Computational protocol: Identification of four prognostic LncRNAs for survival prediction of patients with hepatocellular carcinoma

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[…] The RNA-Seq data of patients in TCGA-LIHC project were downloaded from Genomic Data Commons Data Portal, as well as the corresponding clinical information (). To obtain lncRNA expression profile, we first got ensembl ID of lncRNAs which had been filtered by The Atlas of Noncoding RNAs in Cancer (TANRIC) (), then 12,309 lncRNA ID were used to retrieve the required expression information from above RNA-Seq data. Similarly, 19,817 mRNAs ID were downloaded from GENCODE (release 26) (), then we got the expression profiles of mRNAs from the RNA-Seq data. [...] All bioinformatics analysis and statistical tests were performed with R language (version 3.3.2): (i) limma package for differential expression analysis; (ii) survival package for univariate and multivariate Cox proportional hazards regression survival analysis; (iii) pROC package for ROC curve and the area under the ROC curves (AUC) analysis; (iv) Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Disease Ontology (DO) enrichment analysis were performed with clusterProfiler package (). The co-expression correlation between CTC-297N7.9 and TMEM220 were evaluated with Pearson correlation coefficient. The expression profiles of TMEM220 in normal tissues and cancer cell lines were retrieved from Genotype-Tissue Expression (GTEx) project and Cancer Cell Line Encyclopedia (CCLE) project, respectively (; ). [...] First, nucleotide sequences of each identified lncRNA were downloaded from GENCODE (release 26) (). The probe sequences of microarray were retrieved from matching platform annotation files deposited in Gene Expression Omnibus (GEO) database with R package GEOquery. Next, probes were re-mapped to lncRNA sequences using Magic-BLAST tool (version 1.2.0, from NCBI), and probes which uniquely mapped to the sequence with no mismatch were retained to represent the corresponding lncRNA. For each GEO dataset which focused on HCC, we used GEO2R web application supplied by GEO () to validate differential lncRNA expression. […]

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