A. Ercument Cicek
ABSTRACT
Metabolic networks have become one of the centers of attention in life sciences research with the advancements in the metabolomics field. A vast array of studies analyzes metabolites and their interrelations to seek explanations for various biological questions, and numerous genome-scale metabolic networks have been assembled to serve for this purpose. The increasing focus on this topic comes with the need for software systems that store, query, browse, analyze, and visualize metabolic networks. PathCase Metabolomics Analysis Workbench (PathCaseMAW) is built, released, and running on a manually created generic mammalian metabolic network. The PathCaseMAW system provides a database-enabled framework and web-based computational tools for browsing, querying, analyzing, and visualizing stored metabolic networks. PathCaseMAW editor, with its user-friendly interface, can be used to create a new metabolic network and/or update an existing metabolic network. The network can also be created from an existing genome-scale reconstructed network using the PathCaseMAW SBML parser. The metabolic network can be accessed through a web interface or an iPad application. For metabolomics analysis, Steady-State Metabolic Network Dynamics Analysis (SMDA) algorithm is implemented and integrated with the system. SMDA tool is accessible through both the web-based interface and the iPad application for metabolomics analysis based on a metabolic profile. PathCaseMAW is a comprehensive system with various data input and data access sub-systems. It is easy to work with by design, and is a promising tool for metabolomics research and for educational purposes.
- Fell, D. A. 1997. Understanding the control of metabolism. Portland Press, London, UK.Google Scholar
- Schilling, C.H., Schuster, S., Palsson, B.O., Heinrich, R. 1999. Metabolic Pathway Analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol Prog. 15, 296--303.Google ScholarCross Ref
- Feist, A.M., Palsson, B.O. 2008. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 26, 6, 659--667.Google ScholarCross Ref
- Zelezniak, A., Pers, T.H., Soares, S., Patti, M.E., Patil, K.R. 2010. Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes. PLoS Comput Biol, 6, 4, e1000729.Google ScholarCross Ref
- Patil, K.R., Nielsen, J. 2005. Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci USA 102, 2685--2689.Google ScholarCross Ref
- David, H., Hofmann, G., Oliveira, A.P., Jarmer, H., Nielsen, J. 2006. Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans. Genome Biol 7, R108.Google ScholarCross Ref
- Cicek, A.E., Bederman, I., Henderson, L., Drumm, M.L., Ozsoyoglu, G. 2013. ADEMA: An Algorithm to Determine Expected Metabolite Level Alterations Using Mutual Information PLoS Comput Biol, 9, 1, e1002859. doi:10.1371/journal.pcbi.1002859.Google Scholar
- Duarte, N.C., Becker, S.A., Jamshidi, N., Thiele, I., Mo, M.L., Vo, T.D., Srivas, R., Palsson, B.O. 2007. Global reconstruction of the human metabolic network based on genomic and bibliomic data. PNAS 104, 6, 1777--1782.Google ScholarCross Ref
- Salway, J.G. 2006. Metabolism at a Glance Third Edition. Blackwell Publishing, Malden, MI.Google Scholar
- PathCase-RCMN {http://nashua.case.edu/PathCaseRCMN/Web/}Google Scholar
- Cakmak, A., Qi, X., Cicek, A.E., Bederman, I., Henderson, L., Drumm, M.L., Ozsoyoglu, G. 2012. A New Metabolomics Analysis Technique: Steady-State Metabolic Network Dynamics Analysis. J Bioinform Comput Biol 10, 1, 36.Google ScholarCross Ref
- Cicek, A.E., Ozsoyoglu, G. 2012. Observation Conflict Resolution in Steady-State Metabolic Network Dynamics Analysis. J Bioinform Comput Biol 10, 1, 25.Google ScholarCross Ref
- Cakmak, A., Ozsoyoglu, G., Hanson, R.W. 2012. Querying Metabolism under Different Physiological Constraints. J Bioinform Comput Biol, 8, 2, 247--293.Google ScholarCross Ref
- Cakmak, A., Ozsoyoglu, G., Hanson, R.W. 2012. Managing and Querying Mammalian Metabolic Networks: A Metabolism Query Language and Its Query Processing. In Proceedings of 8th International Conference on Computational Systems Bioinformatics (Stanford, CA, August 10-13, 2009). CSB '09.Google Scholar
- Wishart, D.S., Knox, C., Guo, A.C., Eisner, R., Young, N., Gautam, B., Hau, D.D., Psychogios, N., Dong, E., Bouatra, S., Mandal, R., Sinelnikov, I., Xia, J., Jia, L., Cruz, J.A., Lim, E., Sobsey, C.A., Shrivastava, S., Huang, P., Liu, P., Fang, L., Peng, J., Fradette, R., Cheng, D., Tzur, D., Clements, M., Lewis, A., De Souza, A., Zuniga, A., et. al. 2009. HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res 37(Database issue), D603--610.Google Scholar
- Apple Press Info {http://www.apple.com/pr/library/2011/07/19Apple-Reports-Third-Quarter-Results.html}Google Scholar
- Apple Education {http://www.apple.com/education/ipad/}Google Scholar
- Sabah Newspaper: Turkish Ministry of National Education distributes tablets in schools {http://english.sabah.com.tr/National/2012/02/01/distribution-of-free-tablets-to-students-has-begun}Google Scholar
