Network Analysis

Graph theory: Fundamental principles and concepts of graph theory like nodes, edges, degree, shortest path, connectedness, centrality measures, etc.

Network structures: Different types of network structures such as scale-free networks, small-world networks, random graphs, etc.

Topological analysis: Analyzing the network topology, analyzing the hierarchical structure of the network, clustering algorithms, etc.

Data preprocessing: Preprocessing gene expression data, quality control, normalization, missing value imputation, etc.

Gene regulatory networks (GRNs): Building GRNs, detecting regulatory modules, analyzing transcriptional networks, visualizing motifs, etc.

Interactome networks: Biology interactome network, protein-protein interaction (PPI) network, protein-DNA interaction (PDI) network, etc.

Functional annotation: Function annotation analysis for genes, discovering functional profile of gene set or network, etc.

Network dynamics: Analysis of the evolution of gene networks, analysis of network stability and convergence, etc.

Pathway enrichment analysis: Identifying enriched pathways, GO (gene ontology) enrichment analysis, metabolic pathway analysis, etc.

Network visualization: Network visualization of gene expression data, PPI networks, hierarchies, etc.

Machine learning: Popular machine learning techniques for network analysis, feature selection, classification and clustering analysis.

Statistical analysis: Network analysis using statistical techniques such as correlation, regression, etc.

Protein-Protein Interaction Networks: Description of the interactions among proteins.

Gene Regulatory Networks: Description of the interactions between genes and their regulatory elements.

Metabolic Networks: Description of the chemical reactions occurring in the cell and the associated metabolites.

Signal Transduction Networks: Description of the interactions between signaling molecules and their receptors.

Disease Networks: Identification of disease-associated genes and their interactions.

Co-expression Networks: Description of the correlation between gene expression levels.

Protein-DNA Interaction Networks: Description of the interactions between proteins and DNA.

Gene Ontology Networks: Description of the functional relationships among genes.

miRNA Networks: Description of the interactions among miRNAs and their target genes.

Pathway Analysis Networks: Identification of the pathways involved in a biological process or disease.