Computational protocol: Oncogenic ALK regulates EMT in non-small cell lung carcinoma through repression of the epithelial splicing regulatory protein 1

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Protocol publication

[…] 100nt Paired-end RNA-Seq was performed on H2888 cells treated with TAE-684 for 48 and 72 hours. Untreated H2228 were used as control. The reads were aligned to hg19 reference using Tophat aligner []. Cuffdiff was used to identify differentially expressed genes in cells treated with ALK inhibitor (TAE-684) and cells treated with DMSO (controls) (FDR 0.05 cutoff) []. Hyper-geometric test was performed on both the up-regulated and down-regulated genes upon ALK inhibition against MSigDB C2 CGP signature sets []. […]

Pipeline specifications

Software tools TopHat, Cufflinks
Databases MSigDB
Application RNA-seq analysis
Diseases Adenocarcinoma, Carcinoma, Non-Small-Cell Lung, Lymphoma
Chemicals Tyrosine