Figure 5
An overlap between a network cluster obtained by the Potts model algorithm [31] and the best-matching GO groups from the public cellular component GOA. The cluster contains 11 proteins: 10 subunits of RNA polymerase II and a Vpr protein from Human immunodeficiency virus 1. RNA polymerase II is a well-characterized and stable multi-subunit complex that is formed due to the physical interactions of its subunits. RNA polymerase II is involved in the mRNA synthesis for all eukaryotic protein-coding genes. Vpr protein from HIV has diverse function and regulates the expression of many cellular genes during HIV infection as well as accelerates the production of viral proteins. A – The portion of GO classification overlapping with network cluster. The figure shows the part of the GO classification hierarchy with the bottom node being the GO group that has the statistically the best overlap with the Potts cluster. GO groups are depicted as rectangles and the parent-child relation in the GO tree is shown as a line with an arrow. Only those parent GO groups that have a statistically significant overlap with the Potts cluster are shown. The numbers above the line show the number of proteins common with the Potts cluster (before the slash) and the total number of proteins in the GO group. The Δc value below the arrow is the number of standard deviations by which the overlap is bigger than the overlap expected by random chance. B – The network cluster overlapping with GO classification from Figure A. Highlighted proteins belong to the best overlapping GO group from cellular component classification DNA-directed RNA polymerase II, core complex (GO:0005665).