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

Laurila, Kirsti; Autio, Reija; Kong, Lingjia; Närvä, Elisa; Hussein, Samer; Otonkoski, Timo; Lahesmaa, Riitta; Lähdesmäki, Harri (2014)

 
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Laurila, Kirsti
Autio, Reija
Kong, Lingjia
Närvä, Elisa
Hussein, Samer
Otonkoski, Timo
Lahesmaa, Riitta
Lähdesmäki, Harri
2014

BioData Mining 7 1
32
Terveystieteiden yksikkö - School of Health Sciences
This publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited.
doi:10.1186/s13040-014-0032-2
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Julkaisun pysyvä osoite on
https://urn.fi/URN:NBN:fi:uta-201502031051

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BioMed Central open access
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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.
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