Introduction


Overlapping genes are frequently observed in all kinds of genomes. These overlapping genes are defined as a pair of genes whose transcripts are overlapped. Recently, many cases of overlapping genes are studied in a various eukaryotic organisms to investigate the evolutionary mechanism of them. But their origin and expression mechanism is not clearly elucidated. For the investigating of evolutionary aspect of overlapping genes, we implemented EVOG(Evolution Visualizer for Overlapping Genes), a Web-based DB with a novel visualization interface. EvOG supports all overlapping genes which are common in a subset of Human, Chimpanzee, Cow, Mouse, Chicken, Rat, Zebrafish, Drosophila, and Xenopus tropicalis. It also provides a manually curated database to show the evolutionary features of overlapping genes. EVOG DB components includes a number of overlapping genes (10120 in Human, 10026 in Chimpanzee, 853 in Orangutan, 213 in Rhesus, 3595 in Cow, 99 in Horse, 1 in Platypus, 213 in Dog, 25 in Cat, 1451 in Chicken, 3 in ZebraFinch, 115 in Opossum, 8667 in Mouse, 6892 in Rat, 535 in X. tropicalis, 50 in Medaka, and 1805 in Zebrafish). So people can easily retrieve the overlapping genes which are common in a few specified genomes. EvoG DB is very effective and easy to use in the comparative analysis to investigate evolutionary process of overlapping genes. Also EvOG DB supports a nice visualization interface to show the comparative configuration of those overlapping genes of multiple species along the whole chromosome scale. We apply this EVOG as a main tool to investigate the human evolution and disease by comparing the expression profiling of overlapping genes. In the near future EvOG will include the whole genomes of more than 20 species to compare the common overlapping genes. EvOG is implemented in JAVA and now is available at http://neobio.cs.pusan.ac.kr/evog/.

  A. Overview

  This snapshot shows one overlapping gene pairs {AUP1, HTRA2}, which appears commonly on Human, Chimp, Cow and Mouse. Each red(blue) segment denotes sense(anti-sense) transcript(the interval of each gene). a small thick segment denotes the exon and the thin line denotes the intro part. The vertical scale is aligned in the same scale.

  B. Control panel & main display

  EvOG supports two different viewing scales, (a) absolute scale and (b) zooming: fit to panel size. Absolute scale is a fixed viewing scale to include the overlapping genes appeared in multiple genomes. Zooming makes the viewing scale to fit the actual size. User can enlarge the viewing interval by selecting the scale lines by mouse.(click and dragging to the end of selected interval).

gene information (species, chromosome, gene name, accession number) and position control ruler

display gene's detail information (gene range, exon, intron)

  C. Alternative transcripts display option

  There are two displaying options to show a transcript with more than two different spanning regions. In the following example, HTRA2 has two different descriptions. You can view these multiple interval description for a single transcript by choosing the number of base lines(a single one or one in each separating line. When more than two different configurations of a transcript are overlapping, then the overlapping region is colored in black.(See the upper figure.).

alternative transcripts display option (single base line - overlap region : black color)

alternative transcripts display option (multi base line) :ex) HTRA2

  D. Zoom-in by dragging region

  Users can freely zoom in/out a specified region to investigate the overlapping regions of gene pairs. The right button return the viewing window to the initial configuration(absolute size).

zoom-in operation : drag some region in Gene position bar

  E. Measuring the Degree of Overlapping region in each Gene Pair

  We can measure the degree of overlapping genes in terms of the size of ORG(Overlapping Region of Genes) and TOI(Total Overlapping Interval). Using EvoG, we can observe two values ,|ORG| and |TOI|, on the right end of in each sub-figures obtained. |ORG| means the size(in terms of basepair) of ORG. If |ORG| > 0, that means overlapping positive. Otherwise that is the overlapping negative pair, where two genes are disjoint on a single chromosome. And |TOI| is total length of the minimal interval including the pair of the overlapping genes. |ORG| and |TOI| are two main parameters to reconstruct the phylogenetic tree from a set of overlapping positive and negative gene pairs.


Graphics Application Lab., Dept. of Computer Science,
Molecular Biology & Phylogeny Lab.,
Pusan National University
San-30, Jangjeon-dong, Keumjeong-gu, Pusan, 609-735, South Korea.
Phone: +82-51-582-5009 Fax: +82-51-515-2208