J Integr Bioinform - Knowledge enrichment analysis for human tissue-specific genes uncover new biological insights.

Tópicos

{ gene(2352) biolog(1181) express(1162) }
{ cancer(2502) breast(956) screen(824) }
{ first(2504) two(1366) second(1323) }
{ concept(1167) ontolog(924) domain(897) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ activ(1138) subject(705) human(624) }
{ inform(2794) health(2639) internet(1427) }
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{ intervent(3218) particip(2042) group(1664) }
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{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
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{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
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{ signal(2180) analysi(812) frequenc(800) }
{ sampl(1606) size(1419) use(1276) }
{ data(3008) multipl(1320) sourc(1022) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
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{ high(1669) rate(1365) level(1280) }
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{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }

Resumo

The expression and regulation of genes in different tissues are fundamental questions to be answered in biology. Knowledge enrichment analysis for tissue specific (TS) and housekeeping (HK) genes may help identify their roles in biological process or diseases and gain new biological insights. In this paper, we performed the knowledge enrichment analysis for 17,343 genes in 84 human tissues using Gene Set Enrichment Analysis (GSEA) and Hypergeometric Analysis (HA) against three biological ontologies: Gene Ontology (GO), KEGG pathways and Disease Ontology (DO) respectively. The analyses results demonstrated that the functions of most gene groups are consistent with their tissue origins. Meanwhile three interesting new associations for HK genes and the skeletal muscle tissue genes are found. Firstly, Hypergeometric analysis against KEGG database for HK genes disclosed that three disease terms (Parkinson's disease, Huntington's disease, Alzheimer's disease) are intensively enriched. Secondly, Hypergeometric analysis against the KEGG database for Skeletal Muscle tissue genes shows that two cardiac diseases of "Hypertrophic cardiomyopathy (HCM)" and "Arrhythmogenic right ventricular cardiomyopathy (ARVC)" are heavily enriched, which are also considered as no relationship with skeletal functions. Thirdly, "Prostate cancer" is intensively enriched in Hypergeometric analysis against the disease ontology (DO) for the Skeletal Muscle tissue genes, which is a much unexpected phenomenon.

Resumo Limpo

express regul gene differ tissu fundament question answer biolog knowledg enrich analysi tissu specif ts housekeep hk gene may help identifi role biolog process diseas gain new biolog insight paper perform knowledg enrich analysi gene human tissu use gene set enrich analysi gsea hypergeometr analysi ha three biolog ontolog gene ontolog go kegg pathway diseas ontolog respect analys result demonstr function gene group consist tissu origin meanwhil three interest new associ hk gene skelet muscl tissu gene found first hypergeometr analysi kegg databas hk gene disclos three diseas term parkinson diseas huntington diseas alzheim diseas intens enrich second hypergeometr analysi kegg databas skelet muscl tissu gene show two cardiac diseas hypertroph cardiomyopathi hcm arrhythmogen right ventricular cardiomyopathi arvc heavili enrich also consid relationship skelet function third prostat cancer intens enrich hypergeometr analysi diseas ontolog skelet muscl tissu gene much unexpect phenomenon

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