A comprehensive regulatory network resource for human long non-coding RNAs (lncRNAs) and cancer genes. LnCaNet contains the pre-computed 8,494,907 significant co-expression pairs of 9641 lncRNAs and 2544 well-classified cancer genes in 2922 matched TCGA samples. In detail, we integrated 10 cancer gene lists from public database and calculate the co-expression with all the lncRNAs in 11 TCGA cancer types separately. Based on the resulted 110 co-expression networks, we identified 17 common regulatory pairs related to extracellular space shared in 11 cancers. We expect LnCaNet will enable researcher to explore lncRNA expression pattern, their affected cancer genes and pathways, biological significance in the context of specific cancer types and other useful annotation related to particular kind of lncRNA-cancer gene interaction.
Integrates experimentally supported long-non coding (lncRNA) disease associations. LncRNADisease hosts experimentally and/or computationally supported data, exceeding an over 40-fold lncRNA-disease associations. This database supplies the transcriptional regulatory relationships among lncRNA, messenger RNA (mRNA) and micro-RNA (miRNA). In addition, it allows the names of diseases to be mapped according to the ontology of the diseases.
Informs about RNAs and DNA methylation. Lnc2Meth is an online resource that assists in comprehension of the expression of protein-coding or non-coding transcripts. Its purpose is to clarify the regulatory relationships between human lncRNAs and associated DNA methylation in different diseases.
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. The Lnc2Cancer database contains 1057 manually curated associations between 531 lncRNAs and 86 human cancers. Each association includes lncRNA and cancer name, the lncRNA expression pattern, experimental techniques, a brief functional description, the original reference and additional annotation information. Lnc2Cancer provides a user-friendly interface to conveniently browse, retrieve and download data. Lnc2Cancer also offers a submission page for researchers to submit newly validated lncRNA-cancer associations.
Provides all species and covers functional and disease-specific roles for all long non-coding RNAs (lncRNAs) validated. EVLncRNAs contains about 1543 lncRNAs from 77 species along with their annotated functions, interaction partners and relevant diseases. The database allows users to submit novel experimentally validated lncRNAs and related diseases or associated components. It can be searched by any keywords, such as lncRNA name, alias, disease name, experimental methods, associated components and level of interaction.
Allows users to explore disease associations and non-coding RNAs (ncRNA) function from the perspective of disease similarity. DincRNA is a bioinformatics resource for disease similarity calculation and non-coding RNA functional analysis that provides web pages for users to query disease similarity score, ncRNA functional similarity score, and ncRNA-disease prioritization score. It also includes a search engine to query entities involving disease names, DOIDs, long non-coding RNA (lncRNA) symbols and microRNA (miRNA) symbols, and a batch processing function.
A tool to explore and to compare the expression profiles of conserved loci among various tissues in three organisms. Conversed loci are pairs of adjacent homologous protein-coding genes shared between one or more species. Expression profiles are based on RNA-seq data from many sources to derive tissue enrichment or specificity. Classifications of transcripts are based on the latest release of ENSEMBL, which will be updated in a timely manner. In addition to protein-coding genes, expression profiles of yet-to-be-characterized long non-coding RNAs (lncRNAs) are included.
Allows users to obtain multiple types of information on interesting cardio-ncRNAs. Cardio_ncRNA combines information on about 13 249 curated relationships between about 9503 ncRNAs and 139 cardiovascular diseases (CVDs). It provides a Web interface for users to browse, search and download data sets in the database and submit novel data into the database. This database is searchable by ncRNA names or disease names.
Combines multiple quantitative assessments of the associations between lncRNAs and cancer. Lnc2Catlas employs three quantified ranking methods, assessing secondary structure disruptions, lncRNA-protein interactions, and co-expression networks to evaluate associations. It assists users in prioritization of candidate lncRNAs and eases the understanding of the associations between lncRNAs and cancer.
Collects long non-coding RNA (IncRNA) data obtained from the analysis of RNA-Seq data from 50 samples. KTCNlncDB is a platform devoted to Keratoconus (KTCN) transcriptome. It is a unique resource that will be interest for researchers working in the fields of molecular biology, medicine and biotechnology. The database will significantly contribute to KTCN-related research and also other tasks aimed at deciphering the biology of lncRNAs.
Contains experimentally supported interactions among lncRNAs, Environmental factors (EFs) and phenotypes. DLREFD offers an overview of the relationship between lnRNAs and EFs. It provides useful information for the diagnosis and prevention of diseases related to both genetic and EFs. This database has permitted identification of new disease indications for Food and Drug Administration (FDA)-approved drugs, which is named drug repositioning.
Provides precise data about the associations between heart diseases (HDs) and non-coding RNAs (ncRNAs) from a variety of sources. HDncRNA is a database including two search methods, (i) a global search, in which users can input target information by texting any keywords such as species, disease name, ncRNA type, ncRNA name, in the search bar and (ii) a detailed search, in which three conditions are provided for users to get precise information.
Collects experimentally supported lncRNA–miRNA–mRNA interactions. LncCeRBase is an online resource developed to be helpful in understanding the regulatory mechanisms of lncRNA in complex diseases. Users select a lncRNA, miRNA or mRNA in the Browse page of the web site. It returns a list of matched lncRNA-miRNA-mRNA triplet associations, containing the name (lncRNA, miRNA, and mRNA), PubMed ID, associated disease/tissue, description, title and pathway name.
Allows users to search for the prioritization scores of disease-lncRNA associations. lncRNADis is a database for querying prioritization scores of lncRNA-disease pairs. Users can choose between several methods for prioritization: SemFunSim_PBPA_RWR, Resnik_PBPA_RWR, Wang_PBPA_RWR, PSB_PBPA_RWR, Lin _PBPA_RWR, SemFunSim_PBPM_RWR, Resnik_PBPM_RWR, Wang_PBPM_RWR, PSB_PBPM_RWR, Lin _PBPM_RWR. lncRNADis is part of DincRNA, a bioinformatics resource for disease similarity calculation and non-coding RNA functional investigation.
Contains experimental and predicted associations between long non-coding RNA (lncRNA) and environmental factor (EF). LncEnvironmentDB aims to simplify the research for understanding the contribution of the environment-lncRNA interaction to environmental human disease. This database is useful for studying the relationships of lncRNA and EF. It can serve to estimate potential disease-related EFs by integrating lncRNA-EF associations and EF-disease associations.
Allows the exploration of non-coding RNAs (ncRNAs) with oncogenic potential in human cancers. oncoNcRNA characterizes the somatic copy number alterations (SCNAs) of over 58,000 long non-coding RNAs (lncRNAs), 34,000 piwi-interacting RNAs (piRNAs), 2700 microRNAs (miRNAs), 600 transfer RNAs (tRNAs) and 400 small nucleolar RNAs (snoRNAs) in 64 human cancer types. It enables researchers to rapidly and intuitively analyze the oncogenic potential of ncRNAs of interest. Indeed, we have discovered a large number of ncRNAs which are frequently amplified or deleted within and across tumor types.
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