LncRNAfunc 2.0: an evidence-integrated knowledgebase for regulatory and functional interpretation of lncRNAs in cancer
5 affiliations
- 1Department of Clinical Laboratories, The Second Affiliated Hospital of Xi’an Jiaotong University , Xi’an 710004 ,
- 2Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center , Xi’an, Shaanxi 710061 ,
- 3Institute of Genetics and Developmental Biology, Xi’an Jiaotong University Health Science Center , Xi’an, Shaanxi 710061 ,
- 4School of Life Sciences, Zhengzhou University , Zhengzhou 450001 ,
- 5Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX 77030 ,
Abstract
Long non-coding RNAs (lncRNAs) play diverse regulatory roles in cancer, yet their functional interpretation remains largely based on molecular associations and computational predictions, while experimentally derived evidence is fragmented across heterogeneous resources. Here, we present lncRNAfunc 2.0, an updated knowledgebase for systematic functional interpretation of cancer lncRNAs through multi-source evidence integration. Compared with the previous version, lncRNAfunc 2.0 reprocesses pan-cancer data from The Cancer Genome Atlas, incorporates normal-tissue and cancer-cell-line contexts from GTEx and CCLE, substantially expands binding and interaction evidence, and introduces perturbation evidence for lncRNAs and their regulators. These resources are integrated with association-based analyses and computational predictions as complementary evidence for interpreting lncRNA-associated regulatory relationships. lncRNAfunc 2.0 organizes functional knowledge into six biological dimensions: dysregulation, upstream regulation, lncRNA-mediated mRNA regulation, transcript remodeling, protein regulation, and tumor phenotypes. This framework connects regulatory determinants of lncRNAs with their downstream molecular relationships and phenotypic associations, including mRNA regulation, alternative splicing, protein regulation, survival, molecular and immune phenotypes, and drug response. Overall, lncRNAfunc 2.0 provides an evidence-integrated framework for exploring context-dependent lncRNA functions and regulatory mechanisms across cancers. lncRNAfunc 2.0 is freely available at https://lncrnafunc.xu-bioinfo.com/.
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BibTeX
@article{yang2026lncrnafunc,
title = {{LncRNAfunc 2.0: an evidence-integrated knowledgebase for regulatory and functional interpretation of lncRNAs in cancer}},
author = {Mengyuan Yang and Jiawei Li and Xingzheng Lu and Jiajia Liu and Xiaobo Zhou and Lijuan Zhao and Xiaokang Wu and Yungang Xu},
journal = {Nucleic Acids Research},
year = {2026},
month = nov,
doi = {10.1093/nar/gkag1145},
url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1145/9012872},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - LncRNAfunc 2.0: an evidence-integrated knowledgebase for regulatory and functional interpretation of lncRNAs in cancer
AU - Mengyuan Yang
AU - Jiawei Li
AU - Xingzheng Lu
AU - Jiajia Liu
AU - Xiaobo Zhou
AU - Lijuan Zhao
AU - Xiaokang Wu
AU - Yungang Xu
PY - 2026
DA - 2026/11/05
JO - Nucleic Acids Research
DO - 10.1093/nar/gkag1145
UR - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1145/9012872
AB - Long non-coding RNAs (lncRNAs) play diverse regulatory roles in cancer, yet their functional interpretation remains largely based on molecular associations and computational predictions, while experimentally derived evidence is fragmented across heterogeneous resources. Here, we present lncRNAfunc 2.0, an updated knowledgebase for systematic functional interpretation of cancer lncRNAs through multi-source evidence integration. Compared with the previous version, lncRNAfunc 2.0 reprocesses pan-cancer data from The Cancer Genome Atlas, incorporates normal-tissue and cancer-cell-line contexts from GTEx and CCLE, substantially expands binding and interaction evidence, and introduces perturbation evidence for lncRNAs and their regulators. These resources are integrated with association-based analyses and computational predictions as complementary evidence for interpreting lncRNA-associated regulatory relationships. lncRNAfunc 2.0 organizes functional knowledge into six biological dimensions: dysregulation, upstream regulation, lncRNA-mediated mRNA regulation, transcript remodeling, protein regulation, and tumor phenotypes. This framework connects regulatory determinants of lncRNAs with their downstream molecular relationships and phenotypic associations, including mRNA regulation, alternative splicing, protein regulation, survival, molecular and immune phenotypes, and drug response. Overall, lncRNAfunc 2.0 provides an evidence-integrated framework for exploring context-dependent lncRNA functions and regulatory mechanisms across cancers. lncRNAfunc 2.0 is freely available at https://lncrnafunc.xu-bioinfo.com/.
SN - 0305-1048
SN - 1362-4962
ER -