LIVE: a manually curated encyclopedia of experimentally validated interactions of lncRNAs

An, Gaole; Sun, Jiaqi; Ren, Chao; Ouyang, Zhangyi; Zhu, Lingyun; Bo, Xiaochen; Peng, Shaoliang; Shu, Wenjie

doi:10.1093/database/baz011

Cited by 7 publications

(3 citation statements)

References 16 publications

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“…Similar to RAID, it collects both experimental data, predictions and text-mining associations and adds probabilistic scores to rank the interacting pairs [65]. In addition, there are specialized repositories that focus on just one class of RNAs, as LnChrom and LIVE that contain only lncRNA interaction data [66,67].…”

Section: Predicted Rna-rna Networkmentioning

confidence: 99%

Non-coding RNA regulatory networks

Panni

Lovering

Porras

et al. 2020

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

289

202

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It is well established that the vast majority of human RNA transcripts do not encode for proteins and that non-coding RNAs regulate cell physiology and shape cellular functions. A subset of them are involved in gene regulation at different levels, from epigenetic gene silencing to post-transcriptional regulation of mRNA stability. Notably, the aberrant expression of many non-coding RNAs has been associated with aggressive pathologies. Rapid advances in network biology indicates that the robustness of cellular processes is the result of specific properties of biological networks such as scale-free degree distribution and hierarchical modularity, suggesting that regulatory network analyses could provide new insights on gene regulation and dysfunction mechanisms. In this study we present an overview of public repositories where non-coding RNA-regulatory interactions are collected and annotated, we discuss unresolved questions for data integration and we recall existing resources to build and analyse networks.

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Section: Predicted Rna-rna Networkmentioning

confidence: 99%

Non-coding RNA regulatory networks

Panni

Lovering

Porras

et al. 2020

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

289

202

View full text Add to dashboard Cite

show abstract

“… Overview of current ncRNA databases: The available databases have been grouped into five categories: basic genomic annotation (green), expression profile (blue), molecular interactions (light grey), Disease association (orange) and ncRNA type (dark grey). The corresponding boxes are shaded in yellow if the details are present in the respective databases [ 78 , 79 , 80 , 81 , 82 , 83 , 84 , 85 , 86 , 87 , 88 , 89 , 90 , 91 , 92 , 93 , 94 , 95 , 96 , 97 , 98 , 99 , 100 , 101 ]. …”

Section: Figurementioning

confidence: 99%

Non-Coding RNA Databases in Cardiovascular Research

Balamurali

Stoll

2020

ncRNA

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Cardiovascular diseases (CVDs) are of multifactorial origin and can be attributed to several genetic and environmental components. CVDs are the leading cause of mortality worldwide and they primarily damage the heart and the vascular system. Non-coding RNA (ncRNA) refers to functional RNA molecules, which have been transcribed into DNA but do not further get translated into proteins. Recent transcriptomic studies have identified the presence of thousands of ncRNA molecules across species. In humans, less than 2% of the total genome represents the protein-coding genes. While the role of many ncRNAs is yet to be ascertained, some long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been associated with disease progression, serving as useful diagnostic and prognostic biomarkers. A plethora of data repositories specialized in ncRNAs have been developed over the years using publicly available high-throughput data from next-generation sequencing and other approaches, that cover various facets of ncRNA research like basic and functional annotation, expressional profile, structural and molecular changes, and interaction with other biomolecules. Here, we provide a compendium of the current ncRNA databases relevant to cardiovascular research.

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“…In LncCeRBase [ 30 ] there are details for ceRNAs, and lncRNAs containing genomic variants that disturb ceRNA network regulation [ 31 ]. All kinds of interactions of lncRNAs are available in LIVE [ 32 ]. Variations in lncRNAs can be found from lncRNASNP [ 33 ] and disease-associations from LncRNADisease [ 34 ].…”

Section: Databases For Rna Variationsmentioning

confidence: 99%

Systematics for types and effects of RNA variations

Vihinen

2020

RNA Biology

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Systematics is described for annotation of variations in RNA molecules. The conceptual framework is part of Variation Ontology (VariO) and facilitates depiction of types of variations, their functional and structural effects and other consequences in any RNA molecule in any organism. There are more than 150 RNA related VariO terms in seven levels, which can be further combined to generate even more complicated and detailed annotations. The terms are described together with examples, usually for variations and effects in human and in diseases. RNA variation type has two subcategories: variation classification and origin with subterms. Altogether six terms are available for function description. Several terms are available for affected RNA properties. The ontology contains also terms for structural description for affected RNA type, post-transcriptional RNA modifications, secondary and tertiary structure effects and RNA sugar variations. Together with the DNA and protein concepts and annotations, RNA terms allow comprehensive description of variations of genetic and non-genetic origin at all possible levels. The VariO annotations are readable both for humans and computer programs for advanced data integration and mining.

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LIVE: a manually curated encyclopedia of experimentally validated interactions of lncRNAs

Cited by 7 publications

References 16 publications

Non-coding RNA regulatory networks

Non-coding RNA regulatory networks

Non-Coding RNA Databases in Cardiovascular Research

Systematics for types and effects of RNA variations

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