Can we estimate correct size of human interactome?
A recent study published in Nature methods estimates that the human interactome contains approximately ~130,000 binary interactions, most of which remain to be mapped, and the fraction of interactions identified so far represents approximately 8% of the full interactome. Figure repoted by Venkatesan et al. are four fold less than previously reported study in journal PNAS which estimated the number of interactions in humans to be ~650,000. An estimate of the human interactome can establish the magnitude of work required to map protein-protein interactions. Similar kind of estimates have been used during Human Genome Project, although after sequencing it was revealed that the number of genes is much lower than had been expected or estimated. This ambiguity about size of human interactome is due to unresolved differentiation between sets of protein pairs that can interact (biophysical interactions) and do interact (biological interactions). With 22,500 protein-coding genes, nearly 250 million protein pairs need to be tested to map whole human interactome, which is only possible with appllication of high-throughput approaches. Study also revelas that high-throughput yeast two-hybrid (HT-Y2H) interactions for human proteins are more precise than literature-curated interactions supported by a single publication, which is very much according to observation made by Cusick et al. Although previously it was suggested that biological complexity of organisms can not be explained merely by the number of genes but may be by the number of physiologically relevant interactions, it may be interesting to note that nematode Caenorhabditis elegans appears to have a similar number of genes as humans, and now the size of interactome appears of same order. So the big question is why we are so different from Caenorhabditis elegans?
- M. P. H. Stumpf, T. Thorne, E. de Silva, R. Stewart, H. J. An, M. Lappe, C. Wiuf (2008). From the Cover: Estimating the size of the human interactome Proceedings of the National Academy of Sciences, 105 (19), 6959-6964 DOI: 10.1073/pnas.0708078105
- Kavitha Venkatesan, Jean-François Rual, Alexei Vazquez, Ulrich Stelzl, Irma Lemmens, Tomoko Hirozane-Kishikawa, Tong Hao, Martina Zenkner, Xiaofeng Xin, Kwang-Il Goh, Muhammed A Yildirim, Nicolas Simonis, Kathrin Heinzmann, Fana Gebreab, Julie M Sahalie, Sebiha Cevik, Christophe Simon, Anne-Sophie de Smet, Elizabeth Dann, Alex Smolyar, Arunachalam Vinayagam, Haiyuan Yu, David Szeto, Heather Borick, Amélie Dricot, Niels Klitgord, Ryan R Murray, Chenwei Lin, Maciej Lalowski, Jan Timm, Kirstin Rau, Charles Boone, Pascal Braun, Michael E Cusick, Frederick P Roth, David E Hill, Jan Tavernier, Erich E Wanker, Albert-László Barabási, Marc Vidal (2008). An empirical framework for binary interactome mapping Nature Methods, 6 (1), 83-90 DOI: 10.1038/nmeth.1280
- Michael E Cusick, Haiyuan Yu, Alex Smolyar, Kavitha Venkatesan, Anne-Ruxandra Carvunis, Nicolas Simonis, Jean-François Rual, Heather Borick, Pascal Braun, Matija Dreze, Jean Vandenhaute, Mary Galli, Junshi Yazaki, David E Hill, Joseph R Ecker, Frederick P Roth, Marc Vidal (2009). Literature-curated protein interaction datasets Nature Methods, 6 (1), 39-46 DOI: 10.1038/nmeth.1284
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At very first place we need a reproducible definition of biological interaction. If no of genes as well as interactions are same then what are the factors those determine qualitative and quantitative behavior of system.
May be answer is “Ten Commandments in systems biology” from Denis Nobel. For example no of cancer genes and possible interaction between them is increasing day by day so the no of pathways to trigger the cancer. So It is very misleading to find the causes of cancer from the selection of genes without clear understanding the physiology of cancer and evolution theory of organs.