Multi-Omics Profiling Expression Database: Difference between revisions

Revision as of 14:23, 3 January 2013

Latest revision as of 18:01, 3 December 2023

(36 intermediate revisions by 21 users not shown)

Line 1:

{{infobox biodatabase

<!-- Please do not remove or change this AfD message until the issue is settled -->

{{Article for deletion/dated|page=Model Organism Protein Expression Database|timestamp=20130102183945|year=2013|month=January|day=2|substed=yes|help=off}}

<!-- For administrator use only: {{Old AfD multi|page=Model Organism Protein Expression Database|date=2 January 2013|result='''keep'''}} -->

<!-- End of AfD message, feel free to edit beyond this point -->

{{infobox_biodatabase

|title = MOPED

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

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

|description =

|scope =

|scope = Model Organism Protein Expression Database

|organism =

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

|laboratory =

|author = EugeneRoger KolkerHigdon

|pmidcitation = Higdon R, ''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 | year date=Jan 2012 | month = January2014 | pmid = 22139914 | pmc = 324504024350770 | doi = 10.10931021/nar/gkr1177pr400884c | url pmc=4039175 }}</ref>

|released = 2012

|standard =

|format =

|url = http[https://mopedwww.proteinspire.org/MOPED/ MOPED]

|download =

|webservice =

Line 30 ⟶ 26:

|version=

}}

The '''Multi-Omics Profiling Expression Database''' ('''MOPED''') was an expanding [[Multiomics|multi-omics]] resource that supports rapid browsing of [[transcriptomics]] and [[proteomics]] information from publicly available studies on [[model organism]]s and humans.<ref>{{cite journal |vauthors=Kolker E, Higdon R, Haynes W, Welch D, Broomall W, Lancet D, Stanberry L, Kolker N | title = MOPED: Model Organism Protein Expression Database | journal = Nucleic Acids Res. | volume = 40 | issue = Database issue | pages = D1093–9 |date=Jan 2012 | pmid = 22139914 | pmc = 3245040 | doi = 10.1093/nar/gkr1177 }}</ref> As to date (2021) it has ceased activities and is unaccessible online.<ref>{{cite web |url=https://www.proteinspire.org/MOPED/ |title=Start Moped Web Application |website=www.proteinspire.org |url-status=dead |archive-url=https://web.archive.org/web/20140422231720/https://www.proteinspire.org/MOPED/ |archive-date=2014-04-22}} </ref>

The '''Model Organism Protein Expression Database''' (MOPED) is an expanding proteomics resource that supports rapid browsing of protein expression information from publicly available studies on model organisms and humans. MOPED is designed to simplify the comparison and sharing of proteomics data for the greater research community. MOPED employs the standardized analysis pipeline [https://www.proteinspire.org/ SPIRE] to uniquely provide protein level expression data, meta- analysis capabilities and quantitative data. Data can be queried for specific proteins, 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]], [http://www.pantherdb.org/ Panther], [[Entrez]], [[UniProt]], [[KEGG]], [http://www.theseed.org/wiki/Home_of_the_SEED SEED], and [[Reactome]]. Protein identifiers are integrated from GeneCards (cross-referenced with MOPED), [[Genbank|GI]], [[RefSeq]], [http://www.ebi.ac.uk/ena/about/locus_tag Locus Tag], [[UniProt]], [[WormBase]], and [[Saccharomyces Genome Database|SGD]]. The current version of MOPED (MOPED 2.0, 2012) 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 [http://kolkerlab.proteinspire.org/ Kolker] team at [http://www.seattlechildrens.org/research/ Seattle Children's Research Institute].

==Systematic Protein Investigative Research Environment==

TheMOPED '''Modelis Organismdesigned Proteinto Expressionsimplify Database'''the comparison and sharing of data for the greater research community. (MOPED) isemploys anthe expandingstandardized proteomicsanalysis resourcepipeline that[[Systematic supportsProtein rapidInvestigative browsingResearch ofEnvironment|SPIRE]]<ref>{{cite proteinjournal expression|vauthors=Kolker informationE, fromHigdon publiclyR, availableMorgan studiesP, onSedensky modelM, organismsWelch andD, humans.Bauman MOPEDA, isStewart designedE, toHaynes simplifyW, theBroomall comparisonW, andKolker sharingN of| proteomicstitle data= forSPIRE: theSystematic greaterprotein investigative research community.environment MOPED| employsjournal the= standardizedJ analysisProteomics pipeline| volume [https:= 75 | issue = 1 | pages = 122–6 |date=December 2011 | pmid = 21609792 | doi = 10.1016//wwwj.proteinspirejprot.org2011.05.009 }}</ SPIRE]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]], [http://www.pantherdb.org/ Panther], [[Entrez]], [[UniProt]], [[KEGG]], [http://www.theseed.org/wiki/Home_of_the_SEED SEED], and [[Reactome]]. Protein and gene identifiers are integrated from GeneCards (cross-referenced with MOPED), [[Genbank|GI]], [[RefSeq]], [http://www.ebi.ac.uk/ena/about/locus_tag Locus Tag], [[UniProt]], [[WormBase]], and [[Saccharomyces Genome Database| (SGD]]). The current version of MOPED (MOPED 2.05, 20122014) contains overapproximately 430005 proteinsmillion withtotal atrecords leastincluding one~260 spectral matchexperiments and more than 11 million high certainty~390 spectraconditions. MOPED is developed and supported by the [http://kolkerlab.proteinspire.org/ Kolker] team at [http://www.seattlechildrens.org/research/ [Seattle Children's Research Institute]].

|scope = =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 ==

Line 36 ⟶ 38:

== Further reading ==

{{refbegin}}

* {{cite journal |vauthors=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 = 10.1186/1479-7364-5-6-709 | doi-access = free }}

Kolker E, et al, MOPED: Model Organism Protein Expression Database, Nucleic Acids Research, 2012, 40(D1): 1093-1099. PMID 22139914

{{refend}}

Kolker E, et al, SPIRE: Systematic Protein Investigative Research Environment, Journal of Proteomics, 2011, 75(1): 122-126. PMID 21609792

Stelzer G, et al, In-silico human genomics with GeneCards, Human Genomics, 2011, 5(6): 709–717. PMID 22155609

[[Category:Biological databases]]

[[Category:Proteomics]]

[[Category:Omics]]