A total of 3,437 gene probes were scored as differentially regulated (complete list provided in Table S1), corresponding to about 20% of the microarray gene probes.
We designed the current study as an exploratory analysis expecting a minimal level of false discovery inevitable in analysis of large microarray gene probes.
In certain microarrays, gene probes are printed on the microarray surface according to their chromosomal position or a simple transformation thereof.
(XLS 70 kb) Additional file 8: Microarray data gene probe sets for actively transcribed genes also presented with FUS and Ac-H3K9 (n = 35), EWS and Ac-H3K9 (n = 135), or FUS and EWS and Ac-H3K9 (n = 58) ChIP-seq peaks.
One common example is that microarray datasets use gene probe IDs but metabolic pathways use gene locus names.
Previously, we investigated the transcriptional profiles of peripheral blood mononuclear cells (PBMC) from M. bovis-infected and non-infected control animals using the immuno-specific BOTL-5 microarray (containing 1,391 gene probe sets; Gene Expression Omnibus [GEO] accession: GPL5751) and showed that suppression of innate immune genes was associated with BTB [ 25].
In its singular form, a gene classifier is defined here as a group of microarray gene features (signatures, probes) capable of distinguishing samples in a single chemical-tissue condition between the treated and control.
High-quality cRNA was hybridised to the HG-U95Av2 oligonucleotide microarray, which contains 12 599 gene probe sets, representing approximately 9670 known genes, plus approximately 1495 EST clones (Affymetrix, Santa Clara, CA, USA).
For example, Martin et al. [ 178] broke down a 34,000-probe microarray gene expression dataset into 23 sets of metagenes using clustering techniques.
To measure gene expression in different tissues, we used the Gene Expression Atlas from the Genomics Institute of the Novartis Research Foundation, which consists of Affymetrix microarray gene expression values for 44,776 probe sets across 79 human tissues (Su et al. 2004).
