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Functional interaction networks among groups of genes selected from the data, were built using the Cytoscape [ 52] Reactome FI (Functional Interaction) application [ 53– 55] and visualised with the organic layout.
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The reference structure alignments for the training and validation data are built using our in-house structure alignment tool DeepAlign.
Data sets were built using the OligoGenerator program of [ 20].
Data sets were built using Statistical Analysis Software SASS v.9.2; SAS Institute, Cary, NC), and graphical analyses were conducted with TIBCO Spotfire S+ (v.8.2, TIBCO Spotfire, Somerville, MA) or SAS.
Phylogenetic trees from the post-vaccination data set and the two data sets combined were built using MEGA 2.1 [ 25] and the minimum evolution criterion.
Using all the data several classifiers were built using two machine learning techniques namely Support Vector Machines (SVM) and Neural Networks (NN).
Characterization maps were built using data from both techniques.
Molecular trees of Culicidae and Anophelinae were built using data from previous studies.
Two SVM models were built using data from 219 patients with lung cancer treated using radiotherapy (34 diagnosed with pneumonitis).
Models were built using data for all patients and separately for RF− patients only.
The delta-pair histograms were built using the data publicly available in the OCHEM database.
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