ArticleNucleic acids research2013
Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
39 citing papers in PubMed, 79 citations in OpenAlex.
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- Noncoding elements in wheat defence response to fusarium head blight.Scientific reports · 2025Article
- LncRNA LOC105369504 inhibits tumor proliferation and metastasis in colorectal cancer by regulating PSPC1.Cell death discovery · 2023Article
- LncRNA SNHG14 is beneficial to oxygen glucose deprivation/reoxygenation-induced neuro-2a cell injury via mir-98-5p sequestration-caused BCL2L13 upregulation.Metabolic brain disease · 2022Article
- Long non-coding RNA LSAMP-1 is down-regulated in non-small cell lung cancer and predicts a poor prognosis.Cancer cell international · 2022Article
- Brain Long Noncoding RNAs: Multitask Regulators of Neuronal Differentiation and Function.Molecules (Basel, Switzerland) · 2021Review
- RNA-Seq analysis of blood meal induced gene-expression changes in Aedes aegypti ovaries.BMC genomics · 2021Article
- Long noncoding RNA LINC00346 promotes glioma cell migration, invasion and proliferation by up-regulating ROCK1.Journal of cellular and molecular medicine · 2020Article
- The computational approaches of lncRNA identification based on coding potential:Computational and structural biotechnology journal · 2020Review
- Long Non-coding RNA in Plants in the Era of Reference Sequences.Frontiers in plant science · 2020Review
- Predicting functional long non-coding RNAs validated by low throughput experiments.RNA biology · 2019Article
- LncRNA-SNHG15 enhances cell proliferation in colorectal cancer by inhibiting miR-338-3p.Cancer medicine · 2019Article
- Hepatic transcriptome analysis from HFD-fed mice defines a long noncoding RNA regulating cellular cholesterol levels.Journal of lipid research · 2019Article
- The novel lncRNAeLife · 2019Article
- LncRNA DLEU1 contributes to colorectal cancer progression via activation of KPNA3.Molecular cancer · 2018Article
- Long non-coding RNA DLEU1 predicts poor prognosis of gastric cancer and contributes to cell proliferation by epigenetically suppressing KLF2.Cancer gene therapy · 2018Article
- The Role of Long Noncoding RNAs in Central Nervous System and Neurodegenerative Diseases.Frontiers in behavioral neuroscience · 2018Review
- LincRNA FEZF1-AS1 contributes to the proliferation of LAD cells by silencing p57 expression.Oncotarget · 2017Article
- Identification of long non-coding transcripts with feature selection: a comparative study.BMC bioinformatics · 2017Article
- LincRNAFEZF1-AS1 represses p21 expression to promote gastric cancer proliferation through LSD1-Mediated H3K4me2 demethylation.Molecular cancer · 2017Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In silico prediction of genomic long non-coding RNAs (lncRNAs) is prerequisite to the construction and elucidation of non-coding regulatory network. Chromatin modifications marked by chromatin regulators are important epigenetic features, which can be captured by prevailing high-throughput approaches such as ChIP sequencing. We demonstrate that the accuracy of lncRNA predictions can be greatly improved when incorporating high-throughput chromatin modifications over mouse embryonic stem differentiation toward adult Cerebellum by logistic regression with LASSO regularization. The discriminating features include H3K9me3, H3K27ac, H3K4me1, open reading frames and several repeat elements. Importantly, chromatin information is suggested to be complementary to genomic sequence information, highlighting the importance of an integrated model. Applying integrated model, we obtain a list of putative lncRNAs based on uncharacterized fragments from transcriptome assembly. We demonstrate that the putative lncRNAs have regulatory roles in vicinity of known gene loci by expression and Gene Ontology enrichment analysis. We also show that the lncRNA expression specificity can be efficiently modeled by the chromatin data with same developmental stage. The study not only supports the biological hypothesis that chromatin can regulate expression of tissue-specific or developmental stage-specific lncRNAs but also reveals the discriminating features between lncRNA and coding genes, which would guide further lncRNA identifications and characterizations.
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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 Socratic graph.