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Article: Consensus Comparative Analysis of Human Embryonic Stem Cell-Derived Cardiomyocytes

TitleConsensus Comparative Analysis of Human Embryonic Stem Cell-Derived Cardiomyocytes
Authors
Issue Date2015
PublisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.action
Citation
PLoS One, 2015, v. 10 n. 5, p. e0125442 How to Cite?
AbstractGlobal transcriptional analyses have been performed with human embryonic stem cells (hESC) derived cardiomyocytes (CMs) to identify molecules and pathways important for human CM differentiation, but variations in culture and profiling conditions have led to greatly divergent results among different studies. Consensus investigation to identify genes and gene sets enriched in multiple studies is important for revealing differential gene expression intrinsic to human CM differentiation independent of the above variables, but reliable methods of conducting such comparison are lacking. We examined differential gene expression between hESC and hESC-CMs from multiple microarray studies. For single gene analysis, we identified genes that were expressed at increased levels in hESC-CMs in seven data-sets and which have not been previously highlighted. For gene set analysis, we developed a new algorithm, consensus comparative analysis (CSSCMP), capable of evaluating enrichment of gene sets from heterogeneous data sources. Based on both theoretical analysis and experimental validation, CSSCMP is more efficient and less susceptible to experimental variations than traditional methods. We applied CSSCMP to hESC-CM microarray data and revealed novel gene set enrichment (e.g., glucocorticoid stimulus), and also identified genes that might mediate this response. Our results provide important molecular information intrinsic to hESC-CM differentiation. Data and Matlab codes can be downloaded from S1 Data.
Persistent Identifierhttp://hdl.handle.net/10722/218679
ISSN
2015 Impact Factor: 3.057
2015 SCImago Journal Rankings: 1.395
ISI Accession Number ID
Grants

 

DC FieldValueLanguage
dc.contributor.authorZhang, SH-
dc.contributor.authorPoon, E-
dc.contributor.authorXie, D-
dc.contributor.authorBoheler, KR-
dc.contributor.authorLi, RA-
dc.contributor.authorWong, HS-
dc.date.accessioned2015-09-18T06:50:01Z-
dc.date.available2015-09-18T06:50:01Z-
dc.date.issued2015-
dc.identifier.citationPLoS One, 2015, v. 10 n. 5, p. e0125442-
dc.identifier.issn1932-6203-
dc.identifier.urihttp://hdl.handle.net/10722/218679-
dc.description.abstractGlobal transcriptional analyses have been performed with human embryonic stem cells (hESC) derived cardiomyocytes (CMs) to identify molecules and pathways important for human CM differentiation, but variations in culture and profiling conditions have led to greatly divergent results among different studies. Consensus investigation to identify genes and gene sets enriched in multiple studies is important for revealing differential gene expression intrinsic to human CM differentiation independent of the above variables, but reliable methods of conducting such comparison are lacking. We examined differential gene expression between hESC and hESC-CMs from multiple microarray studies. For single gene analysis, we identified genes that were expressed at increased levels in hESC-CMs in seven data-sets and which have not been previously highlighted. For gene set analysis, we developed a new algorithm, consensus comparative analysis (CSSCMP), capable of evaluating enrichment of gene sets from heterogeneous data sources. Based on both theoretical analysis and experimental validation, CSSCMP is more efficient and less susceptible to experimental variations than traditional methods. We applied CSSCMP to hESC-CM microarray data and revealed novel gene set enrichment (e.g., glucocorticoid stimulus), and also identified genes that might mediate this response. Our results provide important molecular information intrinsic to hESC-CM differentiation. Data and Matlab codes can be downloaded from S1 Data.-
dc.languageeng-
dc.publisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.action-
dc.relation.ispartofPLoS One-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.titleConsensus Comparative Analysis of Human Embryonic Stem Cell-Derived Cardiomyocytes-
dc.typeArticle-
dc.identifier.emailBoheler, KR: bohelerk@hku.hk-
dc.identifier.emailLi, RA: ronaldli@HKUCC.hku.hk-
dc.identifier.authorityBoheler, KR=rp01884-
dc.identifier.authorityLi, RA=rp01352-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1371/journal.pone.0125442-
dc.identifier.pmid25938587-
dc.identifier.hkuros251600-
dc.identifier.volume10-
dc.identifier.issue5-
dc.identifier.spagee0125442-
dc.identifier.epagee0125442-
dc.identifier.isiWOS:000353943000069-
dc.publisher.placeUnited States-
dc.relation.projectCell-based Heart Regeneration-
dc.relation.projectEngineering Calcium Homeostasis of hESC-derived cardiomyocytes-
dc.relation.projectOntogenic combinatorial conditioning of 3D human pluripotent stem cell ventricular models for facilitated maturation-

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