Table 1.
Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome pathway analysis. Top pathways with increased or decreased levels of proteins in 2FF- versus DMSO-treated 4T1 cells. FDR calculated through STRING-DB.org. We note that NF-κB and TNF signaling pathways contain common proteins (Supplemental File S2).
| KEGG Pathways | Reactome Pathways | ||||
|---|---|---|---|---|---|
| Decreased | |||||
| Description | Count in network | FDR | Description | Count in network | FDR |
| NF-κB signaling pathway | 9 or 93 | 0.0002 | Vesicle-mediated transport | 23 of 553 | 1.39 × 10−5 |
| RIG-1-like receptor signaling pathway | 6 of 68 | 0.0062 | Membrane trafficking | 22 of 523 | 1.39 × 10−5 |
| Tight Junction | 9 of 165 | 0.0062 | ER to Golgi Anterograde Transport | 12 of 147 | 1.45 × 10−5 |
| Protein processing in the ER | 9 of 161 | 0.0062 | Asparagine N-linked glycosylation | 15 of 269 | 3.02 × 10−5 |
| TNF signaling pathway | 7 of 108 | 0.0068 | Immune system | 38 of 1523 | 4.78 × 10−5 |
| Increased | |||||
| Spliceosome | 16 of 130 | 1.73 × 10−11 | Metabolism of RNA | 33 of 448 | 4.42 × 10−18 |
| Ribosome biogenesis in eukaryotes | 7 of 76 | 5 × 10−4 | Processing of Capped Intron-containing Pre-mRNA | 23 of 212 | 1.02 × 10−15 |
| Huntington’s disease | 8 of 187 | 0.0134 | mRNA splicing – Major Pathway | 19 of 156 | 8.94 × 10−14 |
| DNA replication | 4 of 35 | 0.0134 | Gene Expression (transcription) | 30 of 858 | 7.30 × 10−9 |