Provides resources to decode Pan-Cancer and Interaction Networks of lncRNAs, miRNAs, competing endogenous RNAs(ceRNAs), RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq data and tumor samples. starBase deciphers Protein-RNA and miRNA-target interactions, such as protein-lncRNA, protein-sncRNA, protein-mRNA, protein-pseudogene, miRNA-lncRNA, miRNA-mRNA, miRNA-circRNA, miRNA-pseudogene, miRNA-sncRNA interactions and ceRNA networks from 108 CLIP-Seq datasets.
Enables to explore the transcriptional regulatory networks of noncoding RNAs (ncRNAs) and protein-coding genes (PCGs). ChIPBase is an open database that integrates many ChIPseq peak datasets of trans-acting factors, including transcription factors (TFs), transcription cofactors (TCFs), chromatin-remodeling factors (CRFs), other DNA-binding proteins and histone modifications. The database consists of nine web-based modules and tools.
Provides amount of predicted microRNA (miRNA) targets on the largest available set of human lncRNAs. LncBase offers a comprehensive collection of computationally predicted miRNA recognition elements (MREs) on mouse lncRNAs. It also includes miRNA–lncRNA interactions supported by experimental data for both human and mouse species. This database is composed of two modules: (i) to explore computationally predicted MREs of DIANA-microT-CDS, and (ii) to explore experimentally verified target sites.
A database that collected and curated approximately 480 entries of experimentally supported lncRNA-disease associations, including 166 diseases. LncRNADisease also curated 478 entries of lncRNA interacting partners at various molecular levels, including protein, RNA, miRNA and DNA.
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.
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.
A database that includes a comprehensive collection of transcriptome profiles of protein coding genes, miRNAs and lncRNAs perturbed by knockdown or overexpression in human and mouse. GPA offers a wealth of information on differential expression patterns, comprehensive functional and pathway characterizations, enrichments of transcriptional factors and miRNAs, information flow in interaction network, and associations with cancers and drugs, together with extensive manually curated phenotype annotations.
Provides comprehensive datasets of lncRNA interaction pairs with experimental evidences. lncRInter is a specialized resource of lncRNA interaction pairs with experimental evidences in publications. The datasets are manually curated from scientific literatures and could serve as a solid source data for lncRNA interaction prediction and function study. It also offers user-friendly interfaces and graphic visualizations of lncRNA interaction networks.
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.
Catalogs experimentally determined functional interactions between ncRNAs and proteins, mRNAs or genomic DNA sequences. NPInter integrates the diverse body of experimental knowledge about functional interactions between noncoding RNAs (ncRNAs) (except tRNAs and rRNAs) and protein related biomacromolecules (PRMs) (proteins, mRNAs or genomic DNAs). It sets up a bridge between the coding and noncoding realms.
Furnishes a curated database that stores InRNA-to-target genes. LncRNA2Target allows users to search for the targets of one or multiple lncRNA that target a single gene. Both search types are performed either by browsing a provided catalog of lncRNA names or by inserting lncRNA/target gene IDs/names in a search box. Users can submit new experientially verified IncRNA-target association to the repository.
Collects experimentally validated IncRNA-chromatin interactions. LnChrom includes more than 382000 interaction pairs in up to 260 cell types/tissues in human and mouse. Users can access, for each interaction, to manually-curated metadata, including associated proteins/complexes, chromatin modifying factors and epigenetic modifications and diseases from original publications.