Dataset Information

RPS: a comprehensive database of RNAs involved in liquid-liquid phase separation.

ABSTRACT: Liquid-liquid phase separation (LLPS) is critical for assembling membraneless organelles (MLOs) such as nucleoli, P-bodies, and stress granules, which are involved in various physiological processes and pathological conditions. While the critical role of RNA in the formation and the maintenance of MLOs is increasingly appreciated, there is still a lack of specific resources for LLPS-related RNAs. Here, we presented RPS (http://rps.renlab.org), a comprehensive database of LLPS-related RNAs in 20 distinct biomolecular condensates from eukaryotes and viruses. Currently, RPS contains 21,613 LLPS-related RNAs with three different evidence types, including 'Reviewed', 'High-throughput' and 'Predicted'. RPS provides extensive annotations of LLPS-associated RNA properties, including sequence features, RNA structures, RNA-protein/RNA-RNA interactions, and RNA modifications. Moreover, RPS also provides comprehensive disease annotations to help users to explore the relationship between LLPS and disease. The user-friendly web interface of RPS allows users to access the data efficiently. In summary, we believe that RPS will serve as a valuable platform to study the role of RNA in LLPS and further improve our understanding of the biological functions of LLPS.

SUBMITTER: Liu M

PROVIDER: S-EPMC8728229 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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RPS: a comprehensive database of RNAs involved in liquid-liquid phase separation.

Liu Mengni M Li Huiqin H Luo Xiaotong X Cai Jieyi J Chen Tianjian T Xie Yubin Y Ren Jian J Zuo Zhixiang Z

Nucleic acids research 20220101 D1

Liquid-liquid phase separation (LLPS) is critical for assembling membraneless organelles (MLOs) such as nucleoli, P-bodies, and stress granules, which are involved in various physiological processes and pathological conditions. While the critical role of RNA in the formation and the maintenance of MLOs is increasingly appreciated, there is still a lack of specific resources for LLPS-related RNAs. Here, we presented RPS (http://rps.renlab.org), a comprehensive database of LLPS-related RNAs in 20 ...[more]

PMID: 34718734

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Project description:Objective: Liquid-liquid phase separation (LLPS) is a functional unit formed by specific molecules. It lacks a membrane and has been reported to play a crucial role in tumor drug resistance and growth by regulating gene expression and drug distribution. However, whether LLPS could be used to predict cancer prognosis was not clear. This study aimed to construct a prognostic model for breast cancer based on LLPS-correlated genes (LCGs). Methods: LCGs were identified using the PhaSepDB, gene expression profile and clinical characteristics of breast cancer were obtained from TCGA and cBioportal. The PanCancer Atlas (TCGA) cohort was used as the training cohort to construct the prognostic model, while the Nature 2012 and Nat Commun 2016 (TCGA) cohort and GEO data were used as test cohort to perform external verification. Data analysis was performed with R4.2.0 and SPSS20.0. Results: We identified 140 prognosis-related LCGs (pLCGs) (p< 0.01) in all cohorts, 240 pLCGs (p< 0.01) in the luminal cohort, and 28 pLCGs (p< 0.05) in the triple-negative breast cancer (TNBC) cohort. Twelve genes in all cohorts (training cohort: 5/10-year ROC values were 0.76 and 0.77; verification cohort: 5/10-year ROC values were 0.61 and 0.58), eight genes in the luminal cohort (training cohort: 5/10-year ROC values were 0.79 and 0.75; verification cohort: 5/10-year ROC values were 0.62 and 0.62), and four genes in the TNBC cohort (training cohort: 5/10-year ROC values were 0.73 and 0.79; verification cohort: 5/10-year ROC values were 0.55 and 0.54) were screened out to construct the prognostic prediction model. The 17-gene risk-score was constructed in all cohorts (1/3/5-year ROC values were 0.88, 0.83, and 0.81), and the 11-gene risk-score was constructed in the luminal cohort (1/3/5-year ROC values were 0.67, 0.85 and 0.84), and the six-gene risk-score was constructed in the TNBC cohort (1/3/5-year ROC value were 0.87, 0.88 and 0.81). Finally, the risk-score and clinical factors were applied to construct nomograms in all cohorts (1/3/5-year ROC values were 0.89, 0.79 and 0.75, C-index = 0.784), in the luminal cohort (1/3/5-year ROC values were 0.84, 0.83 and 0.85, C-index = 0.803), and in the TNBC cohort (1/3/5-year ROC values were 0.95, 0.84 and 0.77, C-index = 0.847). Discussion: This study explored the roles of LCGs in the prediction of breast cancer prognosis.

Dataset Information

RPS: a comprehensive database of RNAs involved in liquid-liquid phase separation.

Publications

RPS: a comprehensive database of RNAs involved in liquid-liquid phase separation.

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