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GEPAS Gene Expression Pattern Analysis Suite

GEPAS Gene 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/

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GEPAS Gene Expression Pattern Analysis Suite

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  1. GEPASGene Expression Pattern Analysis Suite Ka-Lok Ng Dept. of Bioinformatics Asia University

  2. 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

  3. Clusters information Click to view the profile

  4. Profile – horiz. & vert. large scale • Cluster 3

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

  6. 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

  7. Extract cluster 6 - PlotCorr • column 1 vs column 2 Threshold = 0.0 Threshold = 0.2

  8. Extract cluster 6 – TreeView Tree width = 2200

  9. Data – K-means cluster

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