Computational protocol: Cancer Genomics Identifies Regulatory Gene Networks Associated with the Transition from Dysplasia to Advanced Lung Adenocarcinomas Induced by c-Raf-1

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Protocol publication

[…] To compare the normalized data from dysplasia, normal lung tissue from transgenic mouse, tumor cells and non-transgenic of different mice, we used the Significance Analysis of Microarrays (SAM) algorithm (ArrayTrack), which contains a sliding scale for false discovery rate (FDR) of significantly up- and down-regulated genes . All data were permuted 100 cycles by using the two classes, unpaired data mode of the algorithm. As cut-off for significance an estimated FDR of 0.001 was chosen. Moreover, a cut-off for fold-change of differential expression of 2 was used. The full description of the Extraction protocol, labeling and hybridization protocol and data processing is obtainable in the GEO DATA base under http://www.ncbi.nlm.nih.gov/geo/ (accession number GSE14277). […]

Pipeline specifications

Software tools SAM, ArrayTrack
Application Gene expression microarray analysis
Organisms Mus musculus
Diseases Adenocarcinoma, Dysplastic Nevus Syndrome, Lung Neoplasms, Neoplasms, Precancerous Conditions
Chemicals Guanine, Tyrosine