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LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs

We describe LincSNP 2.0 (http://bioinfo.hrbmu.edu.cn/LincSNP), an updated database that is used specifically to store and annotate disease-associated single nucleotide polymorphisms (SNPs) in human long non-coding RNAs (lncRNAs) and their transcription factor binding sites (TFBSs). In LincSNP 2.0, we have updated the database with more data and several new features, including (i...

NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases

NSDs–ncRNAs association data remains unavailable. *To whom correspondence should be addressed. Tel: +86 451 86605788; Fax: +86 451 86605788; Email: Correspondence may also be addressed to Shangwei Ning

Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers

Lnc2Cancer (http://www.bio-bigdata.net/lnc2cancer) is a manually curated database of cancer-associated long non-coding RNAs (lncRNAs) with experimental support that aims to provide a high-quality and integrated resource for exploring lncRNA deregulation in various human cancers. LncRNAs represent a large category of functional RNA molecules that play a significant role in human...

A novel reannotation strategy for dissecting DNA methylation patterns of human long intergenic non-coding RNAs in cancers

Despite growing consensus that long intergenic non-coding ribonucleic acids (lincRNAs) are modulators of cancer, the knowledge about the deoxyribonucleic acid (DNA) methylation patterns of lincRNAs in cancers remains limited. In this study, we constructed DNA methylation profiles for 4629 tumors and 705 normal tissue samples from 20 different types of human cancer by reannotating...

Identification of a Core miRNA-Pathway Regulatory Network in Glioma by Therapeutically Targeting miR-181d, miR-21, miR-23b, β-Catenin, CBP, and STAT3

The application of microRNAs (miRNAs) in the therapeutics of glioma and other human diseases is an area of intense interest. However, it’s still a great challenge to interpret the functional consequences of using miRNAs in glioma therapy. Here, we examined paired deep sequencing expression profiles of miRNAs and mRNAs from human glioma cell lines after manipulating the levels of...

Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer

Recent studies have suggested that long non-coding RNAs (lncRNAs) can interact with microRNAs (miRNAs) and indirectly regulate miRNA targets though competing interactions. However, the molecular mechanisms underlying these interactions are still largely unknown. In this study, these lncRNA–miRNA–gene interactions were defined as lncRNA-associated competing triplets (LncACTs), and...

miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs

In this study, we describe miRSponge, a manually curated database, which aims at providing an experimentally supported resource for microRNA (miRNA) sponges. Recent evidence suggests that miRNAs are themselves regulated by competing endogenous RNAs (ceRNAs) or ‘miRNA sponges’ that contain miRNA binding sites. These competitive molecules can sequester miRNAs to prevent them...

LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs

Shangwei Ning 0 Zuxianglan Zhao 0 Jingrun Ye 0 Peng Wang Hui Zhi Ronghong Li Tingting Wang Xia Li 0 Equal contributors College of Bioinformatics Science and Technology, Harbin Medical University

SNP@lincTFBS: An Integrated Database of Polymorphisms in Human LincRNA Transcription Factor Binding Sites

Large intergenic non-coding RNAs (lincRNAs) are a new class of functional transcripts, and aberrant expression of lincRNAs was associated with several human diseases. The genetic variants in lincRNA transcription factor binding sites (TFBSs) can change lincRNA expression, thereby affecting the susceptibility to human diseases. To identify and annotate these functional candidates...

Identifying a Polymorphic ‘Switch’ That Influences miRNAs' Regulation of a Myasthenia Gravis Risk Pathway

The significant roles of genetic variants in myasthenia gravis (MG) pathogenesis have been demonstrated in many studies, and recently it has been revealed that aberrant level/regulation of microRNAs (miRNAs) might contribute to the initiation and progression of MG. However, the dysfunction of miRNA associated with single nucleotide polymorphisms (miRSNPs) has not been well...

mirTarPri: Improved Prioritization of MicroRNA Targets through Incorporation of Functional Genomics Data

MicroRNAs (miRNAs) are a class of small (19–25 nt) non-coding RNAs. This important class of gene regulator downregulates gene expression through sequence-specific binding to the 3′untranslated regions (3′UTRs) of target mRNAs. Several computational target prediction approaches have been developed for predicting miRNA targets. However, the predicted target lists often have high...

Community of protein complexes impacts disease association

One important challenge in the post-genomic era is uncovering the relationships among distinct pathophenotypes by using molecular signatures. Given the complex functional interdependencies between cellular components, a disease is seldom the consequence of a defect in a single gene product, instead reflecting the perturbations of a group of closely related gene products that...

A novel method to quantify gene set functional association based on gene ontology

Numerous gene sets have been used as molecular signatures for exploring the genetic basis of complex disorders. These gene sets are distinct but related to each other in many cases; therefore, efforts have been made to compare gene sets for studies such as those evaluating the reproducibility of different experiments. Comparison in terms of biological function has been...

Prioritizing human cancer microRNAs based on genes’ functional consistency between microRNA and cancer

The identification of human cancer-related microRNAs (miRNAs) is important for cancer biology research. Although several identification methods have achieved remarkable success, they have overlooked the functional information associated with miRNAs. We present a computational framework that can be used to prioritize human cancer miRNAs by measuring the association between cancer...