cytoscape visualization with negative edge

Illustrator) and adjust labelsġ5 Dealing with ‘hairballs’: zoom or filterġ6 Visual Features Node and edge attributes Visual attributesĪttribute color Arrow shape Visual Features Node and edge attributes Represent properties of genes, interactions Text (string), integer, float, Boolean, list Visual attributes Node, edge visual properties Colour, shape, size, borders, opacity. Use layout to interpret network Local relationships Guilt-by-association Dense clusters Global relationships Visualise multiple types of dataįorce-directed: nodes repel and edges pull Good for up to 500 nodes Bigger networks give hairballs - reduce number of edges Advice: try force directed first, or hierarchical for tree-like networks Tips for better looking networks Manually adjust layout Load network into a drawing program (e.g. We also can have a pathway network : nodes (circle) are representing a gene-set and edge represents the number of overlapping genesġ1 Network basics (ii) - layout and visual attributes Node (circle) are going to represent gene and are going to be related by edges (lines). A gene gene network or a pathway network. We can have 2 types of network when we speak about the output of a pathway enrichment analysis. Node (molecule) Gene Protein Transcript Drug MicroRNA … A simple mapping one molecule - node one interaction - edge A more realistic mapping Cell localization cell cycle cell type taxonomy Physiologically relevant Edges - diverse relationships Critical: what do nodes and edges mean? Edge (interaction) Genetic interaction Physical protein interaction Co-expression Signaling interaction Metabolic reaction DNA-binding Directed or undirected? Edges and nodes : a network is composed of 2 elements : edges and nodes. We also can have a pathway network : nodes (circle) are representing a gene-set and edge represents the number of overlapping genes Physical, regulatory, genetic, functional interactions Useful for discovering relationships in large data sets Better than tables in Excel Visualize multiple data types together Discover interesting patterns Network analysis Finding sub-networks with certain properties (densely connected, co-expressed, frequently mutated, clinical characteristics) Finding paths between nodes (or other network “motifs”) Finding central nodes in network topology (“hub” genes)Ī simple mapping one molecule - node one interaction - edge A more realistic mapping Cell localization cell cycle cell type taxonomy Physiologically relevant Edges - diverse relationships Critical: what do nodes and edges mean? Edges and nodes : a network is composed of 2 elements : edges and nodes. Biochemical reactions - Small-scale, fewer genes - Concentrated from decades of literature - Simplified cellular logic, noisy - Abstractions: directed, undirected - Large-scale, genome-wide - Constructed from omics data integrationħ Networks Represent relationships of biological molecules TODO: What: Schedules first part of talk How Bridge: So this is all about networks.Ħ Pathways vs Networks - Detailed, high-confidence consensus “Integration of biological networks and gene expression data using Cytoscape”, Nature Protocols, 2, (2007). Jüri Reimand High-throughput Biology: From Sequence to Networks April 27-May 3, 2015Ī specific example of this workflow: Cline, et al. In collaboration with Cold Spring Harbor Laboratory & New York Genome CenterĤ Module 3 Lab Cytoscape & Enrichment Map

Cytoscape visualization with negative edge