Using the NONCODE Database Resource.

Curr Protoc Bioinformatics

Institute of Computing Technology Chinese Academy of Sciences, Bioinformatics Research Group, Advanced Computing Research Laboratory, Beijing, China.

Published: June 2017

NONCODE is a comprehensive database that aims to present the most complete collection and annotation of non-coding RNAs, especially long non-coding RNAs (lncRNA genes), and thus NONCODE is essential to modern biological and medical research. Scientists are producing a flood of new data from which new lncRNA genes and lncRNA-disease relationships are continually being identified. NONCODE assimilates such information from a wide variety of sources including published articles, RNA-seq data, micro-array data and databases on genetic variation (dbSNP) and genome-wide associations (GWAS). NONCODE organizes all this information and makes it freely available to the public via the Internet. The NONCODE protocol provides step-by-step instructions on how to browse and search lncRNA information such as sequence, expression, and disease relationships, how to use the tools for functional prediction, species conservation assays, blast analysis, identifier conversion, and, finally, how to submit sequences to identify lncRNA genes. As of Dec 2016, NONCODE has cataloged 487,851 lncRNA genes sequenced from 16 species. © 2017 by John Wiley & Sons, Inc.

Download full-text PDF

Source
http://dx.doi.org/10.1002/cpbi.25DOI Listing

Publication Analysis

Top Keywords

lncrna genes
16
non-coding rnas
8
noncode
7
lncrna
5
noncode database
4
database resource
4
resource noncode
4
noncode comprehensive
4
comprehensive database
4
database aims
4

Similar Publications

KDM6A facilitates Xist upregulation at the onset of X inactivation.

Biol Sex Differ

January 2025

Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, 98195, USA.

Background: X chromosome inactivation (XCI) is a female-specific process in which one X chromosome is silenced to balance X-linked gene expression between the sexes. XCI is initiated in early development by upregulation of the lncRNA Xist on the future inactive X (Xi). A subset of X-linked genes escape silencing and thus have higher expression in females, suggesting female-specific functions.

View Article and Find Full Text PDF

Early missed abortion is defined as a pregnancy of ≤ 12 weeks in which there is a cessation of life in the developing embryo or fetus, leading to its retention within the uterine cavity without being spontaneously expelled promptly. This condition is commonly observed and significantly impacts human reproductive health. This study aimed to identify key genes related to ferroptosis that could serve as novel biomarkers for early missed abortion.

View Article and Find Full Text PDF

While ultrasonography effectively diagnoses Hashimoto's thyroiditis (HT), exploring its transcriptomic landscape could reveal valuable insights into disease mechanisms. This study aimed to identify HT-associated RNA signatures and investigate their potential for enhanced molecular characterization. Samples comprising 31 HT patients and 30 healthy controls underwent RNA sequencing of peripheral blood.

View Article and Find Full Text PDF

FcγRI plays a pro-inflammatory role in the immune response to Chlamydia respiratory infection by upregulating dendritic cell-related genes.

Int Immunopharmacol

January 2025

Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Institute of Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China. Electronic address:

Background: FcγRI, a pivotal cell surface receptor, is implicated in diverse immune responses and is ubiquitously expressed on numerous immune cells. However, its role in intracellular bacterial infections remains understudied.

Methods: Wild-type (WT) and FcγRI knockout (FcγRI-KO) mice were inoculated intranasally with a specific dose of C.

View Article and Find Full Text PDF

Comprehensive characterization of the transcriptional landscape in Alzheimer's disease (AD) brains.

Sci Adv

January 2025

Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN 46202, USA.

Alzheimer's disease (AD) is the leading dementia among the elderly with complex origins. Despite extensive investigation into the AD-associated protein-coding genes, the involvement of noncoding RNAs (ncRNAs) and posttranscriptional modification (PTM) in AD pathogenesis remains unclear. Here, we comprehensively characterized the landscape of ncRNAs and PTM events in 1460 samples across six brain regions sourced from the Mount Sinai/JJ Peters VA Medical Center Brain Bank Study and Mayo cohorts, encompassing 33,321 long ncRNAs, 92,897 enhancer RNAs, 53,763 alternative polyadenylation events, and 900,221 A-to-I RNA editing events.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!