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Permanent URL to this publication: http://dx.doi.org/10.5167/uzh-18206

Moll, A G; Lindenmeyer, M T; Kretzler, M; Nelson, P J; Zimmer, R; Cohen, C D (2009). Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays. PLoS ONE, 4(3):e4702-8pp.

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Background: Alternative mRNA processing mechanisms lead to multiple transcripts (i.e. splice isoforms) of a given gene
which may have distinct biological functions. Microarrays like Affymetrix GeneChips measure mRNA expression of genes
using sets of nucleotide probes. Until recently probe sets were not designed for transcript specificity. Nevertheless, the reanalysis of established microarray data using newly defined transcript-specific probe sets may provide information about expression levels of specific transcripts.
Methodology/Principal Findings: In the present study alignment of probe sequences of the Affymetrix microarray HGU133A with Ensembl transcript sequences was performed to define transcript-specific probe sets. Out of a total of 247,965 perfect match probes, 95,008 were designated ‘‘transcript-specific’’, i.e. showing complete sequence alignment, no crosshybridization, and transcript-, not only gene-specificity. These probes were grouped into 7,941 transcript-specific probe sets and 15,619 gene-specific probe sets, respectively. The former were used to differentiate 445 alternative transcripts of 215
genes. For selected transcripts, predicted by this analysis to be differentially expressed in the human kidney, confirmatory real-time RT-PCR experiments were performed. First, the expression of two specific transcripts of the genes PPM1A (PP2CA_HUMAN and P35813) and PLG (PLMN_HUMAN and Q5TEH5) in human kidneys was determined by the transcriptspecific array analysis and confirmed by real-time RT-PCR. Secondly, disease-specific differential expression of single transcripts of PLG and ABCA1 (ABCA1_HUMAN and Q5VYS0_HUMAN) was computed from the available array data sets and confirmed by transcript-specific real-time RT-PCR.
Conclusions: Transcript-specific analysis of microarray experiments can be employed to study gene-regulation on the
transcript level using conventional microarray data. In this study, predictions based on sufficient probe set size and foldchange are confirmed by independent means


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Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > University Hospital Zurich > Clinic for Nephrology
04 Faculty of Medicine > Institute of Physiology
07 Faculty of Science > Institute of Physiology
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
Deposited On:14 Apr 2009 08:35
Last Modified:05 Apr 2016 13:12
Publisher:Public Library of Science (PLoS)
Publisher DOI:10.1371/journal.pone.0004702
PubMed ID:19277110

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