KEGGanim: pathway animations for high-throughput data

[?] Select an existing high-throughput dataset

Uploaded datasets and public micorarray data (GEO, ArrayExpress):

[?] Manage and upload own datasets

g:PEDaM [?] is a light-weight file manager for gene expression data uploads.

Data folder actions: [?] [Create new folder]
[?] [Use my existing folder]

News

19.10.20 - KEGG database update. Update your existing datasets.

24.01.17 - KEGG database update. Regarding that, please remember to update your datasets.

26.10.15 - NOTICE: *BUG FIX*! We uncovered and fixed a bug that caused KNN impute option to mistreat datasets. All datasets with KNN impute option active are likely affected and have to be uploaded again. We apologise for any inconvenience.

19.02.15 - KEGG database update.

04.10.13 - Minor layout changes on web page (You won't notice). Also reminding You to update Your datasets.

24.01.12 - KEGG database update! Updates are going to be now on regular basis. If You get software errors or malformed images, try to update Your dataset!
Have You noticed the 'Animation filters' tab in 'Animate' box? You can have gene names drawn on image, select genes and samples to display aswell use different color schemes!

25.07.10 - Added support for all KEGG organisms and support for compound visualisation

02.09.09 - Fixed problems caused by KEGG ftp internal makeover; some other improvments / fixes.

Introduction

KEGGanim is a novel web-based tool for visualizing experimental data in the context of biological pathways. KEGGanim produces animations or static images of KEGG pathways by overlaying public or user uploaded high-thourghput data over handdrawn KEGG pathway maps.

KEGGanim visualisation highlights dynamic changes over experimental conditions (time, treatment, dosage, tissue, disease) and allows the user to observe important subpathways and key genes that influence other parts of the pathway.

The simple user interface of KEGGanim allows to quickly search pathways for specific genes and use a large collection of public microarray data. In addition to microarray experiments, KEGGanim also accepts proteomics data and user-specified input of many different gene, probe and protein identifier types for various organisms.

KEGGanim quick-start:

KEGGanim visualisation procedure consists of three essential steps presented in three orange blocks.

Select a dataset in the top orange block.
Example data and previously uploaded files are shown on the left side of the block. Data upload and management module g:PEDaM is available on the right.
Select a pathway in the middle orange block.
An alphabetical list of KEGG pathways is available in the dropdown menu. Click Start the animation! to start the animation below.
Finetune and Animate again using the bottom orange block.
CineFilm section on the left extracts conditions from pathways into compact images. ReAnimate section on the right allows filtering of pathway components and experimental conditions.

Examples:

Example 1
Endothelin-1 effect on fibroblasts (Xu et al [GEO:GDS860]) in human Prion disease pathway [KEGG:05020].
Example 2
Yeast diauxic shift dataset (DeRisi et al [GEO:GDS37]) in cell cycle [KEGG:04111].
Example 3
CineFilm image displaying three conditions from the dataset for the myocardial remodeling in response to LVAD dataset (Hall et al [GEO:GDS558]) in the apoptosis pathway [KEGG:04210].

Tips & Tricks:

Files uploaded in g:PeDAM automatically appear in dataset selection drop-down menu.
Most of the standard gene/probeset/protein identifiers for different species may be used in uploaded datasets. IDs are always treated in case insensitive manner.
The KEGGanim GIF animation can be stored on a local computer (right+click and Save as..). It is easy to include the animation in a Powerpoint presentation.
Links like [?] provide pop-up windows with KEGGanim help and documentation.