Current approaches integrating large scale data and information from a
variety of sources to reveal molecular basis of cellular events do not
adequately benefit from pathway information. Here, we portray a network structure based pathway enrichment system that fuses and exploits model and data: signalling pathways are taken as the biological models while microarray and ChIP-seq data are the sample input data sources among many other alternatives. Our model- and data-driven hybrid system allows to quantitatively assessing the biological activity of a cyclic pathway and simultaneous enrichment of the significant paths leading to the ultimate cellular response. Signal Transduction Score Flow (SiTSFlow) algorithm is the fundamental constituent of proposed network structure based pathway enrichment system. SiTSFlow algorithm converts each pathway into a cascaded graph and then gene scores are mapped onto the protein nodes. Gene scores are transferred to en route of the pathway to form a final activity score describing behaviour of a specific process in the pathway while enriching of the gene node scores. Because of cyclic pathways, the algorithm runs in an iterative manner and it terminates when the node scores converge. The converged final activity score provides a quantitative measure to assess the biological significance of a process under the given experimental conditions. The conversion of cyclic pathways into cascaded graphs is performed by using a linear time multiple source Breadth First Search Algorithm. Furthermore, proposed network structure based pathway enrichment system works in linear time in terms of nodes and edges of given pathways.
In order to explore various biological responses of several processes in a
global signalling network, the selected small pathways have been unified based on their common gene and process nodes. The merge algorithm for pathways also runs in linear time in terms of nodes and edges of given pathways.
In the experiments, SiTSFlow algorithm proved the convergence behaviour of activity scores for several cyclic pathways and for a global signalling network. The biological results obtained by assessing of experimental data by described network structure based pathway enrichment system were in correlation with the expected cellular behaviour under the given experimental conditions.
| Identifer | oai:union.ndltd.org:METU/oai:etd.lib.metu.edu.tr:http://etd.lib.metu.edu.tr/upload/12612951/index.pdf |
| Date | 01 February 2011 |
| Creators | Isik, Zerrin |
| Contributors | Atalay, Mehmet Volkan |
| Publisher | METU |
| Source Sets | Middle East Technical Univ. |
| Language | English |
| Detected Language | English |
| Type | Ph.D. Thesis |
| Format | text/pdf |
| Rights | To liberate the content for public access |
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