- Hucka, M., Finney, A.M., Hoops, S., Keating, S.M., Le Novere, N. 2007. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model definitions. Sept. 26, 2007.Google Scholar
- Das, M. 2009. Parsing BioModels and CellML Models and insertion of data. Masters Project. Case Western Reserve University, Electrical Engineering and Computer Science Department.Google Scholar
- PathCase-Systems Biology Web Site {http://nashua.case.edu/PathwaysSB/Web}Google Scholar
- Cakmak, A., Qi, X., Coskun, S.A., Das, M., Cheng, E., Cicek AE, Lai N, Ozsoyoglu ZM, Ozsoyoglu G: PathCase-SB Architecture and Database Design. BMC Systems Biology 2011, 5:188.Google Scholar
- Elliott, B., Kirac, M., Cakmak, A., Yavas, G., Mayes, S., Cheng, E., Wang, Y., Gupta, C., Ozsoyoglu, G., Ozsoyoglu, Z.M. 2006 PathCase: pathways database system. Bioinformatics, 24: 2526--2533. Google ScholarDigital Library
- Le Novère, N., Bornstein, B., Broicher, A., Courtot, M., Donizelli, M., Dharuri, H., Li, L., Sauro, H., Schilstra, M., Shapiro, B., Snoep, J.L., Hucka, M. 2006. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Research, 34(Database-Issue), 689--691.Google Scholar
- Bornstein, B.J., Keating, S.M., Jouraku, A., Hucka, M. 2008 LibSBML: an API Library for SBML. Bioinformatics, 24, 6, 880--881. Google ScholarDigital Library
- KEGG (Kyoto Encyplopedia of Genes and Genomes) Pathways {http://www.genome.jp/KEGG/pathway.html}Google Scholar
- Kanehisa, M., Goto, S. 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res, 28, 27--30.Google ScholarCross Ref
- Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., Hirakawa, M. 2006. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res, 34, D354--357.Google ScholarCross Ref
- Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., Hirakawa, M. 2010. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res, 38, D355-D360.Google ScholarCross Ref
- PathCase-KEGG {http://nashua.case.edu/PathwaysKegg/Web/Google Scholar
- Johnson, S.R., Qi, X., Cicek, A.E., Ozsoyoglu, G. 2013 iPathCaseKEGG: an iPad interface for KEGG metabolic pathways. Health Inf Sci Syst, 1, 4.Google ScholarCross Ref
- Caspi, R., Altman, T., Dale, J.M., Dreher, K., Fulcher, C.A., Gilham, F., Kaipa, P., Karthikeyan, A.S., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L.A., Paley, S., Popescu, L., Pujar, A., Shearer, A.G., Zhang, P., Karp, P.D. 2010. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Research, 38, D473--9.Google ScholarCross Ref
- Paley, S.M., Karp, P.D. 2002. Evaluation of computational metabolic-pathway predictions for H. pylori. Bioinformatics 18, 715--24.Google ScholarCross Ref
- Karp, P.D., Paley, S.M., Krummenacker, M., Latendresse, M., Dale, J.M., Lee, T., Kaipa, P., Gilham, F., Spaulding, A., Popescu, L., Altman, T., Paulsen, I., Keseler, I.M., Caspi, R. 2010. Pathway Tools version 13.0: Integrated Software for Pathway/Genome Informatics and Systems Biology. Briefings in Bioinformatics, 11, 40--79.Google ScholarCross Ref
- Keseler, I.M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A.G., Mackie, A., Paulsen, I., Gunsalus, R.P., Karp, P.D. 2011. EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Research, 39, D583--590.Google ScholarCross Ref
- Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B., Kanapin, A., Lewis, S., Mahajan, S., May, B., Schmidt, E., Vastrik, I., Wu, G., Birney, E., Stein, L., D'Eustachio, P. 2008. Reactome knowledgebase of biological pathways and processes. Nucleic Acids Res, 37(Database issue), D619--22.Google Scholar
- Matthews, L., D'Eustachio, P., Gillespie, M., Croft, D., de Bono, B., Gopinath, G., Jassal, B., Lewis, S., Schmidt, E., Vastrik, I., Wu, G., Birney, E., Stein, L. 2007. An Introduction to the Reactome Knowledgebase of Human Biological Pathways and Processes. Bioinformatics Primer, NCI/Nature Pathway Interaction Database. doi:10.1038/pid.2007.3Google Scholar
- Vastrik, I., D'Eustachio, P., Schmidt, E., Joshi-Tope, G., Gopinath, G., Croft, D., de Bono, B., Gillespie, M., Jassal, B., Lewis, S., Matthews, L., Wu, G., Birney, E., Stein, L. 2007. Reactome: a knowledge base of biologic pathways and processes. Genome Biology, 8, R39.Google ScholarCross Ref
- Joshi-Tope, G., Vastrik, I., Gopinathrao, G., Matthews, L., Schmidt, E., Gillespie, M., D'Eustachio, P., Jassal, B., Lewis, S., Wu, G., Birney, E., Stein, L. 2003. The Genome Knowledgebase: A Resource for Biologists and Bioinformaticists. Cold Spring Harb Symp Quant Biol., 68, 237--43.Google Scholar
- Pabinger, S., Rader, R., Agren, R., Nielsen, J., Trajanoski, Z. 2011 MEMOSys: Bioinformatics platform for genome-scale metabolic models. BMC Syst Biol, 5, 20.Google ScholarCross Ref
- Ma, H., Sorokin, A., Mazein, A., Selkov, A., Selkov, E., Demin, O., Goryanin, I. 2007. The edinburgh human metabolic network reconstruction and its functional analysis. Mol Syst Biol, 3, 135.Google ScholarCross Ref
- Alshalwi S 2012. PathCase-RCMN: ReconstruCted Metabolic Networks of organisms. Masters Project. Case Western Reserve University, Electrical Engineering and Computer Science Department.Google Scholar
Index Terms
- PathCase-MAW: An Online Metabolic Network Analysis Workbench
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