Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes.

07:00 EST 17th January 2019 | BioPortfolio

Summary of "Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes."

Long non-coding RNAs (lncRNAs) play an important role in gene regulation and are increasingly being recognized as crucial mediators of disease pathogenesis. However, the vast majority of published transcriptome datasets lack high-quality lncRNA profiles compared to protein-coding genes (PCGs). Here we propose a framework to harnesses the correlative expression patterns between lncRNA and PCGs to impute unknown lncRNA profiles. The lncRNA expression imputation (LEXI) framework enables characterization of lncRNA transcriptome of samples lacking any lncRNA data using only their PCG profiles. We compare various machine learning and missing value imputation algorithms to implement LEXI and demonstrate the feasibility of this approach to impute lncRNA transcriptome of normal and cancer tissues. Additionally, we determine the factors that influence imputation accuracy and provide guidelines for implementing this approach.


Journal Details

This article was published in the following journal.

Name: Briefings in bioinformatics
ISSN: 1477-4054


DeepDyve research library

PubMed Articles [15423 Associated PubMed Articles listed on BioPortfolio]

Identification of long non-coding RNAs expressed in knee and hip osteoarthritic cartilage.

Long intergenic non-coding RNAs (lincRNAs) are emerging as key regulators in gene expression; however, little is known about the lincRNA expression changes that occur in osteoarthritis (OA). Here we a...

PLIT: An alignment-free computational tool for identification of long non-coding RNAs in plant transcriptomic datasets.

Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs which play a significant role in several biological processes. RNA-seq based transcriptome sequencing has been extensively used for identi...

Very long intergenic non-coding RNA transcripts and expression profiles are associated to specific childhood acute lymphoblastic leukemia subtypes.

Very long intergenic non-coding RNAs (vlincRNAs) are a novel class of long transcripts (~50 kb to 1 Mb) with cell type- or cancer-specific expression. We report the discovery and characterization of 2...

Emerging roles of long non-coding RNAs in the pathogenesis of Alzheimer's disease.

Alzheimer's disease (AD) is a heterogeneous neurodegenerative disorder and represents the most common form of senile dementia. The pathogenesis of AD is not yet completely understood and no curative t...

Unveiling gibberellin-responsive coding and long noncoding RNAs in maize.

We report coding and long noncoding RNAs in maize upon phytohormone gibberellin stimulation. Plant hormone gibberellin (GA) orchestrates various facets of biological processes. Dissection the transcri...

Clinical Trials [5332 Associated Clinical Trials listed on BioPortfolio]

Evaluation of a Bio-inspired Coding Strategy for Cochlear Implant Users

This study will determine the facilitation, refractoriness and spatial spread effects of auditory nerve fiber responses to electrical stimulation via a cochlear implant. The performance o...

Biomark Study: Predict Intravenous Immunoglobulin Responders in Chronic Inflammatory Demyelinating Polyradiculoneuropathy

This study aims analyze the transcriptome to identify predictive biomarkers of IVIG in CIDP patients. 25 patients with a diagnosis of CIDP according to European criteria, naïve of treatme...

RNA and Heat Shock Protein Biomarkers in Radiation-induced Fibrosis in Breast Cancer

The purpose of this study is to seeking a molecular signature of pathological radiation induced fibrosis based on the response of skin fibroblasts after irradiation, comparing two groups o...

Involvement of SK3 Calcium Channel in Taxane Neuropathy

Taxane neuropathy is a common and long-term side effect of long-term morbidity in patients surviving cancer. No preventive or symptomatic treatment has been shown to be effective. Its path...

Non-coding RNA in the Exosome of the Epithelia Ovarian Cancer

This study aims to analyze the expression of micro-RNA (miRNA) and long non-coding RNA (lncRNA) by next-generation sequencing in patients with high grade serous ovarian cancer (HGSOC) and ...

Medical and Biotech [MESH] Definitions

The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.

Selective perceiving such that the individual protects himself from becoming aware of something unpleasant or threatening, e.g., obscene words are not heard correctly, or violent acts are not seen accurately.

A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.

Testing erythrocytes to determine presence or absence of blood-group antigens, testing of serum to determine the presence or absence of antibodies to these antigens, and selecting biocompatible blood by crossmatching samples from the donor against samples from the recipient. Crossmatching is performed prior to transfusion.

DNA sequences that form the coding region for at least three proteins which regulate the expression of HUMAN T-LYMPHOTROPIC VIRUS 1 and HUMAN T-LYMPHOTROPIC VIRUS 2. The proteins are p21(x), p27(rex), and p40(tax). The tax (trans-activator x) and rex (regulator x) genes are part of pX but are in overlapping reading frames. X was the original designation for the sequences or region (at that time of unknown function) in the long open reading frame (lor) which is now called pX.

Quick Search


DeepDyve research library

Relevant Topic

Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...

Searches Linking to this Article