The Multi-Omics Profiling Expression Database (MOPED) was an expanding multi-omics resource that supports rapid browsing of transcriptomics and proteomics information from publicly available studies on model organisms and humans.[2] As to date (2021) it has ceased activities and is unaccessible online.[3]
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| Content | |
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| Description | MOPED enables discoveries through consistently processed multi-omics data |
| Contact | |
| Research center | Seattle Children's Research Institute |
| Authors | Roger Higdon |
| Primary citation | Higdon R, et al.[1] |
| Release date | 2012 |
| Access | |
| Website | MOPED |
Systematic Protein Investigative Research Environment
editMOPED is designed to simplify the comparison and sharing of data for the greater research community. MOPED employs the standardized analysis pipeline SPIRE[4] to uniquely provide protein level absolute and relative expression data, meta- analysis capabilities and quantitative data. Processed relative expression transcriptomics data were obtained from the Gene Expression Omnibus (GEO). Data can be queried for specific proteins and genes, browsed based on organism, tissue, localization and condition, and sorted by false discovery rate and expression. MOPED empowers users to visualize their own expression data and compare it with existing studies. Further, MOPED links to various protein and pathway data- bases, including GeneCards, Panther, Entrez, UniProt, KEGG, SEED, and Reactome. Protein and gene identifiers are integrated from GeneCards (cross-referenced with MOPED), Genbank, RefSeq, UniProt, WormBase, and Saccharomyces Genome Database (SGD). The current version of MOPED (MOPED 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions. MOPED is developed and supported by the Kolker team at Seattle Children's Research Institute.
Model Organism Protein Expression Database
editMOPED was previously known as the Model Organism Protein Expression Database, before changing its name to the Multi-Omics Profiling Expression Database.[5][6]
References
edit- ^ Higdon R; Stewart E; Stanberry L; Haynes W; Choiniere J; Montague E; Anderson N; Yandl Y; Janko I; Broomall W; Fishilevich S; Lancet D; Kolker N; Eugene Kolker. (Jan 2014). "MOPED enables discoveries through consistently processed proteomics data". J Proteome Res. 13 (1): 107–113. doi:10.1021/pr400884c. PMC 4039175. PMID 24350770.
- ^ Kolker E, Higdon R, Haynes W, Welch D, Broomall W, Lancet D, Stanberry L, Kolker N (Jan 2012). "MOPED: Model Organism Protein Expression Database". Nucleic Acids Res. 40 (Database issue): D1093–9. doi:10.1093/nar/gkr1177. PMC 3245040. PMID 22139914.
- ^ "Start Moped Web Application". www.proteinspire.org. Archived from the original on 2014-04-22.
- ^ Kolker E, Higdon R, Morgan P, Sedensky M, Welch D, Bauman A, Stewart E, Haynes W, Broomall W, Kolker N (December 2011). "SPIRE: Systematic protein investigative research environment". J Proteomics. 75 (1): 122–6. doi:10.1016/j.jprot.2011.05.009. PMID 21609792.
- ^ Kolker, Eugene; Higdon, Roger; Haynes, Winston; Welch, Dean; Broomall, William; Lancet, Doron; Stanberry, Larissa; Kolker, Natali (2011-12-01). "MOPED: Model Organism Protein Expression Database". Nucleic Acids Research. 40 (D1): D1093–D1099. doi:10.1093/nar/gkr1177. ISSN 1362-4962. PMC 3245040. PMID 22139914.
- ^ Montague, Elizabeth; Janko, Imre; Stanberry, Larissa; Lee, Elaine; Choiniere, John; Anderson, Nathaniel; Stewart, Elizabeth; Broomall, William; Higdon, Roger; Kolker, Natali; Kolker, Eugene (2015-01-28). "Beyond protein expression, MOPED goes multi-omics". Nucleic Acids Research. 43 (D1): D1145–D1151. doi:10.1093/nar/gku1175. ISSN 1362-4962. PMC 4383969. PMID 25404128.
Further reading
edit- Stelzer G, Dalah I, Stein TI, Satanower Y, Rosen N, Nativ N, Oz-Levi D, Olender T, Belinky F, Bahir I, Krug H, Perco P, Mayer B, Kolker E, Safran M, Lancet D (October 2011). "In-silico human genomics with GeneCards". Hum. Genomics. 5 (6): 709–17. doi:10.1186/1479-7364-5-6-709. PMC 3525253. PMID 22155609.