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

doi:10.1186/s13040-014-0032-2

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

Department of Computer Science

Research output: Contribution to journal › Article › Scientific › peer-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 language	English
Article number	32
Number of pages	16
Journal	BioData Mining
Volume	7
DOIs	https://doi.org/10.1186/s13040-014-0032-2
Publication status	Published - 13 Dec 2014
MoE publication type	A1 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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1186/s13040-014-0032-2

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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.",

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author = "Kirsti Laurila and Reija Autio and Lingjia Kong and Elisa N{\"a}rv{\"a} and Samer Hussein and Timo Otonkoski and Riitta Lahesmaa and Harri L{\"a}hdesm{\"a}ki",

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doi = "10.1186/s13040-014-0032-2",

language = "English",

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journal = "BioData Mining",

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T1 - Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells

AU - Laurila, Kirsti

AU - Autio, Reija

AU - Kong, Lingjia

AU - Närvä, Elisa

AU - Hussein, Samer

AU - Otonkoski, Timo

AU - Lahesmaa, Riitta

AU - Lähdesmäki, Harri

PY - 2014/12/13

Y1 - 2014/12/13

N2 - 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.

AB - 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.

KW - hESC

KW - hiPSC

KW - Association analysis

KW - SNP

KW - CNV

KW - Gene expression

KW - Exon expression

KW - Transcript expression

KW - EXPRESSION MICROARRAY ANALYSES

KW - RESOLUTION COPY NUMBER

KW - GENE-EXPRESSION

KW - TARGET GENES

KW - PROBE LEVEL

KW - ARRAY DATA

KW - DENSITY

KW - BIOINFORMATICS

KW - NORMALIZATION

U2 - 10.1186/s13040-014-0032-2

DO - 10.1186/s13040-014-0032-2

M3 - Article

SN - 1756-0381

VL - 7

JO - BioData Mining

JF - BioData Mining

M1 - 32

ER -

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

Abstract

Keywords

UN SDGs

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