A study published in Cancer Cell International identifies several long non-coding RNAs that relate to oxaliplatin sensitivity and constructs a predictive and prognostic model for colorectal cancer patients who underwent oxaliplatin-based chemotherapy.
], including the name of cell lines, IC50 value and transcripts express profile of each cell line after oxaliplatin treatment. lncRNAs was extracted from the transcripts based on Homo sapiens GRCh38 file. There were 5710 transcripts were defined as lncRNAs, after mapping to the transcripts ID of GDSC dataset, 1002 lncRNAs were extracted and proceed to the analysis.
The gene expression profile data and the corresponding clinical data of COADREAD patients , LUSC , LUAD , STAD , PAAD and OV were obtained freely from the UCSC Xena database. GSE76092 dataset [] containing the data of two CRC cell lines treatment with oxaliplatin, was downloaded from GEO database. The raw data of the above datasets were preprocessed via background adjustment and quantile normalization.
The prognostic lncRNAs model for the patients was established by Cox regression analysis and characterized by the risk score as previously reported. Based on the previously established formula, the regression coefficient from the multivariate Cox regression model multiplies the expression of the matching lncRNA to determine the risk score []. Then the patients were divided into high- and low-risk group using median of risk score as cut-off value.
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