A Review: Protein Interaction & Behavior Assessment in Host Cells after Novel Drug Compound Administration using Systems Biology Approach

Yesha Modi, Harsh Shinde, Natasha Navet, Richa Arya, Nikita Sushil Kumar, Ved Mishra, Fariya Khan, Satyam Khanna, Ruchi Narula, Prashant Agarwal


To understand complex biological systems requires the integration of experimental and computational research; in other words systems biology approach. Computational biology, through via different software helps in exploration more than one gene expression at a time and also understanding the connectivity, Systems Biology provides a powerful foundation from which to address critical scientific questions head-on. The reviews in this Insight cover many different aspects of this energetic field, although all, in one way or another, illuminate the functioning of modular circuits, including their robustness, design and manipulation. Computational systems biology addresses questions fundamental to our understanding of life, yet progress here will lead to practical innovations in medicine, drug discovery and engineering, In this study we have evaluated thepotentialityof Antifungal Aqueous extracts on Yeast cultures and scientifically proven the same using Cytoscape.


Systems Biology, Proteomics, Protein Profiling, Cytoscape, Network, Nodes & Edges, Attributes, Annotation, Ontology, Gene Ontology etc.

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Altman, R. B., and Raychaudhuri, S. (2001). Whole-genome expression analysis: challenges beyond clustering, Curr Opin Struct Biol 11, 340-7.

Ashburner M., Ball C. A., Blake J. A. and Botstein D., (2000), The Gene Ontology: tool for the unification of biology, Nature Genetics, 25, 25-29.

Avila-Campillo I., Drew K., Lin J., Reiss D. J. and Bonneau R., (2007), BioNetBuilder: automatic integration of biological networks; Bioinformatics1:23(3): 392-3, EPub, PMID: 171385.

Apic G., Ignjatovic T. and Boyer S., (2005), Illuminating drug discovery with biological pathways. FEBS Lett. 579, 1872-1877.

Bell G. W. and Lewitter F. (2006), Visualizing networks; Meth Enzymol. 411:408-21. Doi: 10.1016|50076-6879(06)11022-8 PMID.16939803.

Boone C., Howard B. and Brenda J. Andrews, (2007), Exploring genetic interactions and networks with yeast. Nat. Rev. Genet. 8, 437-449.

Butcher E. C., Berg E. L., and Kunkel E. J., (2004), System biology in drug discovery. Nat Biotechnol, 22:1253-1259.

CajaMurcia F., (2006), Red Espanola de Biologa de Sistemas, Systems biology, 14(1):1931.

Cho C. R., Mark Labow, Mischa Reinhardt, Jan van Oostrum and Manuel C. Peitsch (2006), The application of systems biology to drug discovery. Current Opinion in Chemical Biology, 10(4):294302.

Davierwala A. P., Haynes J., Li Z., Brost R. L., Robinson M. D., and Yu L., (2005), The synthetic genetic interaction spectrum of essential genes. Nat. Genet. 37, 1147-1152.

Dolinski K. and Botstein D., (2005), Changing perspectives in yeast research nearly a decade after the genome sequence. Genome Res., 15, 1611-1619.

Eisen M. B., Spellman P. T., Brown P. O., and Botstein D. (1998). Cluster analysis and display of genome-wide expression patterns, Proc Natl Acad Sci U S A 95, 14863-8.

Fishman M. C. and Porter J. A., (2005), A new grammar for drug discovery. Nature, 437:491-493.

Gary D. B. and Christopher W. V. H., (2003), An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics, 4:2 doi 10, 1186|1471-2105-4-2.

Gavin A.C., Bsche M., Krause R., Grandi P., and Marzioch M. (2002). Functional organization of the yeast proteome by systematic analysis of protein complexes, Nature 415, 141-147.

Goffeau A., Barrell B. G., Bussey H., Davis R. W., Dujon B., Feldmann H., Galibert F., Hoheisel J. D., Jacq C., Johnston M., Louis E. J., Mewes H. W., Murakami Y., Philippsen P., Tettelin H., and Oliver S. G., (1996), Life with 6000 genes. Science, 274, 546.

Ideker T., Thorsson V., Siegel A., and Hood L. (2000). Testing for differentially-expressed genes by maximum likelihood analysis of microarray data, J Comput Biol 7, 805-817.

Ideker T., Ozier O., Schwikowski B., and Siegel A. F., (2002), Discovering regulatory and signaling circuits in molecular interaction networks. Bioinformatics. 18 suppl 1:5233-40; PMID: 12169552.

Kerr, M. K., and Churchill, G. A. (2001). Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments, Proc Natl Acad Sci U S A 98, 8961-5.

Kumar N., Hendriks BS, Janes KA, Graaf D, Lauffenburger DA (2006), Applying computational modeling to drug discovery and development. Drug Discovery Today, 11(1718): 806811.

Lodhi H. and Muggleton S., (2004), Modeling metabolic pathways using stochastic logic programs based Ensemble methods. Second International Conference on Computational Methods in System Biology (CMSB04), LNCS, pages 119133.

Maere Steven, Heymans K. and Kuiper M., (2005). BiNGO: a cytoscape plugin to access overrepresentation of gene ontology categories in biological networks. Bioinformatics 21, 3448-3449, doi: 10.1093|bioinformatics|bti551.

Materi W. and Wishart S., (2007), Computational systems biology in drug discovery and development: methods and applications. Drug Discovery Today, 12(78): 295303.

Noble D., (2006), The Music of Life, Oxford University Press, pages 263-274.

Pilpel, Y., Sudarsanam, P., and Church, G. M. (2001). Identifying regulatory networks by combinatorial analysis of promoter elements, Nat Genet 29, 153-9.

Ren B., Robert F., Wyrick J. J., Aparicio O., Jennings E. G., Simon I., Zeitlinger J., Schreiber J., Hannett N. and Kanin E., (2000). Genome-wide location and function of DNA binding proteins, Science 290, 2306-9.

Rocke, D. M., and Durbin, B. (2001). A model for measurement error for gene expression arrays, J Comput Biol 8, 557-69.

Shannon P., Markiel A., and Ozier O., (2003), Cytoscape: a software invironment for integrated models of biomolecular interaction networks; Genome Res. 13(11):2498-504. Doi: 10.1101|gr|239303. PMC 403769, PMID 1457658.

Shannon P. T., David J Reiss, Richard Bonneau and Nitin S. Baliga, (2006), The Gaggle: an open-source software system for integrating bioinformatics software and data sources, BMC Bioinformatics, 7, 176.

Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Dmitrovsky, E., Lander, E. S., and Golub, T. R. (1999). Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation, Proc Natl Acad Sci U S A 96, 2907-2912.

Tong A. H. Y., Lesage G, Bader GD, Ding H, Xu H, Xin X, and Young J., (2004), Global mapping ofthe yeast genetic interaction network. Science, 303, 808-813.

Uetz, P., Giot L., Cagney G., Mansfield T. A., Judson R. S., Knight J. R., Lockshon D., Narayan V., Srinivasan M., Pochart P., Qureshi-Emili A., Li Y., Godwin B., Conover D., Kalbfleisch T., Vijayadamodar G., Yang M., Johnston M., Fields S. and Rothberg J. M., (2000), A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. J. M. Nature, 403, 623-627.

Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S. and Houfek, T., (2001). Global analysis of protein activities using proteome chips, Science 293, 2101-5.


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