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 = EugeneRoger KolkerHigdon

|pmidcitation = KolkerHigdon ER, ''et al''. <ref name="pmid22139914pmid24350770">{{cite journal |author1=Higdon authorR |author2= KolkerStewart E, Higdon|author3=Stanberry R,L |author4=Haynes W, Welch|author5=Choiniere D,J |author6=Montague E |author7=Anderson N |author8=Yandl Y |author9=Janko I |author10=Broomall W, |author11=Fishilevich S |author12=Lancet D, Stanberry L, |author13=Kolker N |author14=Eugene Kolker. | title = MOPED: Modelenables Organismdiscoveries Proteinthrough Expressionconsistently Databaseprocessed proteomics data. | journal = NucleicJ AcidsProteome Res. | volume = 4013 | issue = Database issue1 | pages = D1093–9107–113 |date=JanuaryJan 20122014 | pmid = 22139914 | pmc = 324504024350770 | doi = 10.10931021/nar/gkr1177pr400884c | url pmc=4039175 }}</ref>

|released = 2012

|standard =

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|version=

}}

The '''Multi-Omics Profiling Expression Database''' ('''MOPED''') iswas an expanding mulit[[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 sharingD, ofBroomall dataW, forLancet theD, greaterStanberry researchL, community.Kolker MOPEDN employs| thetitle standardized= analysis pipeline [httpsMOPED://www.proteinspire.org/ SPIRE]Model toOrganism uniquelyProtein provideExpression proteinDatabase level| expressionjournal data,= meta-Nucleic analysisAcids capabilitiesRes. and| quantitativevolume data.= Data40 can| beissue queried= forDatabase specificissue proteins| andpages gene,= browsedD1093–9 based|date=Jan on2012 organism,| tissue,pmid localization= and22139914 condition| andpmc sorted= by3245040 false| discoverydoi rate= and expression10.1093/nar/gkr1177 MOPED}}</ref> empowers usersAs to visualizedate their own expression data and compare(2021) it withhas existingceased studies. Further, MOPED links to various proteinactivities and pathwayis data-unaccessible bases,online.<ref>{{cite includingweb [[GeneCards]], [http|url=https://www.pantherdbproteinspire.org/MOPED/ Panther],|title=Start [[Entrez]],Moped [[UniProt]],Web [[KEGG]],Application [http://|website=www.theseedproteinspire.org/wiki/Home_of_the_SEED SEED], and [[Reactome]]. Protein identifiers are integrated from GeneCards (cross|url-referencedstatus=dead with MOPED), [[Genbank|GI]], [[RefSeq]], [httparchive-url=https://wwwweb.ebiarchive.ac.ukorg/enaweb/about20140422231720/locus_tag Locus Tag], [[UniProt]], [[WormBase]], and [[Saccharomyces Genome Database|SGD]]. The current version of MOPED (MOPED 2.5, 2014) contains over 43000 proteins with at least one spectral match and more than 11 million high certainty spectra. MOPED is developed and supported by the [httphttps://kolkerlabwww.proteinspire.org/MOPED/ Kolker]|archive-date=2014-04-22}} team at [http:<//www.seattlechildrens.org/research/ Seattle 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 | author vauthors=Stelzer HigdonG, RDalah I, StewartStein ETI, StanberrySatanower LY, HaynesRosen WN, ChoiniereNativ JN, MontagueOz-Levi ED, AndersonOlender NT, YandlBelinky YF, JankoBahir I, BroomallKrug WH, FishilevichPerco SP, LancetMayer DB, Kolker NE, EugeneSafran Kolker.M, Lancet D | title = MOPEDIn-silico enableshuman discoveriesgenomics throughwith consistently processed proteomics data.GeneCards | journal = J ProteomeHum. ResGenomics | volume = 135 | issue = 16 | pages = 107-113709–17 |date=JanOctober 20142011 | pmid = 2435077022155609 | pmc = 3525253 | doi = 10.10211186/pr400884c1479-7364-5-6-709 | doi-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]]