扫码联系客服
A biological information platform for circRNA containing 32,914 human circular RNAs.
(Chen et al., 2016) circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations. Nature.
A machine learning method for predicting circular RNAs from those of non-circularized, expressed exons based on conformational and thermodynamic properties in the flanking introns.
(Liu et al., 2016) Computational identification of circular RNAs based on conformational and thermodynamic properties in the flanking introns. Computational Biology and Chemistry.
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.
(Kalari et al., 2016) BBBomics-Human Blood Brain Barrier Transcriptomics Hub. Frontiers in neuroscience.
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.
(Liu et al., 2015) CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic acids research.
A database and website where merged and unified data sets of circRNAs and the evidence supporting their expression can be accessed, downloaded, and browsed within the genomic context. circBase also provides scripts to identify known and novel circRNAs in sequencing data. There are three main ways of obtaining data from circBase: simple search, list search and conditional retrieval via table browser.
(Glazar et al., 2014) circBase: a database for circular RNAs. Rna.
A machine learning approach focused on distinguishing circularRNA from other lncRNAs using multiple kernel learning.
(Pan and Xiong, 2015) PredcircRNA: computational classification of circular RNA from other long non-coding RNA using hybrid features. Molecular bioSystems.
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 GWAS associated SNPs and potential interaction with disease associated miRNAs.
(Ghosal et al., 2013) Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits. Frontiers in Genetics.
A manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDNA database documents 24713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles. (Wang et al., 2016) NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases. Nucleic Acids Research.
A manually curated resource of piRNAs, which focused on piRNA function analyses as well as piRNA annotation. piRBase has the largest collection of piRNAs among existing databases, and contains at present 77 million piRNA sequences from nine organisms.
(Zhang et al., 2014) piRBase: a web resource assisting piRNA functional study. Database.
A highly user-friendly resource which stores empirically known sequences and other related information on piRNAs reported in human, mouse and rat. piRNABank supports organism and chromosome-wise comprehensive search features including accession numbers, localization on chromosomes, gene name or symbol, sequence homology-based search, clusters and corresponding genes and repeat elements. It also displays each piRNA or piRNA cluster on a graphical genome-wide map.
(Sai Lakshmi and Agrawal, 2008) piRNABank: a web resource on classified and clustered Piwi-interacting RNAs. Nucleic acids research.
An integrated resource for searching the piRNAome of human, mouse and rat. This unique, comprehensive and unified database provides annotation of piRNAs based on their genomic location in gene, intron, intergenic, CDS, UTR, repeat elements, pseudogenes and syntenic regions.
(Sarkar et al., 2014) piRNAQuest: searching the piRNAome for silencers. BMC genomics.
A support vector machine (SVM) classifier to predict potential piRNA targets on protein-coding genes. We trained a support vector machine classifier based on a combination of Miwi CLIP-seq-derived features and position-derived features to predict the potential targets of piRNAs on mRNAs in the mouse.
(Yuan et al., 2015) Computational identification of piRNA targets on mouse mRNAs. Bioinformatics.
Contains the most comprehensive information to date on human small non-coding RNAs (sncRNA) genes and mature sncRNA products.
(Leung et al., 2015) DASHR: database of small human noncoding RNAs. Nucleic acids research.
A manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDNA database documents 24713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles. (Wang et al., 2016) NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases. Nucleic Acids Research.
A manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA.
(Tyagi et al., 2011) HIVsirDB: a database of HIV inhibiting siRNAs. PLoS One.
In silico resources developed to facilitate scientific community fighting against deadly virus EBOLA. EbolaVCR enlists possible vaccine candidates, therapeutic siRNAs and other related resources. Firstly, we predicted and identified experimentally validated epitopes in each of the antigens/proteins of the five known ebolaviruses. Secondly, we generated all the possible overlapping 9mer peptides from the proteins of ebolaviruses. Thirdly, conserved peptides across all the five ebolaviruses (four human pathogenic species) with no identical sequence in the human proteome, based on 1000 Genomes project, were identified. Finally, we identified peptide or epitope-based vaccine candidates that could activate both the B- and T-cell arms of the immune system. In addition, we also identified efficacious siRNAs against the mRNA transcriptome (absent in human transcriptome) of all the five ebolaviruses.
(Dhanda et al., 2016) A web-based resource for designing therapeutics against Ebola Virus. Scientific reports.
A specialized databank for chemically modified siRNAs. siRNAmod contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. siRNAmod browsing option helps user to surf via these five categories: i) modification in sense strand, ii) position of modification in sense strand, iii) modification in antisense strand, iv) position of modification in antisense strand and v) reference.
(Dar et al., 2016) siRNAmod: A database of experimentally validated chemically modified siRNAs. Scientific reports.
A manually curated database having comprehensive details of 1358 siRNA/shRNA targeting viral genome regions. Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. Important fields included in the database are siRNA sequence, virus subtype, target genome region, cell type, target object, experimental assay, efficacy, off-target and siRNA matching with reference viral sequences. Database also provides the users with facilities of advance search, browsing, data submission, linking to external databases and useful siRNA analysis tools especially siTarAlign which align the siRNA with reference viral genomes or user defined sequences. VIRsiRNAdb contains extensive details of siRNA/shRNA targeting 42 important human viruses including influenza virus, hepatitis B virus, HPV and SARS Corona virus. It is possible to perform a quick search based on various database fields i.e. Virus name, siRNA sequence, target region, cell line and Pubmed ID.
(Thakur et al., 2012) VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA. Nucleic acids research.
(Chalk et al., 2005) siRNAdb: a database of siRNA sequences. Nucleic acids research.
A manually curated database having comprehensive details of 1358 siRNA/shRNA targeting viral genome regions. Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. .
(Thakur et al., 2012) VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA. Nucleic acids research.
A comprehensive bioinformatics resource to archive non-coding RNA (ncRNA)-associated cell death interactions. ncRDeathDB documents a total of more than 4600 ncRNA-mediated programmed cell death (PCD) entries in 12 species. ncRDeathDB provides a user-friendly interface to query, browse and manipulate these ncRNA-associated cell death interactions. Furthermore, this resource will help to visualize and navigate current knowledge of the noncoding RNA component of cell death and autophagy, to uncover the generic organizing principles of ncRNA-associated cell death systems, and to generate valuable biological hypotheses.
(Wu et al., 2015) ncRDeathDB: A comprehensive bioinformatics resource for deciphering network organization of the ncRNA-mediated cell death system. Autophagy.
A manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDNA database documents 24713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles.
(Wang et al., 2016) NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases. Nucleic Acids Research.
Contains the most comprehensive information to date on human small non-coding RNAs (sncRNA) genes and mature sncRNA products. DASHR provides a simple user interface for researchers to view sequence and secondary structure, compare expression levels, and evidence of specific processing across all sncRNA genes and mature sncRNA products in various human tissues. DASHR annotation and expression data covers all major classes of sncRNAs including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear, nucleolar, cytoplasmic (sn-, sno-, scRNAs, respectively), transfer (tRNAs), and ribosomal RNAs (rRNAs). DASHR is distinct from other existing databases because it integrates annotations for all major classes of sncRNAs with baseline expression profiles in different human tissues and cell types, making it a very useful resource to the broader scientific community.
(Leung et al., 2015) DASHR: database of small human noncoding RNAs. Nucleic acids research.
(Lestrade and Weber, 2006) snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic acids research.
(Brown et al., 2003) Plant snoRNA database. Nucleic acids research.
最后小编祝大家在2017年里，身体健康，心想事成，元旦快乐！
近期热帖：
2017"生信人"春联征集活动：最后一天了，欢迎留言
