Additional file 1 of Accurate and highly interpretable prediction of gene expression from histone modifications

Additional file 1. Supplementary materials for “Accurate and highly interpretable prediction of gene expression from histone modifications”. S1. Considered epigenomes and classification performance. S2. Hyperparameter search space. S3. Sensitivity analyses. S4. Validation against ChromHMM chromatin states. S5. An alternative approach to binary thresholding. S6. ShallowChrome as a regression model. S7. Cross-epigenome generalisation. S8. Reproducing AttentiveChrome results

SMfinder: Small Molecules Finder for Metabolomics and Lipidomics analysis

SMfinder: Small Molecules Finder for Metabolomics and Lipidomics analysi

Number of high-precision predictions among GO terms for which precision can be confidently estimated

Number of currently annotated (green) versus predicted genes (orange, predictions expected to be correct; gray, predictions expected to be incorrect) for a subset of Gene Ontology (GO) terms for which 30% precision on held-out annotations was achieved while recovering at least 10 positives in the held-out set. The number of predicted genes displayed was limited to 1,000. GO terms were ordered according to similarity of prediction/annotation patterns. Terminal digits of GO term identifiers are shown in parentheses. GO-BP, GO Biological process; GO-CC, GO Cellular component; GO-MF, GO Molecular function.<p><b>Copyright information:</b></p><p>Taken from "A critical assessment of gene function prediction using integrated genomic evidence"</p><p>http://genomebiology.com/2008/9/S1/S2</p><p>Genome Biology 2008;9(Suppl 1):S2-S2.</p><p>Published online 27 Jun 2008</p><p>PMCID:PMC2447536.</p><p></p

Distribution of GO terms at several precision/recall performance points

Proportion of Gene Ontology (GO) terms per evaluation category with a precision/recall performance point that is both above and to the right of a given precision/recall point in the contour plots. GO-BP, GO Biological process; GO-CC, GO Cellular component; GO-MF, GO Molecular function.<p><b>Copyright information:</b></p><p>Taken from "A critical assessment of gene function prediction using integrated genomic evidence"</p><p>http://genomebiology.com/2008/9/S1/S2</p><p>Genome Biology 2008;9(Suppl 1):S2-S2.</p><p>Published online 27 Jun 2008</p><p>PMCID:PMC2447536.</p><p></p

Illustration of evidence underlying predictions for the GO term 'Mitochondrial part'

As described in Figure 6a-e. GO, Gene Ontology.<p><b>Copyright information:</b></p><p>Taken from "A critical assessment of gene function prediction using integrated genomic evidence"</p><p>http://genomebiology.com/2008/9/S1/S2</p><p>Genome Biology 2008;9(Suppl 1):S2-S2.</p><p>Published online 27 Jun 2008</p><p>PMCID:PMC2447536.</p><p></p

Illustration of evidence underlying predictions for the GO term 'Cell adhesion'

As an assessment of predictive usefulness, the precision at 20% recall (P20R) value based on each single data source is shown in parentheses. Expression levels of annotated genes (dark green) and predictions (orange), grouped by Pearson correlation and complete-linkage hierarchical clustering. Protein domains in common among predictions and annotated genes. Largest protein-protein interaction network among predictions and annotated genes. OPHID, Online Predicted Human Interaction Database. Disease and phenotype annotations in common between predictions and annotated genes. Terminal digits of identifiers are shown in parentheses. OMIM, Online Mendelian Inheritance in Man.<p><b>Copyright information:</b></p><p>Taken from "A critical assessment of gene function prediction using integrated genomic evidence"</p><p>http://genomebiology.com/2008/9/S1/S2</p><p>Genome Biology 2008;9(Suppl 1):S2-S2.</p><p>Published online 27 Jun 2008</p><p>PMCID:PMC2447536.</p><p></p