ExoCarta
{{infobox biodatabase
|title = ExoCarta
|logo =File:Database.png
|description = Exosomal proteins, RNA and lipids database
|scope =
|organism =
|center = La Trobe Institute for Molecular Science
|laboratory =
|author = Suresh Mathivanan
|pmid =
|released =
|standard =
|format =
|url = http://www.exocarta.org
|download =
|webservice =
|sql =
|sparql =
|webapp =
|standalone =
|license =
|versioning =
|frequency =
|curation =
|bookmark =
|version=
}}
ExoCarta is a manually curated database of exosomal proteins, RNA and lipids.{{cite journal |last=Mathivanan|first=Suresh|author2=Fahner Cassie J|author3=Reid Gavin E|author4=Simpson Richard J|date=Oct 2011|title=ExoCarta 2012: database of exosomal proteins, RNA and lipids|journal = Nucleic Acids Research|volume=40|issue=Database issue|pages=D1241–4| pmid = 21989406|doi = 10.1093/nar/gkr828| pmc=3245025}}{{cite journal| author=Mathivanan S, Simpson RJ| title=ExoCarta: A compendium of exosomal proteins and RNA | journal=Proteomics | year= 2009 | volume= 9 | issue= 21 | pages= 4997–5000 | pmid=19810033 | doi=10.1002/pmic.200900351 | s2cid=22275212 }}
Exosomes are cell-derived vesicles that are present in many and perhaps all biological fluids, including blood, urine, and cultured medium of cell cultures.{{cite journal
|title=Classification, functions, and clinical relevance of extracellular vesicles
|journal=Pharmacol. Rev.
|volume=64
|issue=3
|pages=676–705
|year=2012
|pmid=22722893
|doi=10.1124/pr.112.005983
|author1=van der Pol E
|author2=Böing, AN
|author3=Harrison P
|author4=Sturk A
|author5=Nieuwland R
|s2cid=7764903
|title=Exosomes: from biogenesis and secretion to biological function
|journal=Immunol. Lett.
|volume=107
|issue=2
|pages=102–8
|year=2006
|pmid=17067686
|doi=10.1016/j.imlet.2006.09.005
|author1=Keller S
|author2=Sanderson MP
|author3=Stoeck A
|author4=Altevogt P
}} The reported diameter of exosomes is between 30 and 100 nm, which is larger than LDL, but much smaller than for example, red blood cells. Exosomes are either released from the cell when multivesicular bodies fuse with the plasma membrane or they are released directly from the plasma membrane.{{cite journal
|title=Exosomes and HIV Gag bud from endosome-like domains of the T cell plasma membrane
|journal=J. Cell Biol.
|volume=172
|issue=6
|pages=932–935
|year=2006
|pmid=16533950
|doi=10.1083/jcb.200508014
|author1=Booth AM
|author2=Fang Y
|author3=Fallon JK
|author4=Yang JM
|author5=Hildreth JE
|author6=Gould SJ
|pmc=2063735}} It is becoming increasingly clear that exosomes have specialized functions and play a key role in, for example, coagulation, intercellular signaling, and waste management. Consequently, there is a growing interest in the clinical applications of exosomes. Exosomes can potentially be used for prognosis, therapy, and biomarkers for health and disease.
Bioinformatics analysis of exosomes
Exosomes contain RNA, proteins, lipids and metabolites that is reflective of the cell type of origin. As exosomes contain numerous bioactive molecules, including proteins, nucleic acids, lipids, sugars, and related conjugates, large scale analysis including proteomics and transcriptomics is often performed.{{Cite journal|last1=Rudraprasad|first1=Dhanwini|last2=Rawat|first2=Aadish|last3=Joseph|first3=Joveeta|date=2022-01-01|title=Exosomes, extracellular vesicles and the eye|url=https://www.sciencedirect.com/science/article/pii/S0014483521004589|journal=Experimental Eye Research|language=en|volume=214|pages=108892|doi=10.1016/j.exer.2021.108892|pmid=34896308|s2cid=245028439|issn=0014-4835|url-access=subscription}} Currently, to analyse these data, non-commercial tools such as FunRich{{Cite journal
| pmid = 25921073
| year = 2015
| last1 = Pathan
| first1 = M
| title = Technical brief funrich: An open access standalone functional enrichment and interaction network analysis tool
| journal = Proteomics
| pages = 2597–601
| last2 = Keerthikumar
| first2 = S
| last3 = Ang
| first3 = C. S.
| last4 = Gangoda
| first4 = L
| last5 = Quek
| first5 = C. Y.
| last6 = Williamson
| first6 = N. A.
| last7 = Mouradov
| first7 = D
| last8 = Sieber
| first8 = O. M.
| last9 = Simpson
| first9 = R. J.
| last10 = Salim
| first10 = A
| last11 = Bacic
| first11 = A
| last12 = Hill
| first12 = A
| last13 = Stroud
| first13 = D. A.
| last14 = Ryan
| first14 = M. T.
| last15 = Agbinya
| first15 = J. I.
| last16 = Mariadasson
| first16 = J. M.
| last17 = Burgess
| first17 = A. W.
| last18 = Mathivanan
| first18 = S
| doi = 10.1002/pmic.201400515
| volume=15
| issue = 15
| s2cid = 28583044
}} can be used to identify over-represented groups of molecules.
References
External links
- [http://www.exocarta.org Official site]
{{Biodatabase-stub}}