When considering all the genes in the data, the proportion of very lowly or not expressed genes was nearly 50% for both mouse and human.
This prevented the introduction of very lowly expressed genes into the conserved co-expression network.
In particular, with edgeR, baySeq and EBSeq in the human data ∼50% or more of the detections were very lowly or not expressed.
If the gene had very lowly detectable RT-PCR signals that did not give a satisfactory PCR amplification, we would not go on carrying out BSP.
Because the set of very lowly expressed genes is enriched for low GERP scores, we filtered out the lowest expressed genes in each tissue.
CD44 was highly expressed in the SR-HER2- basal-like subgroup, with 63% of the tumors being positive compared with 32% for the entire cohort, and was very lowly expressed in the HER2+ groups, with only 14% and 17% of the tumors being positive in the SR+HER2+ and SR-HER2+ groups, respectively.
For nine of these genes (PRIM2A, IGF2R, TFP12, COPG2, KLF14, ABCA1, INPP5F, IGF2AS and BLCAP), the included CpG sites were unmethylated (or very lowly methylated) in the normal human placentas, as well as in the triploid placentas (Table S3 in Additional file 2).
Even upon the analysis of apparently very lowly expressed genes (e.g. SH1000 ssp-lacZ fusion), which display little to no blueness on TSA X-gal plates, we routinely observe expression units in the hundreds [30].
Well, when I worked at the publisher DC Thomson in the early 1960s, I was a very lowly journalist.
The Bioconductor package easyRNASeq [ 23] was used to calculate the RPKM values [ 2], which were utilized to divide the genes into four categories: very lowly or not expressed, lowly, medium or highly expressed genes.
