Genome neighbors

If two genes (white and black circles) are found as neighbors in several genomes, the encoded proteins are predicted to functionally interact. Figure adapted from Eisenberg etal. (2000). 

Fig. 2. The graph representation of various relations among proteins or genes. The pathway and the assembly are representations of biochemical knowledge about the network of molecular interactions. The genome represents the positional correlations of genes. The neighbor, cluster, and hierarchical tree are computationally obtained from a set of binary relations, namely, similarity relations of protein pairs or gene pairs.

GPCR phylogenetic analysis partial neighbor-joining tree of the rhodopsin receptorlike family (A) from Joost andMethner (Genome Biol., 3 research 0063.1-0063.16,2002. http //genomebiology.com/ 2002/3/11/ research/0063). Detailed receptor names are provided in the additional data file 1 of the reference. 

In order to compare the TA and GC asymmetry values in transcribed regions to those in the neighboring intergenic sequences, we have computed Sja and Sgc in adjacent 1-kbp windows along the genome sequence [36, 37]. Figure 7 reports the mean values of these skews for all genes as a function of the distance to the 5 ... 

Williams EJ, Bowles DJ. Coexpression of neighboring genes in the genome of Arabidopsis thaliana. Genome Res 2004 14 1060-1067. 

Lereher MJ, Blumenthal T, Elurst LD. Co-expression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Genome Res 2003 13 238-243. 

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