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COSIE specifications

Information


Unique identifier OMICS_11618
Name COSIE
Alternative name Corrected Splicing Indices for Exon Arrays
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
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Michael B. Stadler

Publication for Corrected Splicing Indices for Exon Arrays

COSIE citations

 (5)
library_books

A robust estimation of exon expression to identify alternative spliced genes applied to human tissues and cancer samples

2014
BMC Genomics
PMCID: 4298068
PMID: 25297679
DOI: 10.1186/1471-2164-15-879

[…] to compare the accuracy in the detection of known splicing events []. First, we tried our method in ESLiMa, ESLiMc and ESLiMt. In parallel, we also tried three published methods: FIRMA [], ARH [] and COSIE []. The most widely used is FIRMA (referred in 75 publications according to Google-Scholar in April 2014), which is based on an extension of the additive model of the RMA method [].The statistic […]

library_books

Transcriptional activity regulates alternative cleavage and polyadenylation

2011
Mol Syst Biol
PMCID: 3202805
PMID: 21952137
DOI: 10.1038/msb.2011.69

[…] Exon array data were normalized by the Robust Multichip Average (RMA) method and were corrected for hybridization bias using the COSIE program (). Expressed genes were selected by the Detection Above Background (DABG) method. Gene expression level was calculated using probesets in constitutive exons, based on NCBI cDNAs/ESTs () […]

library_books

Comparative Analysis of mRNA Isoform Expression in Cardiac Hypertrophy and Development Reveals Multiple Post Transcriptional Regulatory Modules

2011
PLoS One
PMCID: 3142162
PMID: 21799842
DOI: 10.1371/journal.pone.0022391

[…] en exon vs. expression change of its corresponding gene. Since different probes can respond to transcript changes differently, SI values were adjusted by the Corrected Splicing Index for Exon Arrays (COSIE) method . Classification of first, last, and internal exons was based on the RefSeq database. Skipped exons were identified using cDNAs/ESTs . Fox binding sites were analyzed by a method similar […]

library_books

Support vector machines based identification of alternative splicing in Arabidopsis thaliana from whole genome tiling arrays

2011
BMC Bioinformatics
PMCID: 3051901
PMID: 21324185
DOI: 10.1186/1471-2105-12-55

[…] practice a technical bias of exon array platforms leads to a dramatic overestimation of AS in the presence of differential gene expression. To correct for this bias, the authors developed the method COSIE, which adjusts splicing indices using a non-linear model that incorporates probeset-specific response characteristics and saturation effects []. All of these computational methods were developed […]

library_books

R and Bioconductor solutions for alternative splicing detection

2009
Hum Genomics
PMCID: 3525203
PMID: 20038500
DOI: 10.1186/1479-7364-4-2-131

[…] ly as the differential expression of the respective gene increases. This caused an overestimation of AS for the dataset. The authors developed an algorithm, COrrected Splicing Indices for Exon array (COSIE), to correct for this effect. The method was based on a positional dinucleotide modelling approach. The COSIE package can be downloaded from the authors' website http://www.fmi.ch/groups/gbioinf […]


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COSIE institution(s)
Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Basel, Switzerland
COSIE funding source(s)
Novartis Research Foundation

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