Transcriptomics

Dataset Information

4

Transcription profiling by array of human lung from patients with Chronic Obstructive Pulmonary Disorder


ABSTRACT: Chronic obstructive pulmonary disease (COPD) is an inflammatory lung disease with complex pathological features and largely unknown etiologies. Identification and validation of biomarkers for this disease could facilitate earlier diagnosis, appreciation of disease subtypes and/or determination of response to therapeutic intervention. To identify gene expression markers for COPD, we performed genome-wide expression profiling of lung tissue from 56 subjects using the Affymetrix U133 Plus 2.0 array. Lung function measurements from these subjects ranged from normal, un-obstructed to severely obstructed. Analysis of differential expression between cases (FEV1<70%, FEV1/FVC<0.7) and controls (FEV1>80%, FEV1/FVC>0.7) identified a set of 65 probe sets representing discrete markers associated with COPD. Correlation of gene expression with quantitative measures of airflow obstruction (FEV1 or FEV1/FVC) identified a set of 220 probe sets. A total of 31 probe sets were identified that showed evidence of significant correlation with quantitative traits and differential expression between cases and controls. Experiment Overall Design: We assessed genome-wide expression patterns in lung tissue specimens derived from 56 subjects. These subjects were undergoing lobectomy for removal of a suspected tumor, and tissue for our studies was derived from histologically normal tissue distant from the tumor margin. Subjects underwent routine spirometry prior to surgery. Low values for both FEV1 and FEV1/FVC are characteristic features of COPD and associated with the severity of disease. For our studies, Cases (n=15) were defined as subjects with FEV1<70% and FEV1/FVC<0.7 and Controls (n=18) as subjects with FEV1>80% and FEV1/FVC>0.7. A majority of the subjects were diagnosed with adenocarcinoma (n=26) or squamous cell carcinoma (n=19), while other tumor types or benign lesions were found in the remaining subjects (n=11).

INSTRUMENT(S): 418 [Affymetrix]

DISEASE(S): Lung Disease: Chronic Obstructive Pulmonary Disease, Diagnosis: Giant Bullae,Lung Disease: Control, Diagnosis: Non-small Cell Adenocarcinoma,Lung Disease: Control, Diagnosis: Non-small Cell Squamous Cell Carcinoma,Lung Disease: Control, Diagnosis: Lymphoma,Lung Disease: Chronic Obstructive Pulmonary Disease, Diagnosis: Non-small Cell Adenocarcinoma,Lung Disease: Control, Diagnosis: Nsc-mixed,Lung Disease: Control, Diagnosis: Inflammation,Lung Disease: Chronic Obstructive Pulmonary Disease, Diagnosis: Giant Cell Tumor,Lung Disease: Chronic Obstructive Pulmonary Disease, Diagnosis: Emphysema,Lung Disease: Control, Diagnosis: Metastatic Renal Cell Carcinoma,Lung Disease: Chronic Obstructive Pulmonary Disease, Diagnosis: Non-small Cell Squamous Cell Carcinoma,Lung Disease: Control, Diagnosis: Carcinoid

SUBMITTER: Soumyaroop Bhattacharya  

PROVIDER: E-GEOD-8581 | ArrayExpress | 2008-06-18

SECONDARY ACCESSION(S): GSE8581PRJNA101729

REPOSITORIES: GEO, ArrayExpress

Dataset's files

Source:
Action DRS
E-GEOD-8581.README.txt Txt
E-GEOD-8581.idf.txt Idf
E-GEOD-8581.processed.1.zip Processed
E-GEOD-8581.raw.1.zip Raw
E-GEOD-8581.raw.2.zip Raw
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