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starBase
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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.
AtCircDB
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Provides a comprehensive and tissue-specific plant circular RNA database. AtCircDB is an online resource for predicted and validated Arabidopsis hosting circular RNA candidates identified from largescale sequencing data. This database currently hosts four categories of information: (i) circular RNA information, (ii) potential miRNA–circular RNA interaction, (iii) super circular region and (iv) tissue information.
CircNet
Provides the following resources: (i) novel circRNAs, (ii) integrated miRNA-target networks, (iii) expression profiles of circRNA isoforms, (iv) genomic annotations of circRNA isoforms, and (v) sequences of circRNA isoforms. The CircNet database is to our knowledge the first public database that provides tissue-specific circRNA expression profiles and circRNA–miRNA-gene regulatory networks. It not only extends the most up to date catalog of circRNAs but also provides a thorough expression analysis of both previously reported and novel circRNAs. Furthermore, it generates an integrated regulatory network that illustrates the regulation between circRNAs, miRNAs and genes. The CircNet database will be continuously maintained and updated.
CSCD / Cancer-Specific CircRNA Database
Gathers information about all type of circRNAs. CSCD compiles RNASeq datasets in cancer and normal samples added to an integrated circRNA database which principally focus on improvement of functional studies about cancer-specific circRNAs. Searches can be made by sample name, gene symbol or circRNA ID. Users can also performs splicing events prediction or detect potential functional regulation and translation of a specific circRNA by using microRNA response elements (MRE) prediction, RNA binding protein and open reading frame (ORF).
PlantcircBase
Provides the total number of RNA-seq reads in different tissues that support the back-splicing site. PlantcircBase is a database that offers the back-splicing junction sequences of circRNAs, of which the uppercase and lowercase sequences represent the two sides of a back-splicing site, respectively. Diverse bioinformatics tools are available at PlantcircBase: (i) basic tools including browsing, searching and downloading, and (ii) advanced tools, including visualizing structures of circRNAs and predicting circRNAs.
TSCD / Tissue-Specific CircRNA Database
Provides an integrating view to explore the Tissue-Specific (TS) circRNAs in human and mouse tissues. TSCD is an online resource that includes information for TS circRNAs, such as origination of genomic location, conservation across species and visualization of exons structures. Results provided the information for the features and functions of TS circRNAs, thus benefiting the exploring of new RNA biomarkers in organ development and investigating the transcript process in organ differentiation and development disorders.
Circ2Traits
A comprehensive knowledge base of potential association of circular RNAs with diseases in human. Circ2Traits stores information about circRNAs, categorized according to their potential association with diseases, as observed from the genome-wide association study (GWAS) associated single nucleotide polymorphisms (SNPs) and potential interaction with disease associated miRNAs. Users can search by either disease name, or circRNA/miRNA/mRNA/lncRNA identifier, or traits by keyword. The results page will show the circRNAs/miRNAs/mRNAs/lncRNAs potentially associated with disease or traits. Further searching by particular disease name will show the user the whole miRNA-target interaction network for the particular disease. Searching by particular circRNA will show the detailed information about the circRNA.
circRNADb / circular RNA Database
A biological information platform for circRNA containing 32,914 human circular RNAs. This database provides the following main functions to users, including simple search, advanced search, browse, resource download, and information feedback. From a search text box, users can enter the search terms as required, such as chromosome name, gene symbol, transcript, and other keywords to query the circRNA, then the results that matched the query keywords will be listed in the result page.
BBBomics / Blood Brain Barrier omics
A comprehensive portal for blood-brain barrier transcriptomics data, obtained by sequencing mRNA (mRNA-seq) and microRNA (miRNA-seq) of polarized hCMEC/D3 cell monolayers. This data encompasses coding (gene expression, alternate splice forms, expressed single nucleotide variants -eSNVs) and non-coding (microRNA, LincRNA, circular RNA) counts that are easily accessible through BBBomics hub database. We also superimposed the RNA-seq coding data on 285 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, which include canonical, non-canonical, and/or atypical pathways retrievable using BBBomics hub.
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