Weizmann Institute of Science

GeneAnnot: Version 2.2
Release: May, 2012
Affymetrix GeneChips
HG-U95Av2-E
HG-U133A-B
HG-U133 Plus2

Synchronized with
GeneCards Version 3.08

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Novel definition files for human GeneChips based on GeneAnnot

General

Improvements in genome sequence annotation revealed discrepancies in the original probeset/gene assignment in Affymetrix microarrays and the existence of differences between annotations and effective alignments of probes and transcription products. In the current generation of Affymetrix human GeneChips, most probesets include probes matching transcripts from more than one gene and probes which do not match any transcribed sequence. We developed a novel set of custom Chip Definition Files (CDF) and the corresponding Bioconductor libraries for Affymetrix human GeneChips based on the information contained in the GeneAnnot database. GeneAnnot-based custom CDFs include into a unique custom-probeset only those probes matching a single gene. GeneAnnot-based custom CDFs solve the problem of a reliable reconstruction of expression levels; moreover, they eliminate the existence of more than one probeset per gene, which often leads to discordant expression signals for the same transcript. GeneAnnot CDFs are freely distributed and fully compliant with Affymetrix standards and all available software for gene expression analysis.

Details

The novel set of custom GeneChip CDFs and the corresponding Bioconductor probe and annotation libraries, have been designed using GeneAnnot and GeneCards. Custom CDF files are currently available for the human GeneChips HG-U95 set, HG-U133 set and HG-U133 Plus 2.0, based on GeneAnnot version , synchronized with GeneCards Version .

Custom CDF files are fully compliant with Affymetrix standards and were reconstructed using original functions developed with R statistical environment and Bioconductor libraries. They can thus be used with all the software adopting these standards, such as dChip. Indeed, new R packages Bioconductor-compliant have been produced, including CDF, probe and annotation packages for the GeneChip with novel probesets definitions. Bioconductor users can easily take advantage of these libraries since they are compliant with previous libraries for Affymetrix GeneChips: final user should only replace values for "cdfName" and "annotation" slot into AffyBatch objects.

See also this file containing sample R code for custom cdf package use and installation instructions: sample code.

Downloads

Download the latest version of CDFs and related Bioconductor-compliant Packages based on current version of GeneCards and GeneAnnot.
Click here for more details on current package version.

GeneChip	CDF File	CDF package		Probe package		Annotation package
hgu133plus2	CDF File	Win32 CDF	Source CDF	Win32 Probe	Source Probe	Win32 Annotation	Source Annotation
hgu133a	CDF File	Win32 CDF	Source CDF	Win32 Probe	Source Probe	Win32 Annotation	Source Annotation
hgu133b	CDF File	Win32 CDF	Source CDF	Win32 Probe	Source Probe	Win32 Annotation	Source Annotation
hgu95av2	CDF File	Win32 CDF	Source CDF	Win32 Probe	Source Probe	Win32 Annotation	Source Annotation
hgu95b	CDF File	Win32 CDF	Source CDF	Win32 Probe	Source Probe	Win32 Annotation	Source Annotation
hgu95c	CDF File	Win32 CDF	Source CDF	Win32 Probe	Source Probe	Win32 Annotation	Source Annotation
hgu95d	CDF File	Win32 CDF	Source CDF	Win32 Probe	Source Probe	Win32 Annotation	Source Annotation
hgu95e	CDF File	Win32 CDF	Source CDF	Win32 Probe	Source Probe	Win32 Annotation	Source Annotation

Click here for older GeneAnnot CDFs versions.

Reference

Ferrari F, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli GA, Bicciato S.
Novel definition files for human GeneChips based on GeneAnnot
BMC Bioinformatics. 2007 Nov 15;8(1):446