Computational protocol: Pancreatic cancer cell-derived IGFBP-3 contributes to muscle wasting

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Protocol publication

[…] Microarray data GSE16515 and GSE15471 were obtained from NCBI-GEO (www.ncbi.nlm.nih.gov/geo). Expression levels of probes were normalized using RMA and mapped in Affymetrix Human Genome U133 Plus 2.0. Gene expressions in pancreatic cancer samples with fold change > =2 and false discovery rate (FDR) < 0.05 were considered as significant. All comparisons were made between pancreatic cancer tissues and normal tissues. As for gene ontology enrichment analysis, the significantly up- and down-regulated genes were uploaded separately to DAVID Bioinformatics Resource []. The human genome U133 Plus was used as a background for the GO analysis. The GO terms with EASE score < 0.05 were selected for interpretation []. After finding overlapping genes/probes of datasets GSE15471 and GSE16515, Pearson's correlation analysis of fold change of each detected gene in each dataset was performed. Predicted secreted protein genes were annotated regarding gene lists that encode secreted proteins from both The Human Protein Atlas and (www.proteinatlas.org) and GeneCards (www.genecards.org). Heatmaps of selected genes were made using ggplot2 package of software R. […]

Pipeline specifications

Software tools DAVID, Ggplot2
Application Miscellaneous
Organisms Homo sapiens
Diseases Neoplasms, Pancreatic Neoplasms, Carcinoma, Pancreatic Ductal