- Differentiation Between Viral vs. Bacterial Infections:
For machine-learning (SVM) to differentiate between viral and bacterial infections, we used MicroArray dataset GLP96 from: Ramilo O, Allman W, Chung W, Mejias A et al. Gene expression patterns in blood leukocytes discriminate patients with acute infections. Blood 2007 Mar 1;109(5):2066-77. PMID: 17105821
We used GEO2R to compare the bacterial infected datasets and viral infected datasets to get the top 100 differentially expressed genes. We then used the expression of these top differentially expressed genes for SVM.
We used sklearn to train our SVM. We do a logarithmic grid search from 10^-3 to 10^3 for tuning parameters C and gamma. We train using accuracy as our metric and by performing 5 fold cross validation in order to choose the best parameters. Our final parameters were C=1 and gamma=0.001. Our five fold cross validation had an accuracy of 90.8% and our test set had a 100% accuracy.
For gene set enrichment analysis, we used GSEA to run enrichment tests against C7: immunological signatures (189 gene sets) of GSEA's MSigDB database to compare patient sample against healthy samples.
- Mapping bacterial genome to find antibiotic-resistance conferring genes
For our analysis, we used the Antibiotic Resistance Genes Database from: Liu B, Pop M. ARDB-Antibiotic Resistance Genes Database. Nucleic Acids Res. 2009 Jan;37(Database issue):D443-7
- For the web front end, we used a python django server. Our pages were built using the bootstrap styling framework, and analytics were provided using the highcharts.js plotting library.