Multi-Omics Profiling Expression Database: Difference between revisions

Revision as of 05:20, 28 April 2014

Latest revision as of 18:01, 3 December 2023

(21 intermediate revisions by 17 users not shown)

Line 1:

{{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 =

Line 27 ⟶ 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 '''Multi-Omics Profiling Expression Database''' ('''MOPED''') is an expanding multi-omics resource that supports rapid browsing of transcriptomics and proteomics information from publicly available studies on model organisms and humans. MOPED is designed to simplify the comparison and 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 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 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions. 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==

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

TheMOPED '''Multi-Omicsis Profilingdesigned Expressionto Database'''simplify the comparison and sharing of data for the greater research community. ('''MOPED''') isemploys anthe expandingstandardized multi-omicsanalysis resourcepipeline that[[Systematic supportsProtein rapidInvestigative browsingResearch ofEnvironment|SPIRE]]<ref>{{cite transcriptomicsjournal and|vauthors=Kolker proteomicsE, informationHigdon fromR, publiclyMorgan availableP, studiesSedensky onM, modelWelch organismsD, andBauman humans.A, MOPEDStewart isE, designedHaynes toW, simplifyBroomall theW, comparisonKolker andN sharing| oftitle data= forSPIRE: theSystematic greaterprotein investigative research community.environment MOPED| employsjournal the= standardizedJ analysisProteomics pipeline| volume = 75 | issue = [https:1 | pages = 122–6 |date=December 2011 | pmid = 21609792 | doi = 10.1016//wwwj.proteinspirejprot.org/2011.05.009 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 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions. MOPED is developed and supported by the [http://kolkerlab.proteinspire.org/ Kolker] team at [http://www.seattlechildrens.org/research/ [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 ==

Line 36 ⟶ 39:

== 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]]