Gene Commanding Height (GCH) hierarchy in the cancer nucleus and cancer-free resection margins from a surgically removed prostatic adenocarcinoma of a 65y old black man

We profiled the transcriptomes of the dominan nodule (Gleason score 4+5=9) and of the cancer free resection margins of a surgically removed prostate tumor from a 65y old black man. Normalized to the median of valid spots expression data where used to determine the Gene Commanding Height (GCH) Score for every coding and non-coding transcript adequately quantified in all four cancer and four normal tissue samples. The analysis proved that cancer and normal tissue have distinct gene hiearchies. The top three genes in the cancer region were: BAIAP2L1 (BAI1-associated protein 2-like 1 ), FAM71E1 (amily with sequence similarity 71, member E1 ) and MAP6D1 (MAP6 domain containing 1 ), while the top three genes in the cancer-free region were: TOR1A (torsin family 1, member A ), MRPS12 (mitochondrial ribosomal protein S12 ) and GTF2H1 (general transcription factor IIH, polypeptide 1). one gender (male) x one tissue (prostate) x two regions (C65Y = cancer dominant nodule and N65Y = cancer-free (normal) resection margins) Please note that experiments were technically carried out as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed the results as single channel (i.e. 4 raw data files for total 8 samples). The raw data files are linked as Series supplementary files and indicated in the corresponding sample description field.