Relative performance of different methods with regard to the test set and novel set on GO biological process terms (size 101 to 300)

The relative performance of individual groups differs between the test set and novel set. In addition, the performance on the novel set was generally worse than on the test set. This indicates that cross-validation should be used carefully in assessing the relative performance of different algorithms and that evaluation on novel biology is necessary. Asterisks indicate second round submissions. GO, Gene Ontology.<p><b>Copyright information:</b></p><p>Taken from "Predicting gene function in a hierarchical context with an ensemble of classifiers"</p><p>http://genomebiology.com/2008/9/S1/S3</p><p>Genome Biology 2008;9(Suppl 1):S3-S3.</p><p>Published online 27 Jun 2008</p><p>PMCID:PMC2447537.</p><p></p

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods-0

<p><b>Copyright information:</b></p><p>Taken from "Nearest Neighbor Networks: clustering expression data based on gene neighborhoods"</p><p>http://www.biomedcentral.com/1471-2105/8/250</p><p>BMC Bioinformatics 2007;8():250-250.</p><p>Published online 12 Jul 2007</p><p>PMCID:PMC1941745.</p><p></p> using the parameters = 5 and = 10, visualized using Java TreeView [42]. NNN clusters have been colored, internally hierarchically clustered, and the cluster centroids have in turn been hierarchically clustered to provide an easily interpretable tree

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods-2

<p><b>Copyright information:</b></p><p>Taken from "Nearest Neighbor Networks: clustering expression data based on gene neighborhoods"</p><p>http://www.biomedcentral.com/1471-2105/8/250</p><p>BMC Bioinformatics 2007;8():250-250.</p><p>Published online 12 Jul 2007</p><p>PMCID:PMC1941745.</p><p></p>and GO term basis. Each cell represents an AUC score calculated analytically using the Wilcoxon Rank Sum formula; below baseline performance appears in blue, and yellow indicates higher performance. Data set and term combinations for which ten or fewer pairs were able to be evaluated are excluded and appear as gray missing values; functions for which less than 10% of methods were available due to gene exclusion by NNN, QTC, or SAMBA were removed. Visualization provided by TIGR MeV [41]

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods-4

<p><b>Copyright information:</b></p><p>Taken from "Nearest Neighbor Networks: clustering expression data based on gene neighborhoods"</p><p>http://www.biomedcentral.com/1471-2105/8/250</p><p>BMC Bioinformatics 2007;8():250-250.</p><p>Published online 12 Jul 2007</p><p>PMCID:PMC1941745.</p><p></p> using the parameters = 5 and = 10, visualized using Java TreeView [42]. NNN clusters have been colored, internally hierarchically clustered, and the cluster centroids have in turn been hierarchically clustered to provide an easily interpretable tree

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods-3

<p><b>Copyright information:</b></p><p>Taken from "Nearest Neighbor Networks: clustering expression data based on gene neighborhoods"</p><p>http://www.biomedcentral.com/1471-2105/8/250</p><p>BMC Bioinformatics 2007;8():250-250.</p><p>Published online 12 Jul 2007</p><p>PMCID:PMC1941745.</p><p></p>rocesses for which data was available in our analysis. For each algorithm, the maximum AUC across all six data sets was determined, and the resulting AUCs are presented here in descending order per algorithm. NNN correctly clusters genes from substantially more biological processes relative to previous methods

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

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