Improving text clustering for functional analysis of genes

vi Chapter 1 Literature Review and Requirements Analysis 1 1.1 Functional analysis of microarray data 1 1.2 Gene Ontology-based functional analysis 1 1.3 Literature-based functional analysis 4 1.3.1 Assuming similar expressions imply same functional pathway 5 1.3.2 Not assuming similar expressions imply same functional pathway 7 1.4 Hybrid systems 10 1.5 Requirements analysis 11 Chapter 2 Strategic Design 14 2.1 Design overview 14 2.2 Two-step vs. one-step clustering design 15 2.3 Document representation 16 2.4 Choice of text clustering algorithm 18 Chapter 3 BOW-Based System: GeneNarrator 1 20 3.1 Architectural overview of GeneNarrator 1 20 3.2 Detailed description of individual modules 21 3.2.1 DocBuilder 21 3.2.2 LongBOW 21 3.2.3 CrossBOW 23 3.2.4 ArrowSmith 24 3.2.5 GeneSmith 25 3.2.6 BOWviewer 25 Chapter 4 Evaluation of GeneNarrator 1 27 4.1 The gold standard gene list and document set 27 4.2 Evaluating clustering: literature review 28 4.2.1 Subjective judgment 28 4.2.2 Cluster quality measures 29