Tool: KeggExp: a web server for visualizing KEGG pathways maps when analyzing expression profile data
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gravatar for liux.bio
14 months ago by
liux.bio340
China
liux.bio340 wrote:

Overview

KeggExp is a biologist-friendly web server to integrate KEGG pathways and expression profile data (data generated by Microarray, RNA-seq, or mass spectrometry). It aims to adopt interactive visualization techniques to help researchers find key kegg pathways or genes that are worth further attention in analyzing expression profile data. Compared with existing tools, it has following new features:

  • It presents simultaneously pathway map and dendgrogram & heatmap of hierarchical clustering results of the genes in the pathway.
  • It provides interactive operations connecting the pathway map and the dendgrogram & heatmap; users can click to select co-expressed genes in the dendgrogram & heatmap and then highlight them in the pathway map.
  • It presents a button for each experimental group; users can click one button and then highlight the differentially-expressed genes/proteins in the pathway map.
  • It provides interactive operations to visualize multiple pathways in sequence.

Main features

Visualize pathway map and dendgrogram & heatmap

After users select one pathway, KeggExp automatically downloads pathway map and perform clustering analysis for the genes in the pathway, then simultaneously presents pathway map and dendgrogram & heatmap.


enter image description here


Highlight co-expressed genes in the pathway map

Users could select co-expressed genes in the dendgrogram & heatmap, and highlight them in the pathway map.


enter image description here


Highlight differentially-expressed genes/proteins in the pathway map

When users click one experimental group, the up-expressed genes will become red and the down-expressed genes will become green.


enter image description here


Operations for visualizing multiple pathways

One pathway often have cross talks with other pathways. Users can click pathway box in the pathway map and then explore the corresponding pathway. The pathways that have been explored are listed in the left top, users can select one pathway they want to explore.


enter image description here


Availability

KeggExp is available at http://www.fgvis.com/expressvis/KeggExp. If any questions or suggestions, feel free to contact me.

ADD COMMENTlink modified 12 months ago • written 14 months ago by liux.bio340

Powerful. I will recommend to my colleagues. Two small bugs. 1. the try samples cannot be downloaded correctly. 2.heatmap cannot show negative value. BTW, how does it calculate the group expression per gene?

For 1. enter image description here For 2. enter image description here

ADD REPLYlink modified 14 months ago • written 14 months ago by Zhilong Jia1.4k

For the first bug, the browser should be allowed to download multiple files simultaneously.


For the second bug, heatmap is designed to not to show negative value. The expression profile data should be processed data, in which the fold change of one gene between group A and group B could be calculated with ValueA/ValueB; that is to say, the expression value should not be transformed to log2 value. PS: you could double click one gene in the heatmap and show this gene's expression with scattermap.


As for the group expression per gene, we use the average of values of all the replicates in the group.


Many thanks for your feedback. I will add more information to the tutorial.

ADD REPLYlink written 14 months ago by liux.bio340
  1. try to download it at the deployed website. you will see the downloaded files as follow. enter image description here

  2. The expression profile data should be processed data, in which the fold change of one gene between group A and group B could be calculated with ValueA/ValueB. Actually, it is one group, not group A/group B, per column. In most cases, logging (or voomming in limma) the data will make it follow a normal distribution. A negative value can be used in the form of ValueA/ValueB.

Thank you. KEGGexp is useful.

ADD REPLYlink modified 14 months ago • written 14 months ago by Zhilong Jia1.4k
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