Following Stenberg et al. (2009) approach, to compare ubiquitously expressed genes to tissue-specific genes, genes were classified as "ubiquitous" if they had expression value of at least 6 in all 26 adult and larval tissues present in the FlyAtlas database (Chintapalli et al. 2007).
Based on statistical analysis of RPKM abundance for the 34,136 contigs, 34,124 had expression value and 856 contigs had the top 2.5% RPKM value accounting for almost 9% of the total expression abundance from all 34,124 contigs (Additional file 11D).
By 48H, all genes had expression values that were not different from baseline.
Two classes of outliers were then defined: high-outliers had expression values greater than the median plus the interquartile range (IQR), and low-outliers had expression values less than the median minus the IQR.
Probes within each array were averaged on a gene-level and filtered to remove entries that had expression values below the median value of negative control probes.
The coefficient was calculated using all samples that had expression values for both genes in the analysis, with a minimum requirement of 10 common samples.
Only three novel miRNAs (Cass_miRC, Cass_mirE and Cass_miRI) had expression values higher than 10 normalized reads in at least one library.
Genes in the cluster must have had expression values for at least three of the five time points from both the tud progeny females and male datasets to be included in the cluster.
Fourteen genes had expression values in the endometrium of between 100 and 1,000 RPKM (AGT, APOD, AZGP1, CLEC3B, COL1A2, COL3A1, IP1, ISG15, LUM, PDZK1, PIP, PLAT, PRSS16, SAA1 and SPARCL1).
Of the 70 genes originally identified in the study by van't Veer and colleagues [ 10], 18 genes had expression values positively associated with good prognosis, while 52 were associated with metastatic recurrence.
Asymmetrically expressed genes (biallelic) have expression values lower than the cutoff of 1.25× fold.
