ArticleOncotarget2015
LncRNA ontology: inferring lncRNA functions based on chromatin states and expression patterns.
Article in Oncotarget, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The prognostic significance of UCA1 for predicting clinical outcome in patients with digestive system malignancies.Oncotarget · 2017Pooled it
- Circulating IncRNA DRAIC as a potential serum biomarker for predicting lymphatic and vascular spread in pancreatic cancer.Journal of medical biochemistry · 2026Article
- Global changes in gene expression and splicing in alcoholic liver disease.Scientific reports · 2026Article
- miRNA-lncRNA Cross-Regulation Landscape in Cancer: From Molecular Mechanisms to Therapeutic and Diagnostic Applications.Cancers · 2026Review
- Global Changes in Gene Expression and Splicing in Alcoholic Liver Disease.Research square · 2025Article
- Computational Resources for lncRNA Functions and Targetome.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Prediction of lncRNA functions using deep neural networks based on multiple networks.BMC genomics · 2023Article
- Noncoding RNAs as Key Regulators for Cardiac Development and Cardiovascular Diseases.Journal of cardiovascular development and disease · 2023Review
- The correlation of long non-coding RNAs IFNG-AS1 and ZEB2-AS1 with IFN-γ and ZEB-2 expression in PBMCs and clinical features of patients with coronary artery disease.Molecular biology reports · 2022Article
- Ontologies and Knowledge Graphs in Oncology Research.Cancers · 2022Review
- Brain Long Noncoding RNAs: Multitask Regulators of Neuronal Differentiation and Function.Molecules (Basel, Switzerland) · 2021Review
- Alcohol use disorder causes global changes in splicing in the human brain.Translational psychiatry · 2021Article
- Long Noncoding RNAs: New Regulators of Resistance to Systemic Therapies for Gastric Cancer.BioMed research international · 2021Review
- LINC00662 promotes cell viability and metastasis in esophageal squamous cell carcinoma by sponging miR-340-5p and upregulating HOXB2.Thoracic cancer · 2020Article
- Computational Models in Non-Coding RNA and Human Disease.International journal of molecular sciences · 2020Article
- Long non‑coding RNA FER1L4 inhibits cell proliferation and metastasis through regulation of the PI3K/AKT signaling pathway in lung cancer cells.Molecular medicine reports · 2019Article
- Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes.Scientific reports · 2019Article
- Non-coding RNAs as Regulators of Lymphangiogenesis in Lymphatic Development, Inflammation, and Cancer Metastasis.Frontiers in oncology · 2019Review
- KCNQ1OT1/miR-217/ZEB1 feedback loop facilitates cell migration and epithelial-mesenchymal transition in colorectal cancer.Cancer biology & therapy · 2019Article
- LINC00312 represses proliferation and metastasis of colorectal cancer cells by regulation of miR-21.Journal of cellular and molecular medicine · 2018Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accumulating evidences suggest that long non-coding RNAs (lncRNAs) perform important functions. Genome-wide chromatin-states area rich source of information about cellular state, yielding insights beyond what is typically obtained by transcriptome profiling. We propose an integrative method for genome-wide functional predictions of lncRNAs by combining chromatin states data with gene expression patterns. We first validated the method using protein-coding genes with known function annotations. Our validation results indicated that our integrative method performs better than co-expression analysis, and is accurate across different conditions. Next, by applying the integrative model genome-wide, we predicted the probable functions for more than 97% of human lncRNAs. The putative functions inferred by our method match with previously annotated by the targets of lncRNAs. Moreover, the linkage from the cellular processes influenced by cancer-associated lncRNAs to the cancer hallmarks provided a "lncRNA point-of-view" on tumor biology. Our approach provides a functional annotation of the lncRNAs, which we developed into a web-based application, LncRNA Ontology, to provide visualization, analysis, and downloading of lncRNA putative functions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.