Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells

Kirsti Laurila, Reija Autio*, Lingjia Kong, Elisa Närvä, Samer Hussein, Timo Otonkoski, Riitta Lahesmaa, Harri Lähdesmäki

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

2 Citations (Scopus)

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.

Original languageEnglish
Article number32
Number of pages16
JournalBIODATA MINING
Volume7
DOIs
Publication statusPublished - 13 Dec 2014
MoE publication typeA1 Journal article-refereed

Keywords

  • hESC
  • hiPSC
  • Association analysis
  • SNP
  • CNV
  • Gene expression
  • Exon expression
  • Transcript expression
  • EXPRESSION MICROARRAY ANALYSES
  • RESOLUTION COPY NUMBER
  • GENE-EXPRESSION
  • TARGET GENES
  • PROBE LEVEL
  • ARRAY DATA
  • DENSITY
  • BIOINFORMATICS
  • NORMALIZATION

Cite this