Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays
Standard
Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays. / Moll, Anton G; Lindenmeyer, Maja T; Kretzler, Matthias; Nelson, Peter J; Zimmer, Ralf; Cohen, Clemens D.
In: PLOS ONE, Vol. 4, No. 3, 2009, p. e4702.Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review
Harvard
APA
Vancouver
Bibtex
}
RIS
TY - JOUR
T1 - Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays
AU - Moll, Anton G
AU - Lindenmeyer, Maja T
AU - Kretzler, Matthias
AU - Nelson, Peter J
AU - Zimmer, Ralf
AU - Cohen, Clemens D
PY - 2009
Y1 - 2009
N2 - 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 re-analysis 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 HG-U133A 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 cross-hybridization, 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 transcript-specific 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 fold-change are confirmed by independent means.
AB - 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 re-analysis 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 HG-U133A 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 cross-hybridization, 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 transcript-specific 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 fold-change are confirmed by independent means.
KW - ATP Binding Cassette Transporter 1
KW - ATP-Binding Cassette Transporters
KW - Cohort Studies
KW - DNA Probes
KW - Diabetic Nephropathies
KW - Gene Expression Profiling
KW - Humans
KW - Kidney
KW - Kidney Transplantation
KW - Oligonucleotide Array Sequence Analysis
KW - Phosphoprotein Phosphatases
KW - Plasminogen
KW - Protein Phosphatase 2C
KW - RNA Splicing
KW - RNA, Messenger
KW - Reverse Transcriptase Polymerase Chain Reaction
KW - Sequence Alignment
KW - Tissue Donors
KW - Transcription, Genetic
KW - Comparative Study
KW - Journal Article
KW - Research Support, N.I.H., Extramural
KW - Research Support, Non-U.S. Gov't
U2 - 10.1371/journal.pone.0004702
DO - 10.1371/journal.pone.0004702
M3 - SCORING: Journal article
C2 - 19277110
VL - 4
SP - e4702
JO - PLOS ONE
JF - PLOS ONE
SN - 1932-6203
IS - 3
ER -
