2022
DOI: 10.1038/s41467-022-28421-6
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Abstract: Long noncoding RNAs (lncRNAs) are recently implicated in modifying immunology in colorectal cancer (CRC). Nevertheless, the clinical significance of immune-related lncRNAs remains largely unexplored. In this study, we develope a machine learning-based integrative procedure for constructing a consensus immune-related lncRNA signature (IRLS). IRLS is an independent risk factor for overall survival and displays stable and powerful performance, but only demonstrates limited predictive value for relapse-free surviv… Show more

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Cited by 201 publications
(113 citation statements)
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“…An adjusted p < 0.05 was recognized as statistically significant. Single-sample gene set enrichment analysis (ssGSEA) was performed to calculate the relative abundance of TICs in the TME of ccRCC ( Charoentong et al, 2017 ), ssGSEA is a popular enrichment algorithm, which was extensively utilized in medical studies ( Liu et al, 2022b ; Liu et al, 2022c ). Meanwhile, the CIBERSORT, TIMER2.0, CIBERSORT-ABS,QUANTISEQ, MCPCOUNTER, xCell, and EPIC algorithms were applied to quantify the abundance of 22 TICs to illuminate the potential calculation errors generated by diverse algorithms ( Chen et al, 2018 ).…”
Section: Methodsmentioning
confidence: 99%
“…An adjusted p < 0.05 was recognized as statistically significant. Single-sample gene set enrichment analysis (ssGSEA) was performed to calculate the relative abundance of TICs in the TME of ccRCC ( Charoentong et al, 2017 ), ssGSEA is a popular enrichment algorithm, which was extensively utilized in medical studies ( Liu et al, 2022b ; Liu et al, 2022c ). Meanwhile, the CIBERSORT, TIMER2.0, CIBERSORT-ABS,QUANTISEQ, MCPCOUNTER, xCell, and EPIC algorithms were applied to quantify the abundance of 22 TICs to illuminate the potential calculation errors generated by diverse algorithms ( Chen et al, 2018 ).…”
Section: Methodsmentioning
confidence: 99%
“…To estimate the stromal and immune cells in tumor tissues, the Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) algorithm was adopted to calculate the stromal score, immune score, and tumor purity of each patient based on ssGSEA ( Yoshihara et al, 2013 ; Liu et al, 2021a ; Liu et al, 2021b ; Liu et al, 2021c ; Liu et al, 2022a ; Liu et al, 2022b ). To evaluate the proportion of 22 immune cells, the abundance of immune cell infiltration in the low-NOP2-expressing and high-NOP2-expressing groups was estimated using the cell type identification by estimating the relative subsets of RNA transcripts (CIBERSORT) algorithm ( Newman et al, 2015 ).…”
Section: Methodsmentioning
confidence: 99%
“…We performed LASSO-Cox regression analysis in the training set ( p < 0.05), and the risk score was calculated as follows: where is the coefficient, and is the expression value of each selected miRNA. LASSO is a popular algorithm which was extensively utilized in medical studies ( Liu et al, 2022a ), ( Liu et al, 2022b ), ( Liu et al, 2022c ), ( Liu et al, 2022d ). The risk signature for predicting survival was assessed by the AUC value.…”
Section: Methodsmentioning
confidence: 99%