Modelling the Correlation Between the Activities of Adjacent Genes in Drosophila

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2005 Jan 22

PMID 15659243

Citations 14

Authors

Helene H Thygesen

Aeilko H Zwinderman

Affiliations

Soon will be listed here.

Abstract

Background: Correlation between the expression levels of genes which are located close to each other on the genome has been found in various organisms, including yeast, drosophila and humans. Since such a correlation could be explained by several biochemical, evolutionary, genetic and technological factors, there is a need for statistical models that correspond to specific biological models for the correlation structure.

Results: We modelled the pairwise correlation between the expressions of the genes in a Drosophila microarray experiment as a normal mixture under Fisher's z-transform, and fitted the model to the correlations of expressions of adjacent as well as non-adjacent genes. We also analyzed simulated data for comparison. The model provided a good fit to the data. Further, correlation between the activities of two genes could, in most cases, be attributed to either of two factors: the two genes both being active in the same age group (adult or embryo), or the two genes being in proximity of each other on the chromosome. The interaction between these two factors was weak.

Conclusions: Correlation between the activities of adjacent genes is higher than between non-adjacent genes. In the data we analyzed, this appeared, for the most part, to be a constant effect that applied to all pairs of adjacent genes.

Citing Articles

A Catalogue of Putative -Regulatory Interactions Between Long Non-coding RNAs and Proximal Coding Genes Based on Correlative Analysis Across Diverse Human Tumors.

Basu S, Larsson E G3 (Bethesda). 2018; 8(6):2019-2025.

PMID: 29666194 PMC: 5982829. DOI: 10.1534/g3.118.200296.

Gene silencing of porcine MUC13 and ITGB5: candidate genes towards Escherichia coli F4ac adhesion.

Zhou C, Liu Z, Liu Y, Fu W, Ding X, Liu J PLoS One. 2013; 8(7):e70303.

PMID: 23922972 PMC: 3726385. DOI: 10.1371/journal.pone.0070303.

Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation.

Weber C, Hurst L Genome Biol. 2011; 12(3):R23.

PMID: 21414197 PMC: 3129673. DOI: 10.1186/gb-2011-12-3-r23.

Neighbourhood continuity is not required for correct testis gene expression in Drosophila.

Meadows L, Chan Y, Roote J, Russell S PLoS Biol. 2010; 8(11):e1000552.

PMID: 21151342 PMC: 2994658. DOI: 10.1371/journal.pbio.1000552.

Co-expression of neighboring genes in the zebrafish (Danio rerio) genome.

Tsai H, Huang P, Kao C, Wang D Int J Mol Sci. 2010; 10(8):3658-3670.

PMID: 20111688 PMC: 2812831. DOI: 10.3390/ijms10083658.

References

Dorsett D . Distant liaisons: long-range enhancer-promoter interactions in Drosophila. Curr Opin Genet Dev. 1999; 9(5):505-14. DOI: 10.1016/s0959-437x(99)00002-7. View

Bleiweiss R . Mimicry on the QT(L): genetics of speciation in Mimulus. Evolution. 2001; 55(8):1706-9. DOI: 10.1111/j.0014-3820.2001.tb00690.x. View

Llorente B, Durrens P, Malpertuy A, Aigle M, Artiguenave F, Blandin G . Genomic exploration of the hemiascomycetous yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae. FEBS Lett. 2001; 487(1):122-33. DOI: 10.1016/s0014-5793(00)02291-2. View

Oliver B, Parisi M, Clark D . Gene expression neighborhoods. J Biol. 2002; 1(1):4. PMC: 117247. DOI: 10.1186/1475-4924-1-4. View

Ross J, Jiang H, Kanost M, Wang Y . Serine proteases and their homologs in the Drosophila melanogaster genome: an initial analysis of sequence conservation and phylogenetic relationships. Gene. 2003; 304:117-31. DOI: 10.1016/s0378-1119(02)01187-3. View

Cho R, Campbell M, Winzeler E, Steinmetz L, Conway A, Wodicka L . A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell. 1998; 2(1):65-73. DOI: 10.1016/s1097-2765(00)80114-8. View

Fukuoka Y, Inaoka H, Kohane I . Inter-species differences of co-expression of neighboring genes in eukaryotic genomes. BMC Genomics. 2004; 5(1):4. PMC: 331401. DOI: 10.1186/1471-2164-5-4. View

Roy P, Stuart J, Lund J, Kim S . Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature. 2002; 418(6901):975-9. DOI: 10.1038/nature01012. View

Hamilton B . Variations in abundance: genome-wide responses to genetic variation and vice versa. Genome Biol. 2002; 3(10):reviews1029. PMC: 244913. DOI: 10.1186/gb-2002-3-10-reviews1029. View

10.

Cohen B, Mitra R, Hughes J, Church G . A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet. 2000; 26(2):183-6. DOI: 10.1038/79896. View

11.

Kruglyak S, Tang H . Regulation of adjacent yeast genes. Trends Genet. 2000; 16(3):109-11. DOI: 10.1016/s0168-9525(99)01941-1. View

12.

Spellman P, Rubin G . Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol. 2002; 1(1):5. PMC: 117248. DOI: 10.1186/1475-4924-1-5. View

13.

Lercher M, Blumenthal T, Hurst L . Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Genome Res. 2003; 13(2):238-43. PMC: 420373. DOI: 10.1101/gr.553803. View

14.

Parisi M, Nuttall R, Edwards P, Minor J, Naiman D, Lu J . A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults. Genome Biol. 2004; 5(6):R40. PMC: 463073. DOI: 10.1186/gb-2004-5-6-r40. View

15.

Jackson D . Chromatin domains and nuclear compartments: establishing sites of gene expression in eukaryotic nuclei. Mol Biol Rep. 1997; 24(3):209-20. DOI: 10.1023/a:1006873614521. View

16.

Orphanides G, Reinberg D . A unified theory of gene expression. Cell. 2002; 108(4):439-51. DOI: 10.1016/s0092-8674(02)00655-4. View