Noob Enrichment Tsom xam yog ib txoj kev mus kom ze rau lub tsom xam cov noob qhia profile cov ntaub ntawv thiab tau piav nyob rau hauv ib lub Ntawv Los ntawm cov neeg ua hauj lwm hauv lub koom haum Broad lub koom haum.
Lub tswvyim yooj yim yog prompted los ntawm txoj kev soj ntsuam uas kawm noob caj noob ces Uas qhia qhov tseem ceeb tshaj plaws nyob rau hauv qhia theem ntawm ob lub xeev los yog phenotypes yog tsis muaj mechanistic pom. tiag mas, Nws ua rau kev txiav txim zoo coj ib tug noob sib koom ib txhia txuas nrog kev txuas mus los, thiab nug cov lus nug – yog qhov tseem ceeb tshaj plaws qhia tej txheeb cais tseem ceeb enrichment Nyob rau hauv cov noob uas muaj ntau yam qhia?
A noob xaiv tau, ua ntej, rau ntau yam e.g. Lub noob noob paub tias yuav tsum cawv los ntawm- los yog under-expression ntawm ib micro-RNA, los yog saib tsam ib txheej xaiv raws li chromosomal qhov chaw, los yog noob uas molecular function, cellular tivthaiv thiab / los yog tej yam uas tau muab siv cov lus los ntawm cov lus no Noob Ontology.
Ib kom zoo dua rau txoj kev GSEA yog tias nws tseem tau incorporate koj teev tseg, Tsis yog cov transcripts nrog ib arbitrarily xaiv txawv expression Harbor. Kuv paub tseeb tias muaj coob tus neeg nyeem qhov no yuav xav – "Yuav ua li cas thiaj siv tau cov ntaub ntawv tag nrho cov ntaub ntawv? Feem ntau kuv yuav tsuas xav txog noob nrog >2 (LOS YOG lwm favourite tus nqi)-kev qhia txawv." Yog vim li cas txoj kev yog valid yog tias noob expressed ntawm qib qis los yog nrog variance loj ntawm replicates tsis contribute rau lub ntsiab metric siv los ntawm GSEA, 'qhab nees’ (ES).
GSEA tej hauj lwm los ntawm thawj zaug ranking tus nqi qhia rau txhua lub noob los ntawm teeb liab sib piv – xam qhov txawv ntawm qhov tseem ceeb ntawm cov qauv uas sawv cev rau txhua phenotype thiab scaling lawv los ntawm qhov uas cov qauv deviations. Qhov no txhais tau tias noob uas loj sib txawv hauv qhia theem ntawm lub xeev sib txawv thiab me variation ntawm biological replicates yog ranked mas.
Kauj ruam tom ntej yog tias cov ES, Tus thawj txheeb cais generated los ntawm GSEA, xam tau tias yog ib qho uas teev tseg – hauv tus kab mob GSEA manual, Cov ntaub ntawv software excellently, nws lub xeev:
"Tag nrho cov noob yog xub ranked los ntawm lawv lub teeb liab rau nrov piv, Ces tus ES yog xam los ntawm "taug kev" cia lub ranked daim ntawv teev cov noob ua kom a khiav-summ txheeb cais thaum lub noob yog nyob rau hauv lub noob txheej thiab kev xav nws tseem tsis tau. Qhov no magnitude Qhov increment nyob ntawm seb tus kab mob increment nyob ntawm seb correlation Lub noob uas muaj ib tug nraj. Tus ES yog qhov ntau deviation ntawm xoom ces yuav tsum taug kev hauv daim ntawv. A Positive ES indicates noob enrichment ntawm tus saum toj kawg nkaus daim ntawv ranked; a Negative ES indicates noob enrichment ntawm tus Qab ranked npe."
Qhov tseem ceeb tshaj plaws yog qhov tseem ceeb tshaj plaws normalised Raws li noob teeb loj thiab ces ib tug cuav xwm xam tias yog xam tau tias yog, muab tus kwv yees li ntawm cuav xwm. GSEA siv ib tug heev so default tus nqi ntawm 25%, Nws yog suitable rau hypothesis tiam nrog ib tug kuj loj biological replicates.
Zaum ua hauj lwm rau cov ntaub ntawv los ntawm tib neeg Qauv tseem siv tau GSEA, tiam sis yuav tsum tautauware – noob cim GSEA yog ib tug neeg siv GSEA.txhais lus" Los ntawm lawv haiv neeg sib npaug zos.. identifiers siv rau noob los ntawm koj hom paj uas muaj tuaj rau lub microarray yog converted rau hauv cov cim rau lawv tib neeg orthologues, Ces siv nyob rau hauv cov tsom xam. Subramanian thiab lug txhawb cov miv thov tias no conversion muaj tsawg los yog tsis nyhuv hlauv taws xob ntawm GSEA; Nws tau siv ntse nyob rau ntau hom uas tsis yog-tib neeg hom, Tiam sis tau kawg no yuav tsum tau khaws nco thaum investigating tau paub meej.
Rau ib excellent, qhov tob, ntsuam xyuas txog tej cuab yeej uas muaj cuab yeej, tham:
Lwm qhov zoo ntawm tswv yim txog pathway tsom xam, Tshwj xeeb tshaj yog rau cov paub cov R txheeb cais pob yog ntawm no.
nyeem ntawv ntxiv
Ib tug Trackback
[...] data genome-wide for differentially-expressed transcripts. Using the Broad Institute’s marvellous GSEA tool, I assessed the statistical evidence that specific Gene Ontology terms and pathways were [...]