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Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome.

Thévenin A, Ein-Dor L, Ozery-Flato M, Shamir R - Nucleic Acids Res. (2014)

Bottom Line: We find a significant concentration of functional groups both in terms of their distance within the same chromosome and in terms of their dispersal over several chromosomes.The result holds for all three types of functional groups that we tested.Hence, the human genome shows substantial concentration of functional groups within chromosomes and across chromosomes in space.

View Article: PubMed Central - PubMed

Affiliation: Genome Informatics, Faculty of Technology and Institute for Bioinformatics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld 33615, Germany IBM Research-Haifa, Mount Carmel, Haifa 3498825, Israel.

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Proximity criteria and pathway concentration. (a) Criteria for chromosome concentration of co-functioning genes. Circles correspond to genes and the red circles are all the members of a group with a common function. (i): concentration within a chromosome (intra-chromosomal). Here clustering/concentration is gauged based on pairwise linear distance (in base pairs or in the number of intervening genes) between co-functioning genes. (ii): dispersal across chromosomes (inter-chromosomal). Out of the 23 pairs of chromosomes, 18 do not contain the group's genes, so this group is concentrated in few chromosomes. This measure takes into account only the chromosomes on which the co-functioning genes reside and ignores the relative locations within each chromosome. (iii): concentration in the 3D space. Curved lines show positions of chromosomal segments in space, with the genes on them. The group is concentrated in space. By identifying the chromosome each segment belongs to, one can distinguish between proximity of inter- and intra-chromosomal gene pairs, and analyze them separately. (b) Pathway concentration in few chromosomes. For each number j of chromosomes, the plots show the number of pathways whose genes reside in at most j chromosomes. Plots for the real genome (red curve) and for an average over 106 random genomes (blue curve) are shown. The shaded area around the blue curve shows ±1 standard deviation. Inset: Zoom in on the region of a small number of chromosomes.
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Figure 1: Proximity criteria and pathway concentration. (a) Criteria for chromosome concentration of co-functioning genes. Circles correspond to genes and the red circles are all the members of a group with a common function. (i): concentration within a chromosome (intra-chromosomal). Here clustering/concentration is gauged based on pairwise linear distance (in base pairs or in the number of intervening genes) between co-functioning genes. (ii): dispersal across chromosomes (inter-chromosomal). Out of the 23 pairs of chromosomes, 18 do not contain the group's genes, so this group is concentrated in few chromosomes. This measure takes into account only the chromosomes on which the co-functioning genes reside and ignores the relative locations within each chromosome. (iii): concentration in the 3D space. Curved lines show positions of chromosomal segments in space, with the genes on them. The group is concentrated in space. By identifying the chromosome each segment belongs to, one can distinguish between proximity of inter- and intra-chromosomal gene pairs, and analyze them separately. (b) Pathway concentration in few chromosomes. For each number j of chromosomes, the plots show the number of pathways whose genes reside in at most j chromosomes. Plots for the real genome (red curve) and for an average over 106 random genomes (blue curve) are shown. The shaded area around the blue curve shows ±1 standard deviation. Inset: Zoom in on the region of a small number of chromosomes.

Mentions: We set out to test the tendency of genes with a common function to cluster in the genome using three complementary measures (Figure 1a): inter-chromosomally, by measuring the number of chromosomes co-functioning genes are distributed on; intra-chromosomally, using the genomic distances between co-functioning genes, and in 3D space, by measuring the proximity in the nucleus between co-functioning genes. These three approaches are complementary and each addresses a different aspect of the concentration.


Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome.

Thévenin A, Ein-Dor L, Ozery-Flato M, Shamir R - Nucleic Acids Res. (2014)

Proximity criteria and pathway concentration. (a) Criteria for chromosome concentration of co-functioning genes. Circles correspond to genes and the red circles are all the members of a group with a common function. (i): concentration within a chromosome (intra-chromosomal). Here clustering/concentration is gauged based on pairwise linear distance (in base pairs or in the number of intervening genes) between co-functioning genes. (ii): dispersal across chromosomes (inter-chromosomal). Out of the 23 pairs of chromosomes, 18 do not contain the group's genes, so this group is concentrated in few chromosomes. This measure takes into account only the chromosomes on which the co-functioning genes reside and ignores the relative locations within each chromosome. (iii): concentration in the 3D space. Curved lines show positions of chromosomal segments in space, with the genes on them. The group is concentrated in space. By identifying the chromosome each segment belongs to, one can distinguish between proximity of inter- and intra-chromosomal gene pairs, and analyze them separately. (b) Pathway concentration in few chromosomes. For each number j of chromosomes, the plots show the number of pathways whose genes reside in at most j chromosomes. Plots for the real genome (red curve) and for an average over 106 random genomes (blue curve) are shown. The shaded area around the blue curve shows ±1 standard deviation. Inset: Zoom in on the region of a small number of chromosomes.
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Related In: Results  -  Collection

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Figure 1: Proximity criteria and pathway concentration. (a) Criteria for chromosome concentration of co-functioning genes. Circles correspond to genes and the red circles are all the members of a group with a common function. (i): concentration within a chromosome (intra-chromosomal). Here clustering/concentration is gauged based on pairwise linear distance (in base pairs or in the number of intervening genes) between co-functioning genes. (ii): dispersal across chromosomes (inter-chromosomal). Out of the 23 pairs of chromosomes, 18 do not contain the group's genes, so this group is concentrated in few chromosomes. This measure takes into account only the chromosomes on which the co-functioning genes reside and ignores the relative locations within each chromosome. (iii): concentration in the 3D space. Curved lines show positions of chromosomal segments in space, with the genes on them. The group is concentrated in space. By identifying the chromosome each segment belongs to, one can distinguish between proximity of inter- and intra-chromosomal gene pairs, and analyze them separately. (b) Pathway concentration in few chromosomes. For each number j of chromosomes, the plots show the number of pathways whose genes reside in at most j chromosomes. Plots for the real genome (red curve) and for an average over 106 random genomes (blue curve) are shown. The shaded area around the blue curve shows ±1 standard deviation. Inset: Zoom in on the region of a small number of chromosomes.
Mentions: We set out to test the tendency of genes with a common function to cluster in the genome using three complementary measures (Figure 1a): inter-chromosomally, by measuring the number of chromosomes co-functioning genes are distributed on; intra-chromosomally, using the genomic distances between co-functioning genes, and in 3D space, by measuring the proximity in the nucleus between co-functioning genes. These three approaches are complementary and each addresses a different aspect of the concentration.

Bottom Line: We find a significant concentration of functional groups both in terms of their distance within the same chromosome and in terms of their dispersal over several chromosomes.The result holds for all three types of functional groups that we tested.Hence, the human genome shows substantial concentration of functional groups within chromosomes and across chromosomes in space.

View Article: PubMed Central - PubMed

Affiliation: Genome Informatics, Faculty of Technology and Institute for Bioinformatics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld 33615, Germany IBM Research-Haifa, Mount Carmel, Haifa 3498825, Israel.

Show MeSH