Abstract
GenePath is an automated system for reasoning about genetic networks, wherein a set of genes have various influences on one another and on a biological outcome. It acts on a set of experiments in which genes are knocked-out or overexpressed, and the outcome of interest is evaluated. Implemented in Prolog, GenePath uses abductive inference to elucidate network constraints based on background knowledge and experimental results. Two uses of the system are demonstrated: synthesis of a consistent network from abduced constraints, and qualitative reasoning-based approach that generates a set of networks consistent with the data. In practice, as illustrated by an example on aggregation of a soil amoeba Dictyostelium discoideum, a combination of constraint satisfaction and qualitative reasoning produces a small set of plausible networks.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Akutsu, T., Miyano, S., Kuhara, S.S.: Inferring qualitative relations in genetic networks and methabolic pathways. Bioinformatics 16, 727–734 (2000)
Avery, L., Wasserman, S.: Ordering gene function: the interpretation of epistasis in regulatory hierarchies. Trends in Genetics 8, 312–316 (1992)
Bratko, I.: Prolog programming for artificial intelligence, 3rd edn. Addison-Wesley, Reading (2001)
Dutilh, B.: Analysis of data from microarray experiments, the state of the art in gene network reconstruction. Literature thesis, Theoretical biology and Bioinformatics, Utrecht University (1999)
Flach, P.: Simply logical: Intelligent reasoning by example. John Wiley & Sons, New York (1994)
Hughes, T.R., Marton, M.J., Jones, A.R., Roberts, C.J., Stoughton, R., Armour, C.D., Bennett, H.A., Coffey, E., Dai, H., He, Y.D., Kidd, M.J., King, A.M., Meyer, M.R., Slade, D., Lum, P.Y., Stepaniants, S.B., Shoemaker, D.D., Gachotte, D., Chakraburtty, K., Simon, J., Bard, M., Friend, S.H.: Functional discovery via a compendium of expression profiles. Cell 102, 109–126 (2000)
Kakas, A.C., Kowalski, R.A., Toni, F.: Handbook of logic in Artificial Intelligence and Logic Programming. In: Chapter The role of abduction in logic programming, vol. 5, pp. 235–324. Oxford University Press, Oxford (1998)
Kuspa, A., Sucgang, R., Shaulsky, G.: The promise of a protist: the dictyostelium genome project. Functional and Integrative Genomics 1, 279–293 (2001)
Metzstein, M.M., Stanfield, G.M., Horvitz, H.R.: Genetics of programmed cell death in C. elegans: past, present and future. Trends in Genetics 14, 410–416 (1998)
Peer, D., Nachman, I., Linial, M., Friedmann, N.: Using Bayesian networks to analyze whole genome expression data. Journal of Computational Biology 7, 601–620 (2000)
Riddle, D.L., Swanson, M.M., Albert, P.S.: Interacting genes in nematode dauer larva formation. Nature 14, 668–671 (1981)
Ross-Macdonald, P., Coelho, P.S., Roemer, T., Agarwal, S., Kumar, A., Jansen, R., Cheung, K.H., Sheehan, A., Symoniatis, D., Umansky, L., Heidtman, M., Nelson, F.K., Iwasaki, H., Hager, K., Gerstein, M., Miller, P., Roeder, G.S., Snyder, M.: Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402, 413–418 (1999)
Shrager, J., Langley, P., Pohorille, A.: Guiding revision of regulatory models with expression data. In: Proceedings of the Pacific Symposium on Biocomputing, Lihue, HI, vol. 7, pp. 486–497 (2002)
Souza, G.M., da Silva, A.M., Kuspa, A.: Starvation promotes dictyostelium development by relieving pufa inhibition of pka translation through the yaka kinase pathway. Development 126, 3263–3274 (1999)
Souza, G.M., Lu, S.J., Kuspa, A.: YakA, a protein kinase required for the transition from growth to development in Dictyostelium. Development 125, 2291–2302 (1998)
Stefik, M.: Planning with constraints (MOLGEN: Part 1). Artificial Intelligence 16, 111–140 (1981)
Ullrich, A., Shine, J., Chirgwin, J., Pictet, R., Tischer, E., Rutter, W.J., Goodman, H.M.: Rat insulin genes: construction of plasmids containing the coding sequences. Science 196, 1313–1319 (1977)
Weld, D.S., de Kleer, J.: Readings in Qualitative Reasoning about Physical Systems. Morgan Kaufmann, San Mateo (1990)
Winzeler, E.A., Shoemaker, D.D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J.D., Bussey, H., Chu, A.M., Connelly, C., Davis, K., Dietrich, F., Dow, S.W., El Bakkoury, M., Foury, F., Friend, S.H., Gentalen, E., Giaever, G., Hegemann, J.H., Jones, T., Laub, M., Liao, H., Liebundguth, N., Lockhart, D.J., Lucau-Danila, A., Lussier, M., M’Rabet, N., Menard, P., Mittmann, M., Pai, C., Rebischung, C., Revuelta, J.L., Riles, L., Roberts, C.J., Ross-MacDonald, P., Scherens, B., Snyder, M., Sookhai-Mahadeo, S., Storms, R.K., Veronneau, S., Voet, M., Volckaert, G., Ward, T.R., Wysocki, R., Yen, G.S., Yu, K., Zimmermann, K., Philippsen, P., Johnston, M., Davis, R.W.: Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906 (1999)
Zimmer, C.: The slime alternative — what the behavior of amoebas may tell us. Discover, 86–93 (May 1998)
Zupan, B., Demšar, J., Bratko, I., Juvan, P., Halter, J.A., Kuspa, A., Shaulsky, G.: GenePath: a system for automated construction of genetic networks from mutant data. Bioinformatics 19, 383–389 (2003)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Zupan, B. et al. (2007). Discovery of Genetic Networks Through Abduction and Qualitative Simulation. In: Džeroski, S., Todorovski, L. (eds) Computational Discovery of Scientific Knowledge. Lecture Notes in Computer Science(), vol 4660. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73920-3_11
Download citation
DOI: https://doi.org/10.1007/978-3-540-73920-3_11
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-73919-7
Online ISBN: 978-3-540-73920-3
eBook Packages: Computer ScienceComputer Science (R0)