Dataset Information

Discovery of Gene Regulation Pattern in Lung Cancer by Gene Expression Profiling Using Human Tissues.

ABSTRACT: Lung cancer continues to be one the most prevalent and life threatening cancers worldwide. In order to study the gene regulation pattern in lung cancer for new therapeutics discovery, gene expression profiling using human lung cancer tissues was conducted. The gene expression profiles were established using Affymetrix Human Exon 1.0 ST Array with RNA extracts from six clinical patients (five lung cancer samples and one normal control). The raw data were analyzed with Affymetrix Expression Console and Affymetrix Transcriptome Analysis Console 2.0. The regulation of several genes were further validated using real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR). Here we provide detailed experimental methods and analysis for the microarray data, which have been deposited into Gene Expression Omnibus (GEO) under GSE63571.

SUBMITTER: Fu J

PROVIDER: S-EPMC4313763 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Discovery of Gene Regulation Pattern in Lung Cancer by Gene Expression Profiling Using Human Tissues.

Fu Junjie J Khaybullin Ravil R Liang Xiao X Morin Madeleine M Xia Amy A Yeh Anderson A Qi Xin X

Genomics data 20150301

Lung cancer continues to be one the most prevalent and life threatening cancers worldwide. In order to study the gene regulation pattern in lung cancer for new therapeutics discovery, gene expression profiling using human lung cancer tissues was conducted. The gene expression profiles were established using Affymetrix Human Exon 1.0 ST Array with RNA extracts from six clinical patients (five lung cancer samples and one normal control). The raw data were analyzed with Affymetrix Expression Consol ...[more]

PMID: 25664237

Similar Datasets

Project description:Statins are 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitors that alter the synthesis of cholesterol. Some studies have shown a significant association of statins with improved respiratory health outcomes of patients with asthma, chronic obstructive pulmonary disease and lung cancer. Here we hypothesize that statins impact gene expression in human lungs and may reveal the pleiotropic effects of statins that are taking place directly in lung tissues. Human lung tissues were obtained from patients who underwent lung resection or transplantation. Gene expression was measured on a custom Affymetrix array in a discovery cohort (n = 408) and two replication sets (n = 341 and 282). Gene expression was evaluated by linear regression between statin users and non-users, adjusting for age, gender, smoking status, and other covariables. The results of each cohort were combined in a meta-analysis and biological pathways were studied using Gene Set Enrichment Analysis. The discovery set included 141 statin users. The lung mRNA expression levels of eighteen and three genes were up-regulated and down-regulated in statin users (FDR < 0.05), respectively. Twelve of the up-regulated genes were replicated in the first replication set, but none in the second (p-value < 0.05). Combining the discovery and replication sets into a meta-analysis improved the significance of the 12 up-regulated genes, which includes genes encoding enzymes and membrane proteins involved in cholesterol biosynthesis. Canonical biological pathways altered by statins in the lung include cholesterol, steroid, and terpenoid backbone biosynthesis. No genes encoding inflammatory, proteases, pro-fibrotic or growth factors were altered by statins, suggesting that the direct effect of statin in the lung do not go beyond its antilipidemic action. Although more studies are needed with specific lung cell types and different classes and doses of statins, the improved health outcomes and survival observed in statin users with chronic lung diseases do not seem to be mediated through direct regulation of gene expression in the lung.

Dataset Information

Discovery of Gene Regulation Pattern in Lung Cancer by Gene Expression Profiling Using Human Tissues.

Publications

Discovery of Gene Regulation Pattern in Lung Cancer by Gene Expression Profiling Using Human Tissues.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets