Journal: BMC Genomics
Article Title: Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme
Figure Lengend Snippet: 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).
Article Snippet: Labeled cDNA was hybridized to the Affymetrix GeneChip Test 3 Array to verify quality prior to hybridize to the Affymetrix Human Genome U133A Array.
Techniques: Expressing, Microarray, Sampling, Reverse Transcription Polymerase Chain Reaction, Chromatin Immunoprecipitation, Translocation Assay, Binding Assay, Activation Assay