Table 3 Comparing the biological relevance and novelty of different biclustering solutions
From: BicPAM: Pattern-based biclustering for biomedical data analysis
Dataset | Approach | ♯Bics | Avg.♯Genes ×♯Conds | ♯Bics sig.enriched | Coverage and exclusivity of enriched GO terms |
|---|---|---|---|---|---|
dlblc | BicPAM | 56 | 83 ×7 | 43 (77%) | Highest number of exclusively enriched terms (partial list in Table 4). |
(human | BiModule | 322 | 62 ×4 | 79 (25%) | Absence of closing options leads to redundant and less significant terms. |
genome) | DeBi | 31 | 73 ×6 | 21 (68%) | Loss of relevant terms due to the inability to discover all maximal biclusters. |
|  | CC | 10 | 41 ×33 | 5 (50%) | Exclusive bicluster related with circulatory & cardiovascular system development. |
|  | ISA | 72 | 23 ×8 | 8 (11%) | Exclusive bicluster for extracellular structure organization and heparin binding. |
|  | Plaid | 3 | 12 ×49 | 1 (33%) | Majority of genes modeled in a single background bicluster with general terms. |
|  | Fabia | 10 | 79 ×35 | 6 (60%) | Small bicluster with superior enrichment of antigen binding functions. |
|  | Bexpa | 10 | 16 ×87 | 2 (20%) | Small sets of genes supported by large number of conditions. |
|  | Samba | 100 | 17 ×6 | 18 (18%) | Dedicated terms for antigen processing, peptide cross-linking and disassembly. |
|  | OPSM | 12 | 128 ×5 | 5 (42%) | High variance of ♯ genes and ♯ conditions; some of the biclusters with low ♯ genes (coherency across high ♯ conditions) have exclusive significantly enriched terms. |
hughes | BicPAM | 47 | 360 ×7 | 38 (81%) | Exclusive enriched terms due to flexible coherency and post-processing criteria. |
(yeast | BiModule | 219 | 285 ×4 | 43 (20%) | Terms with lower sig. than terms from noise-tolerant BicPAM solutions. |
genome) | DeBi | 28 | 317 ×7 | 21 (75%) | Terms observed across very small sets of conditions (≤5) are not enriched. |
|  | CC | 10 | 228 ×58 | 6 (60%) | GO terms covered by BicPAM constant biclusters. |
|  | ISA | 8 | 120 ×4 | 5 (63%) | Small biclusters with exclusive significance GO terms: spindle pole and karyogamy. |
|  | Plaid | 8 | 78 ×39 | 3 (38%) | One bicluster with higher significance for fungal-type cell wall assembly. |
|  | Fabia | 10 | 210 ×49 | 5 (50%) | Higher significance observed for actin cortical patch and oxidoreductase GO-terms. |
|  | Bexpa | 72 | 42 ×49 | 1 (10%) | Low number of enriched terms (probably due to the low ♯ genes per bicluster). |
|  | Samba | 120 | 18 ×9 | 11 (9%) | Enriched terms covered by pattern-based biclustering solutions. |
|  | OPSM | 6 | 531 ×4 | 3 (50%) | Exclusive bicluster for the negative regulation of metabolic processes. |
gasch | BicPAM | 149 | 411 ×8 | 123 (83%) | Large diversity of highly significant GO-terms (partial list in Table 4). |
(yeast | BiModule | 653 | 287 ×4 | 159 (24%) | Large but incomplete set of GO-terms as it excludes non-constant biclusters. |
genome) | DeBi | 82 | 310 ×6 | 61 (74%) | Significance of terms slightly differ than BicPAM due to the handling of noise. |
|  | CC | 10 | 203 ×79 | 7 (70%) | Enriched terms appear in BicPAM solutions with higher significance. |
|  | ISA | 23 | 292 ×22 | 18 (78%) | Enriched terms covered by pattern-based biclustering solutions. |
|  | Plaid | 6 | 48 ×12 | 3 (50%) | Biclusters (apart from background layer) with lower enrichments than peers. |
|  | Fabia | 10 | 310 ×41 | 8 (80%) | Bicluster with higher sig. for specific proteasome complexes. |
|  | Bexpa | 10 | 63 ×29 | 3 (33%) | The few biclusters with deviation in size (higher ♯ genes) are significant. |
|  | OPSM | 16 | 212 ×8 | 11 (69%) | One bicluster with higher significance for pre-ribosome functions. |