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ncRNA Related Databases
- miRTarBase (Hsu SD et al.,Nucleic Acids Res. 2011 Jan)
- NPInter (Wu T et al.,Nucleic Acids Res. 2006 Jan:D150-2)
- PRD (Fujimori S et al.,Bioinformation. 2012)
- miRNAMap 2.0 (Hsu SD, Chu CH et al.,Nucleic Acids Res.2008 Jan:D165-9)
- human microRNA disease database (HMDD) (Lu M, Zhang Q et al.,PLoS ONE.2008 Oct)
- miRbase (Kozomara A et al.,Nucleic Acids Res. 2011 D152-D157)
- ncRNA Expression Database (NRED) (Dinger ME, Pang KC et al.,Nucleic Acids Res.2009 Jan)
- lncrnadb (Amaral PP et al.,Nucleic Acids Res 39: D146-151.)
- NONCODE (Liu C, Bai B et al.,Nucleic Acids Res.2005 Jan:D112-5)
- RNAdb (Bateman A, Agrawal S et al.,RNA. 2011 Nov;17(11):1941-6.)
Binding Site Predict Tools
- bindN+ (Wang, L. and Brown, S.J et.al., BMC Syst Biol. 2010 May.)
- miranda (John B et al.,PLoS Biol. 2005 Jul)
- RIsearch(Anne Wenzel et al.,Bioinformatics. 2012 Nov)
- RNAbindR (Terribilini M et al.,Nucleic Acids Research. 2007 Jul)
- RBPDB (Cook KB et al.,Nucleic Acids Res. 2011 Jan)
Other Gene/Protein Sources
- HGNC (Gray KA et al., Nucleic Acids Res. 2013 Jan 1;41)
- UniProt (The UniProt Consortium.,Nucleic Acids Res. 41: D43-D47 (2013))
- HPRD(Keshava Prasad TS et al.,.Nucleic Acids Res. 2009 Jan)
- Pathway Commons (Cerami et al.,Nucl. Acids Res.2010)
- RNApathwaysDB (Milanowska K et al.,Nucleic Acids Res.2013 Jan;41(Database issue):D268-72.)
Search ViRBase by four paths: Keyword, Virus/Host Species, RNA/Protein Symbol and Validated Methods
Search Results and Detail Information
Visualization Represention
Browse By Virus/Host Species and RNA Category
Download&API
Help
Users can search the virus-host ncRNA-associated interactions through four Paths:
Path 1(By Keyword): search the virus-host ncRNA-associated interactions by inputting the keywords(any RNA and Protein Symbol) and fuzzy search supported.
Path 2 (By Virus/Host Species): search the virus-host ncRNA-associated interactions by associated option of Virus/Host Species.
Path 3 (By RNA/Protein Symbol): search the virus-host ncRNA-associated interactions by associated option of RNA categories and RNA/Protein symbols.
Path 4 (By Validated Method): search the virus-host ncRNA-associated interactions by validated Methods and multiple selection supported.
The 'First Node' or 'Second Node' option represents the sub-network of interacting ncRNA/Interactor with the first or second interaction node, the 'Both the Nodes' option represents the sub-network of interacting ncRNA/Interactor with both of interaction nodes.
The 'First Neighbour' represents the sub-network of direct interacting with the center node, the 'Second Neighbour' represents the sub-network of direct or second step interacting with the center node.
Interaction sub-network based on the two nodes of this interaction may help the researchers represents all interacting partners immediately.
bindN+
Web Server: Submit the protein sequences to bindN+ and get the binding locationhttp://bioinfo.ggc.org/bindn+/
Parameter setting
Miranda
Manual Location: The manual and the parameter of Mirandahttp://cbio.mskcc.org/microrna_data/manual.html
Parameter setting
RIsearch
Manual Location: The manual and the parameter of RIsearch
http://rth.dk/resources/risearch/
Parameter setting
RNABindR
Web Server: Submit the protein sequences to RNABindR and get the binding locationhttp://einstein.cs.iastate.edu/RNABindR/
Parameter setting
Table 1 The statistics of the virus-host ncRNA-associated entries by interaction categories.
