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Protocols

MMBGX specifications

Information


Unique identifier OMICS_07624
Name MMBGX
Alternative name Multi-Mapping Bayesian Gene eXpression
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 0.99.26
Stability Stable
Requirements
annmap, oligo, inline, Rcpp
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Ernest Turro

Publication for Multi-Mapping Bayesian Gene eXpression

MMBGX citations

 (6)
library_books

Comparative evaluation of isoform level gene expression estimation algorithms for RNA seq and exon array platforms

2016
Brief Bioinform
PMCID: 5444266
PMID: 26944083
DOI: 10.1093/bib/bbw016

[…] Because MMBGX and eXpress shared the most commonly resolved transcripts and the strongest overall expression and fold change correlations, their data were used in comparing RNA-seq and exon-array platforms in […]

library_books

Evaluation of data discretization methods to derive platform independent isoform expression signatures for multi class tumor subtyping

2015
BMC Genomics
PMCID: 4652565
PMID: 26576613
DOI: 10.1186/1471-2164-16-S11-S3

[…] samples and 10 normal brain samples from TCGA data portal (https://tcga-data.nci.nih.gov/tcga/); obtained the isoform expression of 114,930 transcript variants (equivalent to 35,612 genes) using the Multi-Mapping Bayesian Gene eXpression program []. The estimated expression values were then normalized across the samples, using the locally weighted scatterplot smoothing algorithm [], a non-paramet […]

library_books

Isoform level gene signature improves prognostic stratification and accurately classifies glioblastoma subtypes

2014
Nucleic Acids Res
PMCID: 4005667
PMID: 24503249
DOI: 10.1093/nar/gku121

[…] s and 10 normal brain samples (control samples) from the TCGA data portal (https://tcga-data.nci.nih.gov/tcga). The transcript (isoform)-level and gene-level expression estimates were obtained by the Multi-Mapping Bayesian Gene eXpression algorithm () for Affymetrix whole-transcript arrays, based on Ensemble database (version 56). The estimated expression values were then normalized across the sam […]

library_books

Isoform level expression profiles provide better cancer signatures than gene level expression profiles

2013
Genome Med
PMCID: 3706752
PMID: 23594586
DOI: 10.1186/gm437

[…] The isoform level (transcript-level) and gene level expression estimates were obtained by the Multi-Mapping Bayesian Gene eXpression (MMBGX) algorithm for Affymetrix whole-transcript arrays [], based on the Ensembl database (version 56) [], which contains a total of 114,930 different transcrip […]

call_split

Induction of p16INK4a Is the Major Barrier to Proliferation when Epstein Barr Virus (EBV) Transforms Primary B Cells into Lymphoblastoid Cell Lines

2013
PLoS Pathog
PMCID: 3578823
PMID: 23436997
DOI: 10.1371/journal.ppat.1003187
call_split See protocol

[…] everse transcribed and amplified (using the Applause WT-Amp Plus ST kit – NuGen) and hybridized to Affymetrix Human Exon 1.0ST microarrays by UCL Genomics. Gene level analysis was performed using the MMBGX algorithm to generate gene-level data according ENSEMBL genome annotation version 64, as mapped to the Exon microarray by AnnMap (formerly X:Map), broadly as described previously , .Statistical […]

library_books

Extensive Co Operation between the Epstein Barr Virus EBNA3 Proteins in the Manipulation of Host Gene Expression and Epigenetic Chromatin Modification

2010
PLoS One
PMCID: 2981562
PMID: 21085583
DOI: 10.1371/journal.pone.0013979

[…] and cDNA. This was then hybridised to an Affymetrix Human Exon 1.0ST array and scanned.Array data was extracted using Expression Console software to generate CEL files. CEL files were summarised with MMBGX (Multi-Mapping Bayesian Gene eXpression) v0.99.5 using the X:Map/Ensembl database for Homo Sapiens (GRCh37) v56 (xmap_homo_sapiens_core_56_37a.tgz). MMBGX uses X:Map mappings between probes and […]


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MMBGX institution(s)
Department of Epidemiology and Public Health, Imperial College London, Norfolk Place, London, UK

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