Zolotareva, Olga: Identification of Differentially Expressed Gene Modules in Heterogeneous Diseases. 2021
Content
- Table of contents
- List of figures
- List of tables
- Nomenclature
- 1 Introduction
- 2 Background
- 2.1 Genes and Diseases
- 2.2 Gene Prioritization
- 2.3 Mendelian and Complex diseases
- 2.4 Disease Heterogeneity
- 2.5 Gene expression profiling
- 2.6 Identification of differentially expressed genes and gene sets
- 2.7 Biological networks
- 2.8 Network analysis for medical bioinformatics
- 3 Overview of Biclustering Methods
- 3.1 Introduction to Biclustering
- 3.2 Classification of biclustering methods
- 3.2.1 Input data type
- 3.2.2 Patterns
- 3.2.3 The usage of additional data sources
- 3.2.4 Other constraints
- 3.3 Related works
- 3.3.1 Cheng and Church
- 3.3.2 Plaid
- 3.3.3 xMOTIFs
- 3.3.4 ISA
- 3.3.5 COALESCE
- 3.3.6 QUBIC
- 3.3.7 FABIA
- 3.3.8 BiBit
- 3.3.9 DeBi
- 3.4 Validation approaches
- 4 Methods
- 4.1 Problem definition
- 4.2 DESMOND Algorithm
- 4.2.1 Step 1. Assigning sample sets to edges
- 4.2.2 Step 2. Probabilistic edge clustering
- 4.2.3 Step 3. Post-processing
- 4.3 DESMOND2
- 4.4 Analysis of the runtime complexity
- 4.5 Datasets
- 4.6 Experiments
- 4.6.1 Evaluation with synthetic data and the choice of parameters
- 4.6.2 Evaluation with breast cancer data
- 4.7 Code Availability
- 5 Results and Discussion
- 6 Conclusions
- References