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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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Intra-chromosomal distances. The plot shows the average intra-chromosomal distance between genes from the same group in the real (red) and randomized (blue) genomes. (a) PPIs; (b) Complexes; (c) Pathways. Bins were selected so that the occupancy of pairs from the real genome is uniform (hence the straight red line). The clustering effect is reflected by the larger cumulative fraction in the real genome histograms compared to the random model in the smaller distance bins. The light blue shaded region around the blue curve stands for ±1 standard deviation.
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Figure 2: Intra-chromosomal distances. The plot shows the average intra-chromosomal distance between genes from the same group in the real (red) and randomized (blue) genomes. (a) PPIs; (b) Complexes; (c) Pathways. Bins were selected so that the occupancy of pairs from the real genome is uniform (hence the straight red line). The clustering effect is reflected by the larger cumulative fraction in the real genome histograms compared to the random model in the smaller distance bins. The light blue shaded region around the blue curve stands for ±1 standard deviation.

Mentions: Next, we conducted the more sensitive distribution tail test, focusing on groups with short average distances between members. We partitioned the gene groups into 20 bins based on the distances di defined above, as follows. The distances were sorted, and thresholds were set such that 5% of the distances were between (see Supplementary Information for more details). We then used these thresholds to bin distances for each of 105 random genomes defined as above. We used a lexicographic order of bin frequencies to refine the results (see Supplementary Information). We discovered that for all group types, a statistically significant number of groups tend to cluster within smaller distances than expected at random (all three with P-values , Bonferroni corrected). This tendency is illustrated in Figure 2. The cumulative distributions of the true genome are plotted along with their random counterparts obtained by averaging over the 105 random histograms. The figure shows the enrichment of short distances for each of the three functional group types.


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)

Intra-chromosomal distances. The plot shows the average intra-chromosomal distance between genes from the same group in the real (red) and randomized (blue) genomes. (a) PPIs; (b) Complexes; (c) Pathways. Bins were selected so that the occupancy of pairs from the real genome is uniform (hence the straight red line). The clustering effect is reflected by the larger cumulative fraction in the real genome histograms compared to the random model in the smaller distance bins. The light blue shaded region around the blue curve stands for ±1 standard deviation.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150778&req=5

Figure 2: Intra-chromosomal distances. The plot shows the average intra-chromosomal distance between genes from the same group in the real (red) and randomized (blue) genomes. (a) PPIs; (b) Complexes; (c) Pathways. Bins were selected so that the occupancy of pairs from the real genome is uniform (hence the straight red line). The clustering effect is reflected by the larger cumulative fraction in the real genome histograms compared to the random model in the smaller distance bins. The light blue shaded region around the blue curve stands for ±1 standard deviation.
Mentions: Next, we conducted the more sensitive distribution tail test, focusing on groups with short average distances between members. We partitioned the gene groups into 20 bins based on the distances di defined above, as follows. The distances were sorted, and thresholds were set such that 5% of the distances were between (see Supplementary Information for more details). We then used these thresholds to bin distances for each of 105 random genomes defined as above. We used a lexicographic order of bin frequencies to refine the results (see Supplementary Information). We discovered that for all group types, a statistically significant number of groups tend to cluster within smaller distances than expected at random (all three with P-values , Bonferroni corrected). This tendency is illustrated in Figure 2. The cumulative distributions of the true genome are plotted along with their random counterparts obtained by averaging over the 105 random histograms. The figure shows the enrichment of short distances for each of the three functional group types.

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