| Interaction Category | Validated | Predicted | Unknown | Total |
| Virus-Virus | 133 | 11 | 22 | 166 |
| Virus-Host | 10809 | 8 | 53 | 10870 |
| Host-Virus | 189 | 222 | 42 | 453 |
| Host-Host | 422 | 190 | 146 | 758 |
| Total | 11553 | 431 | 263 | 12247 |
Table 2 The statistics of the virus-host ncRNA-associated entries by virus names.
| Virus Name | Validated | Predicted | Unknown | Total |
| Adeno-associated virus(AAV) | 2 | 0 | 1 | 3 |
| Adenovirus(ADV) | 9 | 0 | 0 | 9 |
| Andes hantavirus(ANDV) | 2 | 0 | 0 | 2 |
| Ascoviruses | 2 | 0 | 0 | 2 |
| Autographa californica nucleopolyhedrovirus(AcMNPV) | 1 | 0 | 0 | 1 |
| Avian leukosis virus(ALV) | 1 | 0 | 0 | 1 |
| BK virus(BKV) | 1 | 0 | 0 | 1 |
| Barley stripe mosaic virus(BSMV) | 0 | 0 | 1 | 1 |
| Bombyx mori nuclearpolyhedrosis virus(BmNPV) | 1 | 0 | 0 | 1 |
| Borna disease virus(BDV) | 1 | 0 | 0 | 1 |
| Bovine viral diarrhea virus(BVDV) | 3 | 0 | 0 | 3 |
| Coxsackievirus B3(CVB3) | 11 | 0 | 0 | 11 |
| Cucumber mosaic virus(CMV) | 8 | 0 | 0 | 8 |
| Cytomegalovirus(CMV) | 12 | 0 | 0 | 12 |
| Dengue virus(DENV) | 8 | 0 | 0 | 8 |
| Enterovirus 71(EV71) | 2 | 0 | 0 | 2 |
| Epstein-Barr virus(EBV) | 5670 | 4 | 16 | 5690 |
| Gallid herpesvirus 2(GaHV-2) | 2 | 0 | 0 | 2 |
| Hendra virus | 0 | 0 | 1 | 1 |
| Hepatitis B virus(HBV) | 84 | 1 | 63 | 148 |
| Hepatitis C virus(HCV) | 71 | 4 | 4 | 79 |
| Hepatitis E virus(HEV) | 2 | 0 | 0 | 2 |
| Herpes B virus(BV) | 1 | 0 | 1 | 2 |
| Herpes simplex virus 1(HSV-1) | 11 | 3 | 2 | 16 |
| Herpes simplex virus 2(HSV-2) | 6 | 0 | 1 | 7 |
| Herpesvirus saimiri(HVS) | 41 | 0 | 0 | 41 |
| Human T-cell leukemia virus 1(HTLV-1) | 4 | 0 | 0 | 4 |
| Human cytomegalovirus(HCMV) | 51 | 0 | 14 | 65 |
| Human immunodeficiency virus 1(HIV-1) | 162 | 16 | 115 | 293 |
| Human papillomavirus 16(HPV16) | 9 | 0 | 0 | 9 |
| Human papillomavirus(HPV) | 21 | 0 | 0 | 21 |
| Human respiratory syncytial virus(RSV) | 10 | 0 | 0 | 10 |
| Influenza A virus H1N1(H1N1) | 65 | 100 | 0 | 165 |
| Influenza A virus H3N2(H3N2) | 16 | 0 | 0 | 16 |
| Influenza A virus H5N1(H5N1) | 1 | 0 | 0 | 1 |
| Influenza A virus(infA) | 55 | 1 | 0 | 56 |
| John Cunningham virus(JCV) | 1 | 0 | 0 | 1 |
| Kaposi's sarcoma-associated herpesvirus(KSHV) | 5120 | 78 | 35 | 5233 |
| Marek's disease virus 1(MDV-1) | 26 | 0 | 0 | 26 |
| Marek's disease virus(MDV) | 3 | 0 | 0 | 3 |
| Merkel cell polyomavirus(MCPyV) | 0 | 2 | 0 | 2 |
| Mink enteritis virus(MEV) | 1 | 0 | 0 | 1 |
