ONCOMINE
ONCOMINE (https://www.oncomine.org) is a web-based bioinformatics service available for analysis of differential gene expression and prediction of co-expressed genes [14]. The expression of these drug resistance-related genes in lung cancer was assessed by extracting data. In this study, 0.05 and 2 were the threshold for p value and fold change, separately. The differential expression of these drug resistance-related genes in lung cancer was analyzed by Student's t test.
GEPIA
GEPIA (http://gepia.cancer-pku.cn/index.html), containing 9736 datasets from the GTEx and the TCGA projects, can effectively conduct online analysis and mining of cancer data for RNA sequence expression [15]. In this study, "Single Gene Analysis" was utilized for analysis of differential expression, phase of pathology and relevant prognosis of these genes. Moreover, “Multiple Gene Comparison” was used for multiple gene comparison analysis of these genes. The threshold for p value was 0.05. These genes were analyzed by Student's t test.
UALCAN
UALCAN (http://ualcan.path.uab.edu/analysis.html) functions as a versatile and robust database available for identifying biomarkers, analyzing expression profiles, and survival analysis, among others [16]. In our study, the "Expression Analysis" module, "LUAD" and "LUSC" datasets were utilized to analyze data of these drug resistance-related genes. Generated by the student's t test, the p value has a threshold value of 0.05.
cBioPortal
cBioPortal (https://www.cbioportal.org), a user-friendly website based on numerous databases, enables visualization of cancer genomics data in multiple dimensions [17]. Genetic variation, gene network, as well as co-expression of these drug resistance-related genes were analyzed by cBioPortal. Both the z scores of mRNA and protein expression were derived from the z score threshold ±2.0.
GeneMANIA
GeneMANIA (http://www.genemania.org), a comprehensive web resource, supplies information on genetic interactions and protein analysis, including Genetic Interactions, Pathways, and Shared protein domains [18]. In this study, protein-protein interaction (PPI) network of these drug resistance-related genes was obtained by GeneMANIA.
STRING
STRING (https://string-db.org), covering up to 5.090 thousand total organisms and 24.6 million proteins, aims to search, evaluate, and combine all available sources of PPI data using computational predictions, knowledge transfer between organisms and so on [19]. In this study, PPI network analysis of drug resistance-related genes was performed by STRING.
TIMER
TIMER (https://cistrome.shinyapps.io/timer/), an accessible and intuitive database, makes it possible to systematically assess the clinical effects of various immune cells on a variety of cancer types [20]. The statistical methods it uses have been validated using pathological estimates. In this study, "Gene Module" was used to fully explore the relationship between the expression of these genes and various immune cells. And the "Clinical Module" was used to perform the survival analysis of various types of immune cells in lung cancer.