|Co-evolution of Presence-Absence Patterns
|HOME OVERVIEW BENCHMARK FAQ GALLERY SOURCE CODE CITING & CREDITS|
The CoPAP Gallery includes two examples of the visualized output produced by the web server. (1) The "toy example" shows an analysis of bacterial genes co-evolutionary network. The dataset in the "toy example" is a phyletic pattern of 20 genes across 19 species. This dataset is the default input if the user presses "Load an example". (2) A large scale search for co-evolving bacterial gene families. The data include 4,258 bacterial COGs (Clusters of Orthologous Genes) across 681 bacterial genomes. The phyletic pattern data were retrieved from eggNOG v2.0 (Muller et al. 2010). The tree topology is based on Wu et al. (2009).
Please refer to the CoPAP output html to view the output in its original form:
1. Global properties of the co-evolutionary network
The global properties are illustrated with graphs that are automatically produced by CoPAP and depicted in three figures: (A) Distribution of the number of interactions; (B) Distribution of interactions significance; (C) Histogram of the number of interactions (degree distribution, same data as in A, illustrated as a histogram)1.1 Global properties of the bacterial genes network
2. Projection of patterns onto the tree
CoPAP automatically produces phylogenetic visualization of the presence and absence pattern for given pair of genes. Using the FigTree applet, http://tree.bio.ed.ac.uk/software/figtree/, the pattern for a given gene is represented as a tree with taxa names colored according to existence in both ('11', red), absence in both ('00', grey), presence in the first only ('10', green), or presence in the second only ('01', blue). Here, the patterns of COG4521 (ABC-type taurine transport system, periplasmic component) and COG4525 (ABC-type taurine transport system, ATPase component) are presented. In this case, the high similarity in their phyletic patterns (as seen by multiple '11', red colored genomes) allows CoPAP to infer multiple co-occurring events and significant co-evolution.
All the 20 positions in the "toy example" data selected for the projection of phyletic pattern using Archaeopteryx (Han, Zmasek 2009). Here, different genes are represented by columns, in which presence and absence are colored green, and purple, respectively.
3. Analysis of the network using Cytoscape
CoPAP provides advanced network visualization and analysis by automatically loading the network to the Cytoscape platform (Smoot et al. 2011).
(A) The global view of the network.
(B) Clusters of co-evolving genes representing functional modules.
All 572 Clusters of co-evolving genes are available here
1. Motility-related genes
2. Amino acid transport and metabolism functional category
3. Phosphoribosyl metabolism
4. B12 (Cobalamin biosynthesis)
5. NADH:ubiquin oneoxidoreductase complex
Muller, J, D Szklarczyk, P Julien, et al. 2010. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res 38:D190-195.