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Protocols

MADS specifications

Information


Unique identifier OMICS_07628
Name MADS
Alternative name Microarray Analysis of Differential Splicing
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 1.0
Stability No
Requirements
GeneBASE, rpy
Maintained No

Versioning


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Publication for Microarray Analysis of Differential Splicing

MADS citations

 (3)
library_books

The conserved ubiquitin like protein Hub1 plays a critical role in splicing in human cells

2014
PMCID: 4141198
PMID: 24872507
DOI: 10.1093/jmcb/mju026

[…] >0.03 significant). For initial analysis CEL files were processed using AltAnalyze software (version 2.0) with core probe set filtering using DABG (detected above background P-value cutoff 0.05) and microarray analysis of differential splicing (MiDAS exon analysis parameters P-value cutoff 0.05) (; ). The resulting splice index corresponds to differential exon intensity levels in Hub1 knockdown s […]

library_books

Posttranscriptional regulation by RNA binding proteins during epithelial to mesenchymal transition

2013
PMCID: 3827902
PMID: 23715860
DOI: 10.1007/s00018-013-1379-0

[…] lara, CA, USA) were used to identify changes in splicing profiles after ectopic overexpression of ESRP1 in MDA-MB231 mesenchymal cells and after knockdown of ESRP1 and ESRP2 in PNT2 epithelial cells. Microarray analysis of differential splicing plus (MADS+) computational pipeline was used to identify ESRP-regulated changes in splicing. HJAY arrays consist of eight tiled probes per probe set that t […]

call_split

CD28 Costimulation Regulates Genome Wide Effects on Alternative Splicing

2012
PLoS One
PMCID: 3386953
PMID: 22768209
DOI: 10.1371/journal.pone.0040032
call_split See protocol

[…] -corrected probe intensity to the average expression level of all probes for that transcript. Different splicing indices between treatment conditions would indicate differential splicing. We used the microarray analysis of differential splicing (MADS) and microarray detection of alternative splicing (MIDAS) software to calculate probability values of differential splicing for each probeset . For s […]

Citations

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MADS institution(s)
Department of Statistics, Stanford University, Stanford, CA, USA

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