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Figure 3 | BMC Bioinformatics

Figure 3

From: GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs

Figure 3

Comparison of the differential expression calculated by the SAM algorithm for a series of data of mouse microarrays (five sets of six samples) analyzed using three different expression signal calculation algorithms (MAS5.0, FARMS and RMA) with standard CDFs to "probesets" or using RMA with CDFs to "genes" ( GeneMapper CDFs). Each set includes three biological replicates of knock-out (KO) mice for a specific gene compared to three replicates of the corresponding wild-type (WT) mice. The gene KOs are: APOE-/-, IRS2-/-, NRAS-/-, SCD1-/- and ENG+/-. The full name of these genes, the Ensembl ID number (ENSG) and the probesets assigned by Affymetrix are indicated in the top line of each set, labelled Entry (1). The table shows the numbers for the statistical parameters calculated in the comparison, which are: (2) rank of the KO gene across down-regulated genes; (3) rank of the KO gene across all genes; (4) p-value from SAM for the KO gene; (5) d-value from SAM for the KO gene; (6) number of significant gene loci with q-value < 0.10 (this calculation was performed such that all probesets were assigned to specific genes following the Affymetrix assignment or the GeneMapper assignment; therefore the methods are comparable since the number of gene loci indicated are the fraction of total mouse genes assigned); (7) total number of mouse gene loci assigned within the microarray; (8) percentage of significant gene loci with respect to the total. Yellow background indicates the top values for each statistical parameter calculated with each of the four procedures used. The comparison that includes the identical methods for expression calculation (RMA) and for differential expression (SAM) changing only the CDFs is presented in the last two columns, framed with a black line.

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