KEGGanim

Category Cross-Omics>Pathway Analysis/Tools

Abstract KEGGanim is a novel web-based visualization tool that links manually curated 'pathway maps' from the Kyoto Encyclopedia of Genes and Genomes (KEGG) with experimental data from sources like gene expression and proteomics.

KEGGanim produces animations or static images of KEGG pathways by overlaying public or user uploaded high-throughput data over hand drawn KEGG pathway maps.

KEGGanim shows animated figures of pathways with genes and proteins depicted as colored rectangles. Pathway members are painted red or green according to their experimental values in a given dataset.

Animation changes the color values of these rectangles while looping over experimental conditions in the dataset, for instance, moments in a time series, healthy and diseased samples, or samples of healthy tissues.

KEGGanim allows a researcher to observe expression and protein production dynamics in the context of pathway dependencies.

Animating a pathway over consecutive time-points reflects the behavior of master regulatory genes, propagation of signals in the pathway over time, and the avalanche of up- and down regulation caused by the master regulator.

When analyzing a set of conditions or tissues on a microarray, KEGGanim allows you to reason about tissue specificity or the influence of global conditions on the pathway and its components.

KEGGanim combines KEGG pathway data with a matrix of experimental values of genes and proteins.

First, the user needs to select a pathway of interest from a dropdown menu in the web interface, which corresponds to a graphical map downloaded from the KEGG database.

The second input is a matrix containing experimental values for genes and proteins.

A number of gene expression datasets from GEO (see G6G Abstract Number 20013) and ArrayExpress (see G6G Abstract Number 20012) are available in KEGGanim for immediate analysis.

KEGGanim automatically fetches all associations to the genes in the pathway from the g:Profiler software (g:Profiler is a family of tools for functional assessment of gene groups, gene ID mappings, orthology and expression similarity searches.), and creates an animation of the related experimental values over different conditions.

If several probe-sets or proteins match a pathway member, the corresponding node is split into smaller colored areas to reflect different experimental values.

Users can upload their own data for analysis and visualization.

Most common gene and protein IDs and microarray probe-sets are accepted as input, for instance standard names, such as, RefSeq, Entrez, Affymetrix, UniProt, EnsEMBL as well as species-specific IDs.

Uploaded data is optionally centred and normalized, and missing values may be replaced with fixed values or via the k-Nearest Neighbor (kNN) method implementation in GEPAS (see G6G Abstract Number 20273).

Additional options help to interpret the animations and concentrate on specific conditions or components.

KEGGanim tooltips display names and descriptions of genes and proteins when the user hovers over corresponding pathway members.

Line-plots display the amounts of proteins or the gene expression levels.

The user can narrow down the study by selecting a subset of conditions to view.

Experimental values for irrelevant pathway members and related probe- sets may also be excluded from the animation.

The cinefilm feature overcomes the technical difficulty of including animations in printed materials by allowing the user to extract pathway snapshots of time-points or conditions into a separate image.

These features are especially useful in visualizing time-series data.

The Graphics Interchange Format (GIF) animations produced by KEGGanim do Not require special software packages for viewing, and can easily be inserted into presentation slides, web pages, tutorials, etc.

System Requirements

Web-based.

Manufacturer

Manufacturer Web Site KEGGanim

Price Contact manufacturer.

G6G Abstract Number 20390

G6G Manufacturer Number 104027