Additional file 2: of Semantic biomedical resource discovery: a Natural Language Processing framework

contains the list of tools and resources that were in our repository. (PDF 964 kb

Additional file 1: of Semantic biomedical resource discovery: a Natural Language Processing framework

contains extensive results of the experiments. (PDF 803 kb

Limitations of analyzing solely gene expression profiles.

<p>(A) A dummy pathway. (B) The input (artificial) gene expression profile. (C) Functional status of sub-paths–the shaded cells indicate that sub-path A <b>→</b> B–| C is functional in the corresponding samples.</p

The integrated network that reflects the CXCR4 mutation downstream signalling events

<p>The integrated network that reflects the CXCR4 mutation downstream signalling events</p

The MinePath identified sub-paths for the ‘3ER GSE2034-3494-7390’ merged dataset that discriminate between the ER+ and ER- phenotypes in the ErbB pathway.

<p>Edges colored in red indicate regulatory relations functional for the ER- phenotype, green for the ER+ phenotype, and black for relations that are functional for both phenotypes.</p

Semantics of pathway gene relations in MinePath ‘UP’, ‘DOWN’ stand for up-regulation and down-regulation of genes, respectively.

<p>Semantics of pathway gene relations in MinePath ‘UP’, ‘DOWN’ stand for up-regulation and down-regulation of genes, respectively.</p

Part of the WNT signaling pathway for gastric cancer that shows the MinePath discriminant sub-paths.

<p>Green edges indicate discriminant functional relations for GC cases; edges in black indicate discriminant functional relations for both CG and normal cases; undirected yellow edges denote binding/association relations.</p

Contrasted SPIA, GGEA and MinePath results for the p53 pathway using the GSE3494 ER+ vs. ER- dataset.

<p>The legend shows the meaning of the edge colors used to contrast between the results produced by the three pathway analysis methodologies.</p

Venn diagram of the selected (significant) pathways shared among SPIA, GGEA, MinePath and the six significant BrCa/ER pathways

<p>Venn diagram of the selected (significant) pathways shared among SPIA, GGEA, MinePath and the six significant BrCa/ER pathways</p

Predictive performance of MinePath on three BrCa/ER datasets Rows and columns refer to training and test data, respectively.

<p>Bold figures for ‘Average ACC’ indicate superior performance; ‘SP’–sub-path, ‘ACC’–prediction (on unseen/test data) accuracy, ‘AUC’–Area Under the Curve, ‘Average ACC’–average accuracy, i.e., the average accuracy of GSE3494 over GSE2034 (89.5%) and GSE7390 (89.9%) is 89.7%.</p