LNCipedia: a database for annotated human lncRNA transcript sequences and structures

By Pieter-Jan Volders, Kenny Helsens, Xiaowei Wang, Björn Menten, Lennart Martens, Kris Gevaert, Jo Vandesompele, Pieter Mestdagh. Nucleic Acids Res., 2012

520 citations recorded by the source corpus.

Here, we present LNCipedia (http://www.lncipedia.org), a novel database for human long non-coding RNA (lncRNA) transcripts and genes. LncRNAs constitute a large and diverse class of non-coding RNA genes. Although several lncRNAs have been functionally annotated, the majority remains to be characterized. Different high-throughput methods to identify new lncRNAs (including RNA sequencing and annotation of chromatin-state maps) have been applied in various studies resulting in multiple unrelated lncRNA data sets. LNCipedia offers 21 488 annotated human lncRNA transcripts obtained from different sources. In addition to basic transcript information and gene structure, several statistics are determined for each entry in the database, such as secondary structure information, protein coding potential and microRNA binding sites. Our analyses suggest that, much like microRNAs, many lncRNAs have a significant secondary structure, in-line with their presumed association with proteins or protein complexes. Available literature on specific lncRNAs is linked, and users or authors can submit articles through a web interface. Protein coding potential is assessed by two different prediction algorithms: Coding Potential Calculator and HMMER. In addition, a novel strategy has been integrated for detecting potentially coding lncRNAs by automatically re-analysing the large body of publicly available mass spectrometry data in the PRIDE database. LNCipedia is publicly available and allows users to query and download lncRNA sequences and structures based on different search criteria. The database may serve as a resource to initiate small- and large-scale lncRNA studies. As an example, the LNCipedia content was used to develop a custom microarray for expression profiling of all available lncRNAs.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b840eed489006a6554ec3db2a30c846a5a0c673d

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Citations in the corpus

LNCipedia 5: towards a reference set of human long non-coding RNAs (2018, methodology): “In 2012, we released LNCipedia, a database to collect human lncRNA sequences and annotation (19).”
Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer (2016, background): “These include looking for co-expressed genes and lncRNAs as featured in the lncRNAtor database [118], looking at functional similarity patterns (motifs) and predicting RNA structures as featured in LNCipedia and lncRNome [116,119], and integrating epigenomic information as featured in lncRNome [116]”
LncRNA: a link between RNA and cancer. (2014, unknown): “Currently, few lncRNAs are functionally validated[12].”
Long non-coding RNAs and complex diseases: from experimental results to computational models (2016, methodology): “…of lncRNA-related databases have been constructed recently, including databases annotating lncRNA’s sequences or structures such as LNCipedia [37, 38], providing comprehensive information of lncRNAs such as NONCODE [48–52] and lncRNAwiki [175], displaying the experimentally confirmed…”
Non-coding RNA: what is functional and what is junk? (2015, unknown): “…genome Estimated average size (kb) Reference Mammalian lincRNome 53647 2.3 1.4 Managadze et al. (2013) LNCipedia (as of March 2014)* 21487 0.67 1 Volders et al. (2013) FPKM > 1 lincRNAs 35585 1.1** NA Hangauer et al. (2013) Gencode v7 catalog of human ncRNAs 9277 0.29** Median of 0.6*** Derrien…”