Figure 2

Bootstrap box plots of the gene expression intensity of various internal controls. (A) The box plot results show the best 14 internal control candidates, all of which exhibited consistent expression intensity in the NHRI lung adenocarcinoma microarray dataset for each re-sampling process. Moreover, also included are 10 well-known Q-RT-PCR internal controls contained in 23 probe sets on the HG-U133A chip. These are shown as #1–23 in x-axis. The detailed probe set characteristics were shown in Table 1. Except ABCF1, BHLHB2 and LAPTM4A, the gene expression intensities of top 12 internal control candidates, GAPDH, and ACTB from the Boston (B) and the Ann Arbor lung cancer datasets (C) were also compared. DDX5: (DEAD (Asp-Glu-Ala-Asp) box polypeptide 5), PKM2: (pyruvate kinase, muscle), BHLHB2: (basic helix-loop-helix domain containing, class B, 2), GLO1: (glyoxalase I), LAPTM4A: (lysosomal-associated protein transmembrane 4 alpha), SET: (SET translocation (myeloid leukemia-associated)), CLTC: (clathrin, heavy chain (Hc)), MSN: (MSN/ALK fusion; moesin/anaplastic lymphoma kinase fusion protein), ABCF1: (ATP-binding cassette, sub-family F (GCN20), member 1), EPHB3: (EPH receptor B3), CCL5: (chemokine (C-C motif) ligand 5), PTPN21: (protein tyrosine phosphatase, non-receptor type 21), DDR1: (discoidin domain receptor family, member 1), 1–4: ACTB (actin, beta), 5–6: B2M (beta-2-microglobulin), 7–12: GAPDH (glyceraldehyde-3-phosphate dehydrogenase), 13: HMBS (hydroxymethylbilane synthase), 14: HPRT1 (hypoxanthine phosphoribosyltransferase 1), 15–19: RPL13A (ribosomal protein L13a), 20: RPL32 (ribosomal protein L32), 21: SDHA (succinate dehydrogenase complex, subunit A, flavoprotein (Fp)), 22: UBC (ubiquitin C), 23: YWHAZ (tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide).