title: Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells.
abstract: BACKGROUND
  Human genomic variations, including single nucleotide polymorphisms (SNPs) and copy number variations (CNVs), are associated with several phenotypic traits varying from mild features to hereditary diseases. Several genome-wide studies have reported genomic variants that correlate with gene expression levels in various tissue and cell types.
  
  
  RESULTS
  We studied human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) measuring the SNPs and CNVs with Affymetrix SNP 6 microarrays and expression values with Affymetrix Exon microarrays. We computed the linear relationships between SNPs and expression levels of exons, transcripts and genes, and the associations between gene CNVs and gene expression levels. Further, for a few of the resulted genes, the expression value was associated with both CNVs and SNPs. Our results revealed altogether 217 genes and 584 SNPs whose genomic alterations affect the transcriptome in the same cells. We analyzed the enriched pathways and gene ontologies within these groups of genes, and found out that the terms related to alternative splicing and development were enriched.
  
  
  CONCLUSIONS
  Our results revealed that in the human pluripotent stem cells, the expression values of several genes, transcripts and exons were affected due to the genomic variation.
authors: Department of Information and Computer Science, Aalto University School of Science, Espoo, Finland.
authors: Kirsti
authors: K
authors: Laurila
authors: Department of Signal Processing, Tampere University of Technology, Tampere, Finland.|School of Health Sciences, University of Tampere, Tampere, Finland.
authors: Reija
authors: R
authors: Autio
authors: Department of Signal Processing, Tampere University of Technology, Tampere, Finland.|Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
authors: Lingjia
authors: L
authors: Kong
authors: Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
authors: Elisa
authors: E
authors: Närvä
authors: Samuel Lunenfeld Research Institute, Toronto, Canada.|Research Program Unit, Molecular Neurology, Biomedicum Stem Cell Center, University of Helsinki, Helsinki, Finland.
authors: Samer
authors: S
authors: Hussein
authors: Research Program Unit, Molecular Neurology, Biomedicum Stem Cell Center, University of Helsinki, Helsinki, Finland.
authors: Timo
authors: T
authors: Otonkoski
authors: Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
authors: Riitta
authors: R
authors: Lahesmaa
authors: Department of Information and Computer Science, Aalto University School of Science, Espoo, Finland.|Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
authors: Harri
authors: H
authors: Lähdesmäki
keywords: Association analysis; CNV; Exon expression; Gene expression; SNP; Transcript expression; hESC; hiPSC
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