Multi-Omics Profiling Expression Database: Difference between revisions

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{{infobox biodatabase

{{external links|date=August 2013}}

{{infobox_biodatabase

|title = MOPED

|logo =[[File:Database.png]]

|description = MOPED enables discoveries through consistently processed multi-omics data

|description =

|scope =

|scope = Multi-Omics Profiling Expression Database

|organism =

|center = [[Seattle Children's Research Institute]]

|laboratory =

|author = Roger Higdon

|pmidcitation = Higdon R, ''et al''. <ref name="pmid24350770">{{cite journal | author author1= Higdon R, |author2=Stewart E, |author3=Stanberry L, |author4=Haynes W, |author5=Choiniere J, |author6=Montague E, |author7=Anderson N, |author8=Yandl Y, |author9=Janko I, |author10=Broomall W, |author11=Fishilevich S, |author12=Lancet D, |author13=Kolker N, |author14=Eugene Kolker. | title = MOPED enables discoveries through consistently processed proteomics data. | journal = J Proteome Res | volume = 13 | issue = 1 | pages = 107-113107–113 |date=Jan 2014 | pmid = 24350770 | doi = 10.1021/pr400884c |pmc=4039175 }}</ref>

|released = 2012

|standard =

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|version=

}}

The '''Multi-Omics Profiling Expression Database''' ('''MOPED''') iswas an expanding [[Multiomics|multi-omics]] resource that supports rapid browsing of [[transcriptomics]] and [[proteomics]] information from publicly available studies on [[model organismsorganism]]s and humans.<ref>{{cite MOPEDjournal is|vauthors=Kolker designedE, toHigdon simplifyR, theHaynes comparisonW, andWelch sharing of data for the greater research community. MOPED employs the standardized analysis pipeline [https://www.proteinspire.org/ SPIRE] to uniquely provide protein level absolute and relative expression dataD, 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 andBroomall genesW, browsedLancet based on organismD, tissue, localization andStanberry conditionL, andKolker sortedN by| falsetitle discovery rate and expression.= MOPED: empowersModel usersOrganism toProtein visualizeExpression theirDatabase own| expressionjournal data= andNucleic compareAcids itRes. with| existingvolume studies.= Further,40 MOPED| linksissue to= variousDatabase proteinissue and| pathwaypages data-= bases,D1093–9 including|date=Jan GeneCards,2012 Panther,| Entrez,pmid UniProt,= KEGG,22139914 | SEED,pmc and= Reactome.3245040 Protein| anddoi gene= identifiers10.1093/nar/gkr1177 are}}</ref> integratedAs fromto GeneCardsdate (cross-referenced with MOPED2021), Genbank,it RefSeq,has UniProt,ceased WormBase,activities and Saccharomycesis Genomeunaccessible Database (SGD)online.<ref>{{cite web The current version of MOPED (MOPED 2|url=https://www.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditionsproteinspire. org/MOPED/ is|title=Start developedMoped andWeb supportedApplication by|website=www.proteinspire.org the|url-status=dead [http|archive-url=https://kolkerlabweb.proteinspirearchive.org/ Kolker] team at [httpweb/20140422231720/https://www.seattlechildrensproteinspire.org/researchMOPED/ Seattle|archive-date=2014-04-22}} Children's Research Institute].</ref>

==Systematic Protein Investigative Research Environment==

MOPED was previously known as the Model Organism Protein Expression Database, before changing its name to the Multi-Omics Profiling Expression Database.

MOPED is designed to simplify the comparison and sharing of data for the greater research community. MOPED employs the standardized analysis pipeline [[Systematic Protein Investigative Research Environment|SPIRE]]<ref>{{cite journal |vauthors=Kolker E, Higdon R, Morgan P, Sedensky M, Welch D, Bauman A, Stewart E, Haynes W, Broomall W, Kolker N | title = SPIRE: Systematic protein investigative research environment | journal = J Proteomics | volume = 75 | issue = 1 | pages = 122–6 |date=December 2011 | pmid = 21609792 | doi = 10.1016/j.jprot.2011.05.009 }}</ref> 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==

MOPED was previously known as the Model Organism Protein Expression Database, before changing its name to the Multi-Omics Profiling Expression Database.<ref>{{Cite journal |last1=Kolker |first1=Eugene |last2=Higdon |first2=Roger |last3=Haynes |first3=Winston |last4=Welch |first4=Dean |last5=Broomall |first5=William |last6=Lancet |first6=Doron |last7=Stanberry |first7=Larissa |last8=Kolker |first8=Natali |date=2011-12-01 |title=MOPED: Model Organism Protein Expression Database |url=https://doi.org/10.1093/nar/gkr1177 |journal=Nucleic Acids Research |volume=40 |issue=D1 |pages=D1093–D1099 |doi=10.1093/nar/gkr1177 |issn=1362-4962 |pmc=3245040 |pmid=22139914}}</ref><ref>{{Cite journal |last1=Montague |first1=Elizabeth |last2=Janko |first2=Imre |last3=Stanberry |first3=Larissa |last4=Lee |first4=Elaine |last5=Choiniere |first5=John |last6=Anderson |first6=Nathaniel |last7=Stewart |first7=Elizabeth |last8=Broomall |first8=William |last9=Higdon |first9=Roger |last10=Kolker |first10=Natali |last11=Kolker |first11=Eugene |date=2015-01-28 |title=Beyond protein expression, MOPED goes multi-omics |url=http://academic.oup.com/nar/article/43/D1/D1145/2439032/Beyond-protein-expression-MOPED-goes-multiomics |journal=Nucleic Acids Research |language=en |volume=43 |issue=D1 |pages=D1145–D1151 |doi=10.1093/nar/gku1175 |issn=1362-4962 |pmc=4383969 |pmid=25404128}}</ref>

== References ==

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== Further reading ==

{{refbegin}}

* {{cite journal |vauthors=Stelzer authorG, =Dalah KolkerI, EStein TI, HigdonSatanower RY, HaynesRosen WN, WelchNativ N, Oz-Levi D, BroomallOlender WT, LancetBelinky DF, StanberryBahir LI, Krug H, Perco P, Mayer B, Kolker NE, Safran M, Lancet D | title = MOPED:In-silico Modelhuman Organismgenomics Proteinwith Expression DatabaseGeneCards | journal = NucleicHum. Acids Res.Genomics | volume = 405 | issue = Database issue6 | pages = D1093–9709–17 |date=JanOctober 20122011 | pmid = 2213991422155609 | pmc = 32450403525253 | doi = 10.10931186/nar/gkr11771479-7364-5-6-709 | urldoi-access = free }}

* {{cite journal | author = Kolker E, Higdon R, Morgan P, Sedensky M, Welch D, Bauman A, Stewart E, Haynes W, Broomall W, Kolker N | title = SPIRE: Systematic protein investigative research environment | journal = J Proteomics | volume = 75 | issue = 1 | pages = 122–6 |date=December 2011 | pmid = 21609792 | doi = 10.1016/j.jprot.2011.05.009 }}

* {{cite journal | author = 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 | title = In-silico human genomics with GeneCards | journal = Hum. Genomics | volume = 5 | issue = 6 | pages = 709–17 |date=October 2011 | pmid = 22155609 | pmc = 3525253 | doi = | url = }}

{{refend}}

[[Category:Biological databases]]

[[Category:Proteomics]]

[[Category:Omics]]