Gene Expression for Classification Dr. Animesh Sharma
Gene Expression for Classification <ul><li>Snapshot at time = t </li></ul><ul><li>Class: [1,…,p], Gene: [1,...,q],  </li><...
Case Studies <ul><li>On Identifying Marker Genes from Gene Expression Data in a Neural Framework through Online Feature An...
AML - ALL
SRBCT <ul><li>7 markers </li></ul><ul><ul><li>fibroblast growth factor receptor 4 (FGFR)  </li></ul></ul><ul><ul><li>trans...
Thanks I wish everyone a great and highly productive 2007!
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Gene expression analysis

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Gene expression analysis using Featue Selection Multi Layer Perceptron and Non Euclidean Relational Fuzzy c-Means.

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Gene expression analysis

  1. 1. Gene Expression for Classification Dr. Animesh Sharma
  2. 2. Gene Expression for Classification <ul><li>Snapshot at time = t </li></ul><ul><li>Class: [1,…,p], Gene: [1,...,q], </li></ul><ul><li>Sample: [1,…,r] </li></ul><ul><ul><li>Low sample, High Dimension </li></ul></ul><ul><li>Find n<<<p </li></ul><ul><ul><li>Good discriminating power </li></ul></ul><ul><li>Problem: </li></ul><ul><ul><li>‘ r’ too low </li></ul></ul><ul><ul><li>Non linear expression </li></ul></ul><ul><ul><li>Noise in expression data </li></ul></ul>Expression plot of Just 1 Gene! (across 4 Classes and 20 Sample)
  3. 3. Case Studies <ul><li>On Identifying Marker Genes from Gene Expression Data in a Neural Framework through Online Feature Analysis </li></ul><ul><li>( IJIS Wiley ) </li></ul><ul><ul><li>Class (Sample(Tr:Te)): AML (11:14) / ALL (27:20) </li></ul></ul><ul><ul><li>7129 Genes </li></ul></ul><ul><ul><li>FSMLP – 5 Genes, LM NN- 1 Misclassification (MC) </li></ul></ul><ul><ul><ul><li>Golub et al. – 50 Genes, 4 MC (SOM) </li></ul></ul></ul><ul><ul><ul><li>Cho et al. – 25 Genes, 2 MC (MI) </li></ul></ul></ul><ul><li>Discovering biomarkers from gene expression data for predicting cancer subgroups using neural networks and relational fuzzy clustering ( BMC Bioinformatics ) </li></ul><ul><ul><li>Class (Sample(Tr:Te)): EWS (23:6) / BL (8:3) / NB (12:6) / RMS (20:5 ) </li></ul></ul><ul><ul><li>2308 Genes </li></ul></ul><ul><ul><li>FSMLP->NERFCM(Corr) – 20->7 Genes, RBF/SVM - 0 MC </li></ul></ul><ul><ul><ul><li>Khan et al. – 96 Genes, 0 MLP </li></ul></ul></ul><ul><ul><ul><li>Tibshirani et al. – 43 Genes, 0 Nearest Centroid (SM) </li></ul></ul></ul>
  4. 4. AML - ALL
  5. 5. SRBCT <ul><li>7 markers </li></ul><ul><ul><li>fibroblast growth factor receptor 4 (FGFR) </li></ul></ul><ul><ul><li>transmembrane protein (AF1Q) </li></ul></ul><ul><ul><li>NGFI-A binding protein 2 (NAB2) </li></ul></ul><ul><ul><li>cadherin 2, N-cadherin (neuronal) (CDH2) </li></ul></ul><ul><ul><li>EH domain containing 1 (EHD1) </li></ul></ul><ul><ul><li>lymphocyte-specific protein 1 (LSP1 ) </li></ul></ul><ul><ul><li>follicular lymphoma variant translocation 1 (FVT1) </li></ul></ul>A. EWS, B. NHL, C. NB, D. RMS
  6. 6. Thanks I wish everyone a great and highly productive 2007!

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