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Comparison of strategies for identification of regulatory quantitative trait loci of transcript expression traits.

Franceschini N, Wojczynski MK, Göring HH, Peralta JM, Dyer TD, Li X, Li H, North KE - BMC Proc (2007)

Bottom Line: Seventy-six percent of transcripts had a significant heritability and 54% of them had LOD score >or= 1.8.Bivariate genetic analysis of 15 transcripts that had co-localized QTLs on 4q28.2-q31.1 identified significant genetic correlation among some transcripts although no improvement in the magnitude of LOD scores in this region was noted.Similar results were found in analysis of 12 transcripts, that had co-localized QTLs in the 13q34 region.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Epidemiology, University of North Carolina Chapel Hill, Bank of America Center, 137 East Franklin Street, Suite 306, CB #8050, Chapel Hill, North Carolina 27514, USA. noraf@unc.edu

ABSTRACT
In order to identify regulatory genes, we determined the heritability of gene transcripts, performed linkage analysis to identify quantitative trait loci (QTLs), and evaluated the evidence for shared genetic effects among transcripts with co-localized QTLs in non-diseased participants from 14 CEPH (Centre d'Etude du Polymorphisme Humain) Utah families. Seventy-six percent of transcripts had a significant heritability and 54% of them had LOD score >or= 1.8. Bivariate genetic analysis of 15 transcripts that had co-localized QTLs on 4q28.2-q31.1 identified significant genetic correlation among some transcripts although no improvement in the magnitude of LOD scores in this region was noted. Similar results were found in analysis of 12 transcripts, that had co-localized QTLs in the 13q34 region. Principal-component analyses did not improve the ability to identify chromosomal regions of co-localized gene expressions.

No MeSH data available.


Related in: MedlinePlus

Chromosome 4 co-localized gene transcripts univariate and bivariate analyses results (n = 15 transcripts). Each box has the transcript name (in bold) and the univariate transcript LOD score. Genetic correlation (ρG) between two transcripts and p-values are displayed in the outside box along with the bivariate LOD scores. We found two potential networks of regulatory genes among 15 co-expressed transcripts on the 4q28.2 to 4q31.1 region. Five transcripts did not have significant genetic correlation with any other transcript and are not included in this graph.
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Figure 1: Chromosome 4 co-localized gene transcripts univariate and bivariate analyses results (n = 15 transcripts). Each box has the transcript name (in bold) and the univariate transcript LOD score. Genetic correlation (ρG) between two transcripts and p-values are displayed in the outside box along with the bivariate LOD scores. We found two potential networks of regulatory genes among 15 co-expressed transcripts on the 4q28.2 to 4q31.1 region. Five transcripts did not have significant genetic correlation with any other transcript and are not included in this graph.

Mentions: We then performed bivariate analysis of all pairwise co-localized transcripts on 4q28.2-q31.1 and found evidence for genetic correlation of co-localized genes, although without much increase in the magnitude of the LOD score (Figure 1). This analysis identified two networks of gene expressions (Figure 1). We obtained two factors using PCA of the first network (Group 1, SNX4, YWHAQ, ASS, MX2, and ISGF3G gene transcripts). Both factors had significant heritability; however, only Factor 1, loading heavily on the MX2 gene, localized to the 4q28.2-q31.1 region (Table 1), and the magnitude of the LOD score was lower than that of the univariate MX2 gene transcript analysis (LOD = 2.28). The heritability of one factor obtained using PCA for Group 2 transcripts was not significant and further analysis was not performed.


Comparison of strategies for identification of regulatory quantitative trait loci of transcript expression traits.

Franceschini N, Wojczynski MK, Göring HH, Peralta JM, Dyer TD, Li X, Li H, North KE - BMC Proc (2007)

Chromosome 4 co-localized gene transcripts univariate and bivariate analyses results (n = 15 transcripts). Each box has the transcript name (in bold) and the univariate transcript LOD score. Genetic correlation (ρG) between two transcripts and p-values are displayed in the outside box along with the bivariate LOD scores. We found two potential networks of regulatory genes among 15 co-expressed transcripts on the 4q28.2 to 4q31.1 region. Five transcripts did not have significant genetic correlation with any other transcript and are not included in this graph.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2367462&req=5

Figure 1: Chromosome 4 co-localized gene transcripts univariate and bivariate analyses results (n = 15 transcripts). Each box has the transcript name (in bold) and the univariate transcript LOD score. Genetic correlation (ρG) between two transcripts and p-values are displayed in the outside box along with the bivariate LOD scores. We found two potential networks of regulatory genes among 15 co-expressed transcripts on the 4q28.2 to 4q31.1 region. Five transcripts did not have significant genetic correlation with any other transcript and are not included in this graph.
Mentions: We then performed bivariate analysis of all pairwise co-localized transcripts on 4q28.2-q31.1 and found evidence for genetic correlation of co-localized genes, although without much increase in the magnitude of the LOD score (Figure 1). This analysis identified two networks of gene expressions (Figure 1). We obtained two factors using PCA of the first network (Group 1, SNX4, YWHAQ, ASS, MX2, and ISGF3G gene transcripts). Both factors had significant heritability; however, only Factor 1, loading heavily on the MX2 gene, localized to the 4q28.2-q31.1 region (Table 1), and the magnitude of the LOD score was lower than that of the univariate MX2 gene transcript analysis (LOD = 2.28). The heritability of one factor obtained using PCA for Group 2 transcripts was not significant and further analysis was not performed.

Bottom Line: Seventy-six percent of transcripts had a significant heritability and 54% of them had LOD score >or= 1.8.Bivariate genetic analysis of 15 transcripts that had co-localized QTLs on 4q28.2-q31.1 identified significant genetic correlation among some transcripts although no improvement in the magnitude of LOD scores in this region was noted.Similar results were found in analysis of 12 transcripts, that had co-localized QTLs in the 13q34 region.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Epidemiology, University of North Carolina Chapel Hill, Bank of America Center, 137 East Franklin Street, Suite 306, CB #8050, Chapel Hill, North Carolina 27514, USA. noraf@unc.edu

ABSTRACT
In order to identify regulatory genes, we determined the heritability of gene transcripts, performed linkage analysis to identify quantitative trait loci (QTLs), and evaluated the evidence for shared genetic effects among transcripts with co-localized QTLs in non-diseased participants from 14 CEPH (Centre d'Etude du Polymorphisme Humain) Utah families. Seventy-six percent of transcripts had a significant heritability and 54% of them had LOD score >or= 1.8. Bivariate genetic analysis of 15 transcripts that had co-localized QTLs on 4q28.2-q31.1 identified significant genetic correlation among some transcripts although no improvement in the magnitude of LOD scores in this region was noted. Similar results were found in analysis of 12 transcripts, that had co-localized QTLs in the 13q34 region. Principal-component analyses did not improve the ability to identify chromosomal regions of co-localized gene expressions.

No MeSH data available.


Related in: MedlinePlus