GeneFriends takes submitted list of genes and uses a large database of microarray data (4164 Micro array datasets containing 26,113 experimental conditions and 19,080 genes) [ 32], from the Gene Expression Omnibus [ 65, 66] to find genes that are commonly coexpressed with the entered gene list.
Bar-Joseph et al's (2003) continuous representation model for finding differentially expressed genes in time series micro array datasets (which has been used to find more cell-cycle response genes in yeast than conventional clustering methods) is also unable to filter clock influences from treatment response influences on gene expression patterns [ 21].
To determine whether BRE expression has an impact on survival in other patient cohorts, we extended our studies to a large independent, publicly available micro-array dataset of 2,324 patients (see Fig. 3, Kaplan Meier Plotter [ 32] (www.kmplot.com)).
We explored the antisense transcripts in relation to the miRNA targets by extracting the expression data for Arabidopsis miRNA target genes from existing high-resolution (25 36 b.p. probe size) whole-genome tiling micro-array datasets [82], [83].
Previously published micro-array datasets were examined for correlation between LOX expression and metastasis in human breast cancer patients [ 2, 3].
Expression of the gene was examined by exploring a micro array mRNA expression dataset generated on Illumina V3 Human-12 chips in cartilage samples of 33 patients (13 men and 20 women of European descent aged 54 years to 80 years) that underwent joint replacement due to end-stage OA disease.
The expression of these genes was analyzed in the macro- and micro-dissected array datasets.
Datasets available for such tasks include the primary literature, large scale micro array experiments, whole genome two hybrid screenings, full genome sequences, and the patterns of conserved/non-conserved homologues and orthologues in them.
Strong correlation between PCR expression data and micro array values was found (Figure 3).
Tissue micro array (TMA).
BG carried out the micro array protocol.
