apparent homolog) of the 28 human robust circadian genes had identifiable homologs in mouse that were circadian in at least one tissue. Of […]

library_books

A common gene signature across multiple studies relate biomarkers and functional regulation in tolerance to renal allograft

2015
PMCID: 4424816
PMID: 25629549
DOI: 10.1038/ki.2014.395

[…] Data sets were renormalized using a Lowess procedure, log-transformed, and median-centered on genes as previously described., , , , Probe annotation was performed using MADGene to convert and match the genes across array platforms. Data sets were standardized according to the STA group, before their integration and merging on the 1846 consensus genes. The relationshi […]

library_books

Summarizing cellular responses as biological process networks

2013
BMC Syst Biol
PMCID: 3751784
PMID: 23895181
DOI: 10.1186/1752-0509-7-68

[…] y Interaction Database’s curated pathways [] downloaded February 7, 2011. For the rat data, we normalized all data into the Ensembl Peptide ID namespace through a combination of the Synergizer [] and MadGENE [] mapping services. For the human data, we used the same services to normalize all the data into Entrez Gene namespace.Next, we integrated the annotations with the gene interaction networks. […]

library_books

Immune Response and Mitochondrial Metabolism Are Commonly Deregulated in DMD and Aging Skeletal Muscle

2011
PLoS One
PMCID: 3212519
PMID: 22096509
DOI: 10.1371/journal.pone.0026952

[…] h individual data set, non-linear effects such as background or saturation were corrected by LOWESS as previously described .For each GEO platform (GPL), information on probe-sets was gathered in the MADGene database (www.madtools.org) and completed with related information collected from the NCBI Entrez gene database and Unigene databases , . Based on this annotation, genes found as differentiall […]

library_books

High Throughput Analysis of Promoter Occupancy Reveals New Targets for Arx, a Gene Mutated in Mental Retardation and Interneuronopathies

2011
PLoS One
PMCID: 3178625
PMID: 21966449
DOI: 10.1371/journal.pone.0025181

[…] the uncentered correlation coefficient as similarity metric. Results were displayed using the Java TreeView program (http://jtreeview.sourceforge.net/) . Information on probes was retrieved with the MADGene resource and clusters of genes with the same regulation were then functionally annotated using GoMiner (http://discover.nci.nih.gov/gominer/index.jsp) . […]

library_books

Meta analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns

2011
BMC Genomics
PMCID: 3049149
PMID: 21324190
DOI: 10.1186/1471-2164-12-113

[…] d tools (e.g. Connectivity Map, L2L, Oncomine) rely on manual curation of data. Although these tools are extremely useful, they are labor-intensive. Thanks to the automatic microarray annotation tool MADGene [] (see also Additional File , part 6), MADMuscle analyzes all muscle-related data sets from GEO in a fully automatic way. This frees users from the limitations of manually curated data sets, […]


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MADGene institution(s)
INSERM U915, IRT-UN, University of Nantes, France; LINA - COD, University of Nantes, France
MADGene funding source(s)
This work was supported in part by the Regional research funding (BIL project) and the French Muscular Dystrophy Association (AFM).

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