The effect of GeneChip gene definitions on the microarray study of cancers

Abstract

The Affymetrix GeneChip is a popular microarray platform for genome-wide expression profiling and has been widely used in functional genomics especially in the classification of cancers. Due to the updating of genome data, much of the genome information with which the chips were designed is out-of-date and it has been reported that many of the genes/transcripts on the chips differ from their original definition when mapping the probes to the new genome information. Dai et al. have reported that the updated definition can cause as much as 30-50% discrepancy in the genes selected as differentially expressed on a heart tissue expression profiling dataset. Understanding the nature of this difference is therefore very important for the utilization of the data. In this work, with a large cancer dataset as an example, we compared two major definitions and investigated their effects on classification, clustering, discovery of differentially expressed genes and gene-set-based analysis. Results show that the two definitions agree well on clustering and classification results but genes and gene sets discovered as differentially expressed or enriched can be very different. Discoveries based on the Affymetrix definition can cover most of those based on the new definition, but tend to have more false positives.

A Tool to Build Up-To-Date Gene Annotations for Affymetrix Microarrays

“…As microarrays are commonly used for identification of the differentially expressed genes, we analysed several datasets from MoGene-1 and MoGene-2 platforms, and found an increase in accuracy and identification of the differentially expressed genes, which is consistent with previously reported results [3,5].…”

“…It was shown that updated probe set groupings improve both accuracy and precision of the expression profiling studies [3,4]. Lu and Zhang report that for several studies the numbers of genes identified as differentially expressed show 30-50% discrepancy, when analyzed with updated probe set annotations, which is consistent with the results from Dai et al [5].…”

“…As genomic information is corrected, some probes were found to not hybridize to the respective target or to hybridize to multiple regions [3]. Additionally, in the original Affymetrix annotations frequently same gene's expression is measured by several probe sets, with intensity values differing significantly, which complicates the summarization of the results on the gene level.…”

Transcriptional profiling of C57 and DBA strains of mice in the absence and presence of morphine

“…Samples run on different platforms (e.g., [18]), or analyzed with different methods (e.g., [19-22]), can produce varying results. Quality of probes, probes directed at minor splice variants, and mis-annotation of probes can also lead to errors in conclusions (e.g., [23]). Furthermore, for a proportion of mRNAs with altered expression, there may not be a corresponding change in protein expression.…”

25-Hydroxycholesterol acts as an amplifier of inflammatory signaling

“…Raw CEL files were processed at the transcript level using the robust multichip average method (40) with the HuEx10stv2_Hs_ENST (V14) custom content definition files (from http://brainarray.mbni.med. umich.edu) (41)(42)(43). Microarray data have been deposited in GEO (accession: GSE41475).…”