DNA microarray technology is the most notable high throughput technology which emerged for functional genomics in recent years. Patterns in microarray data provide clues of gene functions, cell types, and interactions among genes or gene products. Since the scale of microarray data keeps on growing, there is an urgent need for the development of methods and tools for the analysis of these huge amounts of complex data. / Interesting patterns in microarray data can be patterns appearing with significant frequencies or patterns appearing special trends. Firstly, an algorithm to find biclusters with coherent values is proposed. For these biclusters the subset of genes (or samples) show some similarities, such as low Euclidean distance or high Pearson correlation coefficient. We propose Average Correlation Value (ACV) to measure the homogeneity of a bicluster. ACV outperforms other alternatives for being applicable for biclusters of more types. Our algorithm applies dominant set approach to create sets of sorting vectors for rows of the data matrix. In this way, the co-expressed rows of the data matrix could be gathered. By alternatively sorting and transposing the data matrix the blocks of co-expressed subset are gathered. Weighted correlation coefficient is used to measure the similarity in the gene level and the sample level. Their weights are updated each time using the sorting vector of the previous iteration. Genes/samples which are assigned higher weights contribute more to the similarity measure when they are used as features for the other dimension. Unlike the two-way clustering or divide and conquer algorithm, our approach does not break the structure of the whole data and can find multiple overlapping biclusters. Also the method has low computation cost comparing to the exhaustive enumeration and distribution parameter identification methods. / Next, algorithms to find biclusters with coherent evolutions, more specific, the order preserving patterns, are proposed. In an Order Preserving Cluster (OP-Cluster) genes induce the same relative order on samples, while the exact magnitude of the data are not regarded. By converting each gene expression vector into an ordered label sequence, we transfer the problem into finding frequent orders appearing in the sequence set. Two heuristic algorithms, Growing Prefix and Suffix (GPS) and Growing Frequent Position (GFP) are presented. The results show these methods both have good scale-up properties. They output larger OP-Clusters more efficiently and have lower space and computation space cost comparing to the existing methods. / We propose the idea of Discovering Distinct Patterns (DDP) in gene expression data. The distinct patterns correspond to genes with significantly different patterns. DDP is useful to scale-down the analysis when there is little prior knowledge. A DDP algorithm is proposed by iteratively picking out pairs of genes with the largest dissimilarities. Experiments are implemented on both synthetic data sets and real microarray data. The results show the effectiveness and efficiency in finding functional significant genes. The usefulness of genes with distinct patterns for constructing simplified gene regulatory network is further discussed. / Teng, Li. / Adviser: Laiwan Chan. / Source: Dissertation Abstracts International, Volume: 71-01, Section: B, page: 0446. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 118-128). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. Ann Arbor, MI : ProQuest Information and Learning Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese.
| Identifer | oai:union.ndltd.org:cuhk.edu.hk/oai:cuhk-dr:cuhk_344387 |
| Date | January 2009 |
| Contributors | Teng, Li., Chinese University of Hong Kong Graduate School. Division of Computer Science and Engineering. |
| Source Sets | The Chinese University of Hong Kong |
| Language | English, Chinese |
| Detected Language | English |
| Type | Text, theses |
| Format | electronic resource, microform, microfiche, 1 online resource (vii, 128 leaves : ill.) |
| Rights | Use of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/) |
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