 | |
| Content | |
|---|---|
| Description | Exosomal proteins, RNA and lipids database |
| Contact | |
| Research center | La Trobe Institute for Molecular Science |
| Authors | Suresh Mathivanan |
| Access | |
| Website | http://www.exocarta.org |
ExoCarta is a manually curated database of exosomal proteins, RNA and lipids. [1] [2]
Exosomes are cell-derived vesicles that are present in many and perhaps all biological fluids, including blood, urine, and cultured medium of cell cultures. [3] [4] 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. [5] It is becoming increasingly clear that exosomes have specialized functions and play a key role in, for example, coagulation, intercellular signaling, and waste management. [3] 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. [6] Currently, to analyse these data, non-commercial tools such as FunRich [7] can be used to identify over-represented groups of molecules.
References
- ^ Mathivanan, Suresh; Fahner Cassie J; Reid Gavin E; Simpson Richard J (Oct 2011). "ExoCarta 2012: database of exosomal proteins, RNA and lipids". Nucleic Acids Research. 40 (Database issue): D1241–4. doi: 10.1093/nar/gkr828. PMC 3245025. PMID 21989406.
- ^ Mathivanan S, Simpson RJ (2009). "ExoCarta: A compendium of exosomal proteins and RNA". Proteomics. 9 (21): 4997–5000. doi: 10.1002/pmic.200900351. PMID 19810033. S2CID 22275212.
- ^ a b van der Pol E; Böing, AN; Harrison P; Sturk A; Nieuwland R (2012). "Classification, functions, and clinical relevance of extracellular vesicles". Pharmacol. Rev. 64 (3): 676–705. doi: 10.1124/pr.112.005983. PMID 22722893. S2CID 7764903.
- ^ Keller S; Sanderson MP; Stoeck A; Altevogt P (2006). "Exosomes: from biogenesis and secretion to biological function". Immunol. Lett. 107 (2): 102–8. doi: 10.1016/j.imlet.2006.09.005. PMID 17067686.
- ^ Booth AM; Fang Y; Fallon JK; Yang JM; Hildreth JE; Gould SJ (2006). "Exosomes and HIV Gag bud from endosome-like domains of the T cell plasma membrane". J. Cell Biol. 172 (6): 932–935. doi: 10.1083/jcb.200508014. PMC 2063735. PMID 16533950.
- ^ Rudraprasad, Dhanwini; Rawat, Aadish; Joseph, Joveeta (2022-01-01). "Exosomes, extracellular vesicles and the eye". Experimental Eye Research. 214: 108892. doi: 10.1016/j.exer.2021.108892. ISSN 0014-4835. PMID 34896308. S2CID 245028439.
- ^ Pathan, M; Keerthikumar, S; Ang, C. S.; Gangoda, L; Quek, C. Y.; Williamson, N. A.; Mouradov, D; Sieber, O. M.; Simpson, R. J.; Salim, A; Bacic, A; Hill, A; Stroud, D. A.; Ryan, M. T.; Agbinya, J. I.; Mariadasson, J. M.; Burgess, A. W.; Mathivanan, S (2015). "Technical brief funrich: An open access standalone functional enrichment and interaction network analysis tool". Proteomics. 15 (15): 2597–601. doi: 10.1002/pmic.201400515. PMID 25921073. S2CID 28583044.
External links
 | This Biological database-related article is a stub. You can help Wikipedia by expanding it. |
|
| |
| Content | |
|---|---|
| Description | Exosomal proteins, RNA and lipids database |
| Contact | |
| Research center | La Trobe Institute for Molecular Science |
| Authors | Suresh Mathivanan |
| Access | |
| Website | http://www.exocarta.org |
ExoCarta is a manually curated database of exosomal proteins, RNA and lipids. [1] [2]
Exosomes are cell-derived vesicles that are present in many and perhaps all biological fluids, including blood, urine, and cultured medium of cell cultures. [3] [4] 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. [5] It is becoming increasingly clear that exosomes have specialized functions and play a key role in, for example, coagulation, intercellular signaling, and waste management. [3] 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. [6] Currently, to analyse these data, non-commercial tools such as FunRich [7] can be used to identify over-represented groups of molecules.
References
- ^ Mathivanan, Suresh; Fahner Cassie J; Reid Gavin E; Simpson Richard J (Oct 2011). "ExoCarta 2012: database of exosomal proteins, RNA and lipids". Nucleic Acids Research. 40 (Database issue): D1241–4. doi: 10.1093/nar/gkr828. PMC 3245025. PMID 21989406.
- ^ Mathivanan S, Simpson RJ (2009). "ExoCarta: A compendium of exosomal proteins and RNA". Proteomics. 9 (21): 4997–5000. doi: 10.1002/pmic.200900351. PMID 19810033. S2CID 22275212.
- ^ a b van der Pol E; Böing, AN; Harrison P; Sturk A; Nieuwland R (2012). "Classification, functions, and clinical relevance of extracellular vesicles". Pharmacol. Rev. 64 (3): 676–705. doi: 10.1124/pr.112.005983. PMID 22722893. S2CID 7764903.
- ^ Keller S; Sanderson MP; Stoeck A; Altevogt P (2006). "Exosomes: from biogenesis and secretion to biological function". Immunol. Lett. 107 (2): 102–8. doi: 10.1016/j.imlet.2006.09.005. PMID 17067686.
- ^ Booth AM; Fang Y; Fallon JK; Yang JM; Hildreth JE; Gould SJ (2006). "Exosomes and HIV Gag bud from endosome-like domains of the T cell plasma membrane". J. Cell Biol. 172 (6): 932–935. doi: 10.1083/jcb.200508014. PMC 2063735. PMID 16533950.
- ^ Rudraprasad, Dhanwini; Rawat, Aadish; Joseph, Joveeta (2022-01-01). "Exosomes, extracellular vesicles and the eye". Experimental Eye Research. 214: 108892. doi: 10.1016/j.exer.2021.108892. ISSN 0014-4835. PMID 34896308. S2CID 245028439.
- ^ Pathan, M; Keerthikumar, S; Ang, C. S.; Gangoda, L; Quek, C. Y.; Williamson, N. A.; Mouradov, D; Sieber, O. M.; Simpson, R. J.; Salim, A; Bacic, A; Hill, A; Stroud, D. A.; Ryan, M. T.; Agbinya, J. I.; Mariadasson, J. M.; Burgess, A. W.; Mathivanan, S (2015). "Technical brief funrich: An open access standalone functional enrichment and interaction network analysis tool". Proteomics. 15 (15): 2597–601. doi: 10.1002/pmic.201400515. PMID 25921073. S2CID 28583044.
External links
|
| This Biological database-related article is a stub. You can help Wikipedia by expanding it. |