LncExpDB: an expression database of human long non-coding RNAs

Zhao, Li; Liu, Lin; Jiang, Shuai; Li, Qianpeng; Feng, Changrui; Du, Qiang; Zou, Dong; Xiao, Jingfa; Zhang, Zhang; Ma, Lijiao

doi:10.1093/nar/gkaa850

Cited by 73 publications

(68 citation statements)

References 48 publications

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“…LncExpDB ( https://bigd.big.ac.cn/lncexpdb ; detailed in ( 10 ) in this issue) is an expression database of human long non-coding RNAs (lncRNAs). Based on our previous work on LncBook ( 11 ), LncExpDB houses abundant expression profiles of 101 293 non-redundant, manually-curated lncRNA genes across 337 biological conditions, which can be further classified into nine important biological contexts, namely, normal tissue/cell line, cancer cell line, subcellular localization, exosome, cell differentiation, preimplantation embryo, organ development, circadian rhythm, and virus infection.…”

Section: New Databasesmentioning

confidence: 99%

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021

Li¹,

Zhao²,

Gong³

et al. 2020

Nucleic Acids Research

Self Cite

197

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The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a suite of database resources to support worldwide research activities in both academia and industry. With the explosive growth of multi-omics data, CNCB-NGDC is continually expanding, updating and enriching its core database resources through big data deposition, integration and translation. In the past year, considerable efforts have been devoted to 2019nCoVR, a newly established resource providing a global landscape of SARS-CoV-2 genomic sequences, variants, and haplotypes, as well as Aging Atlas, BrainBase, GTDB (Glycosyltransferases Database), LncExpDB, and TransCirc (Translation potential for circular RNAs). Meanwhile, a series of resources have been updated and improved, including BioProject, BioSample, GWH (Genome Warehouse), GVM (Genome Variation Map), GEN (Gene Expression Nebulas) as well as several biodiversity and plant resources. Particularly, BIG Search, a scalable, one-stop, cross-database search engine, has been significantly updated by providing easy access to a large number of internal and external biological resources from CNCB-NGDC, our partners, EBI and NCBI. All of these resources along with their services are publicly accessible at https://bigd.big.ac.cn.

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Section: New Databasesmentioning

confidence: 99%

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021

Li¹,

Zhao²,

Gong³

et al. 2020

Nucleic Acids Research

Self Cite

197

View full text Add to dashboard Cite

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“…Many free online databases and programs can help to predict the function of identified lncRNAs or circRNAs in cancer development and progression. These include AnnoLnc2 for human lncRNAs annotation [ 229 ], LNCipedia, a comprehensive compendium of human long non-coding RNAs [ 230 ], LncExpDB, an expression database of human lncRNA genes [ 231 ], LincSNP 3.0, a database for single nucleotide polymorphisms (SNPs) in human lncRNAs [ 232 ], lnCAR, a comprehensive resource for lncRNAs in cancers [ 233 ], or databases for circular RNAs such as circBASE [ 234 ] or circInteractome [ 235 ]. Sun et al have identified 246 differentially-expressed lncRNAs in metastatic melanoma cell lines when compared to primary melanomas [ 236 ].…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

The Functional Role of Long Non-Coding RNAs in Melanoma

Wozniak

Czyż

2021

Cancers

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Melanoma is the most lethal skin cancer, with increasing incidence worldwide. The molecular events that drive melanoma development and progression have been extensively studied, resulting in significant improvements in diagnostics and therapeutic approaches. However, a high drug resistance to targeted therapies and adverse effects of immunotherapies are still a major challenge in melanoma treatment. Therefore, the elucidation of molecular mechanisms of melanomagenesis and cancer response to treatment is of great importance. Recently, many studies have revealed the close association of long noncoding RNAs (lncRNAs) with the development of many cancers, including melanoma. These RNA molecules are able to regulate a plethora of crucial cellular processes including proliferation, differentiation, migration, invasion and apoptosis through diverse mechanisms, and even slight dysregulation of their expression may lead to tumorigenesis. lncRNAs are able to bind to protein complexes, DNA and RNAs, affecting their stability, activity, and localization. They can also regulate gene expression in the nucleus. Several functions of lncRNAs are context-dependent. This review summarizes current knowledge regarding the involvement of lncRNAs in melanoma. Their possible role as prognostic markers of melanoma response to treatment and in resistance to therapy is also discussed

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“…LncExpDB was released by China’s National Bio-Information Center in 2020 ( 68 ). The database contains the expression of the lncRNA genes from 101 293 individuals in 337 biological environments and 1977 samples under nine biological conditions.…”

Section: General Platformsmentioning

confidence: 99%

“…On the interface, users can browse the expressions of interested lncRNAs in nine different biological contexts, including cancer tissue/cell lines, normal tissue/cell line, exosome, cell differentiation, subcellular localization, preimplantation embryo, organ development, virus infection and circadian rhythm. Based on a large amount of RNA-seq data, a total of 2907 cancer cells were identified, and oncologists were able to estimate the expression of the lncRNA’s biological function in cancer cells ( 68 ). In the cancer cell line option in the context module, the visual expression of interested lncRNA can be gained in cancer cell line.…”

Section: General Platformsmentioning

confidence: 99%

OUP accepted manuscript

Zhang

Qin

et al. 2021

Database

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Accumulated evidence suggests that the widely expressed long-non-coding RNAs (lncRNAs) are involved in biogenesis. Some aberrant lncRNAs are closely related to pathological changes, for instance, in cancer. Both in tumorigenesis and cancer progression, depending on the interplay with cellular molecules, lncRNAs can modulate transcriptional interference, chromatin remodeling, post-translational regulation and protein modification, and further interfere with signaling pathways. Aiming to the diagnosis/ prognosis markers or potential therapeutical targets, it is important to figure out the specific mechanism and the tissue-specific expressing patterns of lncRNAs. Generally, the bioinformatics analysis is the first step. More and more in silico databases are increasing. But the existing integrative online platforms’ functions are not only having their unique features but also share some common features, which may lead to a waste of time for researchers. Here, we reviewed these web tools according to the functions. For each database, we clarified the data source, analysis method and the evidence that the analysis result is derived from. This review also illustrated examples in practical use for a specific lncRNA by these web tools. It will provide convenience for researchers to quickly choose the appropriate bioinformatics web tools in oncology studies.

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LncExpDB: an expression database of human long non-coding RNAs

Cited by 73 publications

References 48 publications

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021

The Functional Role of Long Non-Coding RNAs in Melanoma

OUP accepted manuscript

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