| Moloney murine leukemia virus(MoMuLV) | 5 | 0 | 0 | 5 |
| Murine cytomegalovirus(MCMV) | 2 | 0 | 0 | 2 |
| Package lentivirus(PLV) | 1 | 0 | 0 | 1 |
| Polyoma virus(PyV) | 1 | 0 | 0 | 1 |
| Porcine reproductive and respiratory syndrome virus(PRRSV) | 2 | 0 | 0 | 2 |
| Primate foamy virus 1(PFV-1) | 1 | 0 | 0 | 1 |
| Pseudorabies virus(PRV) | 1 | 0 | 0 | 1 |
| Reconstructed 1918 influenza virus(r1918) | 0 | 18 | 0 | 18 |
| Reticuloendotheliosis virus(REV) | 1 | 0 | 0 | 1 |
| Rhesus lymphocryptovirus(rLCV) | 10 | 0 | 0 | 10 |
| Severe acute respiratory syndrome coronavirus(SARS-CoV) | 0 | 204 | 0 | 204 |
| Simian immunodeficiency virus(SIV) | 7 | 0 | 0 | 7 |
| Simian virus 40(SV40) | 3 | 0 | 1 | 4 |
| Soybean mosaic virus(SMV) | 1 | 0 | 0 | 1 |
| Tomato aspermy virus(TAV) | 13 | 0 | 0 | 13 |
| Turnip mosaic virus(TuMV) | 1 | 0 | 0 | 1 |
| Vesicular stomatitis virus(VSV) | 4 | 0 | 4 | 8 |
| West Nile virus(WNV) | 1 | 0 | 0 | 1 |
| White spot syndrome virus(WSSV) | 2 | 0 | 4 | 6 |
| Total | 11553 | 431 | 263 | 12247 |
Table 3 The statistics of the virus-host ncRNA-associated entries by host species.
| Host Species | Validated | Predicted | Unknown | Total |
| Aedes albopictus | 1 | 0 | 0 | 1 |
| Anopheles gambiae | 1 | 0 | 0 | 1 |
| Autographa californica | 1 | 0 | 0 | 1 |
| Bombyx mori | 1 | 0 | 0 | 1 |
| Bovine | 3 | 0 | 0 | 3 |
| Brassica napus | 1 | 0 | 0 | 1 |
| Callithrix jacchus | 38 | 0 | 1 | 39 |
| Chlorocebus sabaeus | 1 | 0 | 0 | 1 |
| Cricetulus griseus | 2 | 0 | 0 | 2 |
| Drosophila melanogaster | 2 | 0 | 0 | 2 |
| Gallus gallus | 33 | 0 | 0 | 33 |
| Glycine max | 1 | 0 | 0 | 1 |
| Homo sapiens | 11349 | 209 | 239 | 11797 |
| Litopenaeus vannamei | 1 | 0 | 0 | 1 |
| Macaca mulatta | 10 | 0 | 0 | 10 |
| Mus musculus | 43 | 222 | 5 | 270 |
| Neovison vison | 1 | 0 | 0 | 1 |
| Rattus norvegicus | 14 | 0 | 13 | 27 |
| Saimiri boliviensis | 8 | 0 | 0 | 8 |
| Shrimp | 1 | 0 | 4 | 5 |
| Simian | 3 | 0 | 0 | 3 |
| Solanum lycopersicum | 33 | 0 | 0 | 33 |
| Sus scrofa | 5 | 0 | 0 | 5 |
| Triticum aestivum | 0 | 0 | 1 | 1 |
| Total | 11553 | 431 | 263 | 12247 |
Table 4 The statistics of the virus-host ncRNA-associated entries by ncRNA categories.
| ncRNA Category | Validated | Predicted | Unknown | Total |
| LncRNA | 92 | 204 | 18 | 314 |
| ShRNA | 3 | 0 | 0 | 3 |
| SnoRNA | 5 | 0 | 0 | 5 |
| miRNA | 11462 | 227 | 245 | 11934 |
| Total | 11553 | 431 | 263 | 12247 |