Integrating diverse information to gain more insight into microarray analysis.
Microarray technology provides an opportunity to view transcriptions at genomic level under different conditions controlled by an experiment. From an array experiment using a human cancer cell line that is engineered to differ in expression of tumor antigen, integrin alpha6beta4, few hundreds of differentially expressed genes are selected and are clustered using one of several standard algorithms. The set of genes in a cluster is expected to have similar expression patterns and are most likely to be coregulated and thereby expected to have similar function. The highly expressed set of upregulated genes become candidates for further evaluation as potential biomarkers. Besides these benefits, microarray experiment by itself does not help us to understand or discover potential pathways or to identify important set of genes for potential drug targets. In this paper we discuss about integrating protein-to-protein interaction information, pathway information with array expression data set to identify a set of "important" genes, and potential signal transduction networks that help to target and reverse the oncogenic phenotype induced by tumor antigen such as integrin alpha6beta4. We will illustrate the proposed method with our recent microarray experiment conducted for identifying transcriptional targets of integrin alpha6beta4 for cancer progression.
Loganantharaj
Raja
R
Bioinformatics Research Lab, University of Louisiana, Lafayette, LA 70504, USA. logan@cacs.louisiana.edu
Chung
Jun
J
D000465:Algorithms; D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D039161:Integrin alpha6beta4 / Q000235:genetics / Q000378:metabolism*; D046228:Microarray Analysis; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020543:Proteome / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics
D039161:Integrin alpha6beta4; D020543:Proteome