Table 2.
Summary of statistically significant GeneGo pathway maps (FDR 0.0001) discovered in ANOVA-revealed, differentially regulated genes in PC samples from study 1 and/or study 2
| Unique pathways included* | P† | Hits‡ | Ratio, %§ | SF5‖ |
|---|---|---|---|---|
| GO category: development, n = 11#¶ | ||||
| Regulation of EMT* | 4.22 × 10−10 | 25/64 | 39.1 | B1 |
| IGF-1 receptor signaling | 2.83 × 10−8 | 14/51 | 27.4 | A5 |
| Flt3 signaling | 3.06 × 10−7 | 12/44 | 27.3 | A11 |
| FGFR signaling pathway | 2.69 × 10−6 | 12/53 | 22.6 | A22 |
| EGFR signaling pathway | 3.14 × 10−6 | 13/63 | 20.6 | A23 |
| GO category: cell adhesion and cytoskeleton remodeling, n = 8#¶ | ||||
| TGF, WNT and cytoskeletal remodeling | 4.47 × 10−8 | 31/111 | 27.9 | B2 |
| TGF, WNT and cytoskeletal remodeling | 7.69 × 10−8 | 20/111 | 18.0 | A8 |
| ECM remodeling | 1.89 × 10−7 | 19/52 | 36.5 | B3 |
| Chemokines and cell adhesion | 1.89 × 10−7 | 28/100 | 28.0 | B5 |
| Cytoskeleton remodeling | 2.98 × 10−7 | 28/102 | 27.5 | B6 |
| Cytoskeleton remodeling | 4.81 × 10−7 | 18/102 | 17.6 | A12 |
| PLAU signaling | 6.62 × 10−7 | 11/39 | 28.2 | A14 |
| GO category: immune response, n = 7#¶ | ||||
| Gastrin in inflammatory response | 5.54 × 10−9 | 17/69 | 24.6 | A2 |
| Classical complement pathway | 1.89 × 10−7 | 19/52 | 36.5 | B4 |
| Lectin-induced complement pathway | 3.62 × 10−7 | 18/49 | 36.7 | B7 |
| CD40 signaling | 6.16 × 10−7 | 14/64 | 21.9 | A13 |
| IL-7 signaling in B lymphocytes | 1.93 × 10−6 | 11/43 | 25.6 | A17 |
| GO category: others, n = 7††#¶ | ||||
| Apoptosis and survival–BAD phosphorylation | 1.80 × 10−8 | 13/42 | 31.0 | A3 |
| Translation–regulation of EIF4F activity | 4.85 × 10−8 | 14/53 | 26.4 | A6 |
| Translation–regulation of EIF2 activity | 6.94 × 10−8 | 12/39 | 30.8 | A7 |
| Some pathways of EMT in cancer cells | 1.73 × 10−6 | 12/51 | 23.5 | A16 |
| Signal transduction–AKT signaling | 1.93 × 10−6 | 11/43 | 25.6 | A18 |
FDR indicates false discovery rate; PC, plasma cell; GO, GeneGo; EMT, epithelial to mesenchymal transition; IGF, insulin-like growth factor 1; FGFR, fibroblast growth factor receptor; EGFR, epidermal growth factor receptor; WNT, wingless-type; ECM, extracellular matrix; PLAU, plasminge activator, uroinase; BAD, BCL2-associated agonist of cell death; and NGF, naive grwoth factor.
Designation of GeneGo pathway.
Log (P), indicating the probability that the postulated GeneGo pathway is in fact not involved in the tumor sample.
Number of differentially regulated pathway genes versus total number of genes comprising the pathway.
Ratio of differentially regulated pathway genes to total number of pathway genes.
Number of pathway in panel A or panel B of supplemental Figure 5.
GeneGo category of functionally related, genetic pathway maps. Enrichment analysis scores and ranks the most relevant GeneGo pathways in a given category.
Number of unique GeneGo pathway maps discovered in a given GeneGo category.
Epithelial to mesenchymal transition.
Includes the following GO categories: Apoptosis and survival, NGF activation of NF-κB, G-protein signaling, Some pathways of EMT in cancer cells and signal transduction.