Hiseqmirnaseq

The miRNA (Illumina HiSeq miRNASeq) and mRNA expression (Illumina HiSeq RNASeqV2) profiles of the 10 human cancers were downloaded from TCGA (as of October 2015). We subsequently obtained corresponding lncRNA expression data from the TANRIC database (Li et al., 2015 (link)).

A total of 341 colon cancer cases were enrolled for comprehensively integrated analysis. The colon cancer level 3 RNAseq and miRNASeq of 341 colon cancer samples and corresponding clinical data (S1 File) were downloaded from TCGA database using the Data Transfer Tool (provided by GDC Apps)(https://tcga-data.nci.nih.gov/). The RNAseq and survival data were anonymised before we accessed them. These data were included 341 colon cancer samples and 27 non-cancer samples. That sequence data was derived from Illumina HiSeqRNASeq and Illumina HiSeqmiRNASeq platforms. Our research meets publication guidelines provided by TCGA (http://cancergenome.nih.gov/publications/publicationguidelines).

Individual lung adenocarcinoma RNA sequencing (RNA-seq) data (level 3) and the corresponding clinical data were obtained from the TCGA database. The TCGA database is a public platform with more than 30 cancer types and clinical pathological information for at least 11,000 patients. It has been widely used by a large number of researchers to explore the genetic basis of tumors through high-throughput sequencing. The RNA-seq data were generated by Illumina HiSeq RNA-seq and Illumina HiSeq miRNA-Seq platforms. Exclusion criteria were set as follows: (1) histological diagnosis negating LUAD; (2) presence of a malignancy other than LUAD; (3) lack of complete clinical data. The three RNA expression profiles were integrated and extracted by using the R bioconductor package TCGABiolinks. Genes were annotated using the Ensembl online database. The present study was in compliance with the publication guidelines provided by TCGA, and the data obtained from TCGA did not require approval from an ethics committee.

A total of 418 patients with BCa were enrolled in our comprehensive integrated analysis. Data were downloaded from the TCGA database (http://tcga-data.nci.nih.gov/) using the Data Transfer Tool provided with GDC Apps. For the study, level 3 mRNASeq gene expression data, miRNASeq data, and clinical information of patients were downloaded (http://tcga-data.nci.nih.gov/). Sequencing data were collected using Illumina HiSeq RNASeq and Illumina HiSeq miRNASeq platforms (Illumina, San Diego, CA) and the study was performed in line with the publication guidelines provided by TCGA (http://cancergenome.nih.gov/publicaitons/publicationguidelines). Ethical approval was not necessary in our study because the expression profiles were downloaded from the public database and no new experiments in patients or animals were performed.

DNA methylation profiles, miRNA-Seq data, RNA-seq data and clinical information of UVMs samples were extracted from the TCGA database on March 2018. The DNA methylation profiling data were performed using Infinium 450k Chip. MiRNA-Seq and RNA-seq were executed on Illumina-HiSeq miRNA-seq and RNA-seq platform. The annotation of the lncRNA file was downloaded from GENCODE (https://www.gencodegenes.org/). We divided TCGA UVMs patients into two groups based on the survival time: Alive < 2 years group (survival time was less than 2 years after diagnose) and Alive > 2 years group (survival time was more than 2 years after diagnose).