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Whole-genome expression analysis in the third instar larval midgut of Drosophila melanogaster.

Harrop TW, Pearce SL, Daborn PJ, Batterham P - G3 (Bethesda) (2014)

Bottom Line: The data support functional diversification in subsections of the midgut.Analysis of the expression of gene families that are implicated in the metabolism of xenobiotics suggests that metabolism may not be uniform along the midgut.These data provide a starting point for investigating gene expression and xenobiotic metabolism and other functions of the larval midgut.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia twharrop@gmail.com p.batterham@unimelb.edu.au.

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Multidimensional scaling (MDS) of standardized, log-transformed FPKM values of clustered genes, scaled by α, which is the gene’s membership value for the cluster to which it was assigned, larger points having α values closer to 1. The clusters are supported by the MDS analysis. FPKM, Fragments per kilobase of exon per million fragments mapped.
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fig2: Multidimensional scaling (MDS) of standardized, log-transformed FPKM values of clustered genes, scaled by α, which is the gene’s membership value for the cluster to which it was assigned, larger points having α values closer to 1. The clusters are supported by the MDS analysis. FPKM, Fragments per kilobase of exon per million fragments mapped.

Mentions: To investigate the patterns of gene expression in the subsections of the midgut, fuzzy C-means clustering was performed on standardized, log-transformed FPKM values from a subset of highly expressed genes with variable expression. To construct this gene set, genes with FPKM > 5 in any section or mean FPKM > 3 across all sections (6315 genes) were ranked by variance across all sections, and the top 20% were retained for fuzzy C-means analysis (1263 genes). The retained genes define 8 clusters with differing patterns of expression along the length of the midgut (Figure 1). Multidimensional scaling of a distance matrix of standardized, log-transformed FPKM values (i.e. principal component analysis) supports the separation of the expression clusters (Figure 2). The expression of genes in some clusters reflects the divisions between the anterior, middle, and posterior midgut, corresponding to known physiological or morphological distinctions, and the differential patterns of gene expression indicate that the subsections of the third instar larval midgut may have differences in function. For example, genes in cluster 1 are enriched in the anterior midgut and more lowly expressed in the middle and posterior midgut, whereas cluster 8 contains genes expressed in the posterior and middle midgut. Cluster 5 may reveal differences of expression in morphologically indistinguishable compartments of the larval midgut, as it contains genes specifically expressed in M12–13 but not the other sections of the anterior midgut.


Whole-genome expression analysis in the third instar larval midgut of Drosophila melanogaster.

Harrop TW, Pearce SL, Daborn PJ, Batterham P - G3 (Bethesda) (2014)

Multidimensional scaling (MDS) of standardized, log-transformed FPKM values of clustered genes, scaled by α, which is the gene’s membership value for the cluster to which it was assigned, larger points having α values closer to 1. The clusters are supported by the MDS analysis. FPKM, Fragments per kilobase of exon per million fragments mapped.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4232545&req=5

fig2: Multidimensional scaling (MDS) of standardized, log-transformed FPKM values of clustered genes, scaled by α, which is the gene’s membership value for the cluster to which it was assigned, larger points having α values closer to 1. The clusters are supported by the MDS analysis. FPKM, Fragments per kilobase of exon per million fragments mapped.
Mentions: To investigate the patterns of gene expression in the subsections of the midgut, fuzzy C-means clustering was performed on standardized, log-transformed FPKM values from a subset of highly expressed genes with variable expression. To construct this gene set, genes with FPKM > 5 in any section or mean FPKM > 3 across all sections (6315 genes) were ranked by variance across all sections, and the top 20% were retained for fuzzy C-means analysis (1263 genes). The retained genes define 8 clusters with differing patterns of expression along the length of the midgut (Figure 1). Multidimensional scaling of a distance matrix of standardized, log-transformed FPKM values (i.e. principal component analysis) supports the separation of the expression clusters (Figure 2). The expression of genes in some clusters reflects the divisions between the anterior, middle, and posterior midgut, corresponding to known physiological or morphological distinctions, and the differential patterns of gene expression indicate that the subsections of the third instar larval midgut may have differences in function. For example, genes in cluster 1 are enriched in the anterior midgut and more lowly expressed in the middle and posterior midgut, whereas cluster 8 contains genes expressed in the posterior and middle midgut. Cluster 5 may reveal differences of expression in morphologically indistinguishable compartments of the larval midgut, as it contains genes specifically expressed in M12–13 but not the other sections of the anterior midgut.

Bottom Line: The data support functional diversification in subsections of the midgut.Analysis of the expression of gene families that are implicated in the metabolism of xenobiotics suggests that metabolism may not be uniform along the midgut.These data provide a starting point for investigating gene expression and xenobiotic metabolism and other functions of the larval midgut.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia twharrop@gmail.com p.batterham@unimelb.edu.au.

Show MeSH
Related in: MedlinePlus