Table 1.
Statistical significance of protein pairs' functional coherence in Saccharomyces cerevisiae.
Figure 1.
Functionally coherent modules from the Chen and Yuan [8] study.
(A) Module ID M1 and (B) Module ID M3.
Table 2.
Functional modules evaluated using existing enrichment analysis tools in comparison with HMS.
Table 3.
Percentage of significant (-value
) and highly significant (
-value
) functionally coherent modules from Chen and Yuan [8] and CYS2008 [19].
Figure 2.
Functional coherence analysis of protein complexes and pathways.
Functional coherence analysis of protein complexes from MIPS-curated [15], Ho [17], Gavin [18], and Krogan [16] as well as metabolic pathways from KEGG. Comparison between our HMS scoring, cosine similarity with different -value methods from [22], Jaccard similarity with different
value methods from [22] and GS
[23] methods. (A) Significant Modules (
value
0.05 and (B) Highly Significant Modules (
value
).
Table 4.
HMS results for some KEGG metabolic pathways and MIPS protein complexes [22] classified as insignificant by Chagoyen et al. [22].
Table 5.
Comparison of pair-wise semantic similarity metrics using functionally-associated and non-functional protein pairs.
Table 6.
Skill metrics for Saccharomyces cerevisiae KEGG experiments.
Table 7.
Skill metrics for Saccharomyces cerevisiae MIPS experiments.
Table 8.
Consistency of multi-pathway genes across clusters that enrich the corressponding pathways.
Figure 3.
Effect of different values of on the
score.
Figure 4.
Functional annotation and coherence of hierarchical modules.
The figure shows the overview of the methodology to assess functional coherence and assign annotation to hierarchical functional modules.
Figure 5.
Overview of fuzzy reconstruction of hierarchical modularity.
Figure 6.
An illustration of a hierarchical taxonomy over the set of functional annotation terms
. (A) A DAG view. (B) A level set view.
Figure 7.
Hierarchical functional annotation of a gene module for a gene set
given the taxonomy
in Figure 6.
(A) Functional annotation of genes in by unrelated term sets in
. (B) A hierarchical gene module
. (C) The resulting annotation of the internal (non-leaf) nodes in
.
Figure 8.
Illustration of penalization factor calculation.
(A) Hierarchical annotation of the functional module defined in Figure 7. (B) Dissimilarity score for a parent
and a child
.
Figure 9.
Comparison between the three penalization factor functions considered.