Computational protocol: SLC7A5 Functions as a Downstream Target Modulated by CRKL in Metastasis Process of Gastric Cancer SGC-7901 Cells

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Protocol publication

[…] Statistical analysis for 72 specimens in was carried out by SPSS 18.0 and GraphPad Prism 5.0. P values were calculated by paired t-test and Fisher’s exact text. Those P values < 0.05 were considered statistically significant.The whole genome mRNA microarray expression of from GSE13911 with 38 tumor samples and 31 non-tumor samples were downloaded from NCBI GEO database. We applied the quantile normalization to adjust the global noise among different samples. Then, we screened the most significantly differential expressed genes (p-value <0.05) between tumor and normal samples by R “limma” package. Within the differential expressed genes, the top correlated genes with CRKL was selected by Pearson Correlation test with p-value < 0.05 and 2 fold change between tumor and normal. The heatmap was generated by “ggplot2” package in R. SLC7A5 is one of the correlated genes of CRKL based on Pearson correlation test.For the survival analysis of CRKL and SLC7A5, we use online tool (http://www.kmplot.com/gastric) to generate Kaplan–Meier curves, which include 876 gastric cancer patients with available clinical data. For the expression of the genes, each percentile of expression between the lower and upper quartiles was computed and the best performing threshold was used as the final cutoff for the Univariate Cox regression analysis. Kaplan–Meier survival plot were downloaded from their website and the hazard ratio with 95% confidence and P Value were calculated. […]

Pipeline specifications

Software tools limma, Ggplot2
Applications Miscellaneous, Gene expression microarray analysis
Diseases Stomach Neoplasms