Sequence biases in large scale gene expression profiling data.
We present the results of a simple, statistical assay that measures the G+C content sensitivity bias of gene expression experiments without the requirement of a duplicate experiment. We analyse five gene expression profiling methods: Affymetrix GeneChip, Long Serial Analysis of Gene Expression (LongSAGE), LongSAGELite, 'Classic' Massively Parallel Signature Sequencing (MPSS) and 'Signature' MPSS. We demonstrate the methods have systematic and random errors leading to a different G+C content sensitivity. The relationship between this experimental error and the G+C content of the probe set or tag that identifies each gene influences whether the gene is detected and, if detected, the level of gene expression measured. LongSAGE has the least bias, while Signature MPSS shows a strong bias to G+C rich tags and Affymetrix data show different bias depending on the data processing method (MAS 5.0, RMA or GC-RMA). The bias in the Affymetrix data primarily impacts genes expressed at lower levels. Despite the larger sampling of the MPSS library, SAGE identifies significantly more genes (60% more RefSeq genes in a single comparison).
Siddiqui
Asim S
AS
Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
Delaney
Allen D
AD
Schnerch
Angelique
A
Griffith
Obi L
OL
Jones
Steven J M
SJ
Marra
Marco A
MA
D000818:Animals; D001482:Base Composition; D003596:Cytosine / Q000032:analysis; D004247:DNA / Q000737:chemistry; D020869:Gene Expression Profiling; D005796:Genes; D006147:Guanine / Q000032:analysis; D006801:Humans; D051379:Mice; D015341:Nucleic Acid Probes / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis
D015341:Nucleic Acid Probes; D006147:Guanine; D003596:Cytosine; D004247:DNA