Computational protocol: Decreased expression of Calpain-9 predicts unfavorable prognosis in patients with gastric cancer

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Protocol publication

[…] These data are publically available from the Cancer Genome Atlas and the NCBI Gene Expression Omnibus (accession number: GSE13911). For the TCGA dataset, all level-3 data were downloaded from the TCGA-STAD portal by using TCGA-Assembler software. The mRNA expression in TCGA dataset was measured by RNA sequencing V2. The RSEM (RNA-Seq by Expectation-Maximization) counts were further normalized by TMM (trimmed mean of M value) method to estimate the relative RNA production levels using edgeR software. Then we performed voom analysis to estimate the mean-variance relationship of the log-count. For the GSE13911 dataset reported previously, the mRNA expression was measured by microarray. The probe set intensities were quantified using the GeneChip Operating Software (GCOS) and normalized with GCRMA (GeneChip Robust Multiarray Averaging) using Array Assist Software. Differentially expressed genes in TCGA and GSE13911 datasets were screened with the paired moderated t-test using limma software package, and described in and . […]

Pipeline specifications

Software tools TCGA-assembler, RSEM, edgeR, voom, limma
Databases GEO TCGA Data Portal
Application RNA-seq analysis
Organisms Homo sapiens, Homo sapiens/Mus musculus xenograft
Diseases Vestibulocochlear Nerve Diseases, Neoplasms, Stomach Neoplasms
Chemicals Calcium, Cysteine