GEPAS Gene Expression Pattern Analysis Suite Ka-Lok Ng Dept. of Bioinformatics Asia University.

GEPASGene Expression Pattern Analysis Suite

Ka-Lok Ng

Dept. of Bioinformatics

Asia University

• Prepare a text file with tab delimiter

• Line starts with ‘#’ denotes comment

• http://gepas.bioinfo.cipf.es/

• Tools clustering choose SOTA upload the text file decide the threshold, i.e. 80% RUN

• To view the tree click ‘send to SotaTree’ default parameters RUN

Clusters information

Click to view the profile

Profile – horiz. & vert. large scale

• Cluster 3

Diauxic data

• http://gepas3.bioinfo.cipf.es/cgi-bin/sets/diauxic

Diauxic data

• Tools clustering choose SOTA upload the text file decide the threshold, i.e. 90% RUN

• To view the tree click ‘send to SotaTree’ default parameters RUN

Click on the cluster 6, it has 108 elements

Extract cluster 6 - PlotCorr

• column 1 vs column 2

Threshold = 0.2

Threshold = 0.0

Extract cluster 6 – TreeView

Tree width = 2200

Data – K-means cluster