| PROTEIN 1 | INTERACTION VERB | PROTEIN 2 | FREQUENCY |
| Ca2 | activates | protein kinase | 312 |
| Cln3 | activate | protein kinase | 234 |
| TAP | binds | transcription factor | 192 |
| TNF | activates | protein tyrosine kinase | 133 |
| serine/threonine kinase | binding | RhoA GTPase | 132 |
| Phospholamban | inhibits | ATPase | 114 |
| PRL | activated | transcription factor | 108 |
| Interleukin 2 | activates | transcription factor | 84 |
| Prolactin | activates | transcription factor | 84 |
| AMPA | activated | protein kinase | 78 |
| Nerve growth factor | activates | protein kinase | 78 |
| LPS | inhibited | MHC class II | 75 |
| Heat shock protein | Binding | p59 | 72 |
| EPO | activated | STAT5 | 63 |
| EGF | activated | PP2A | 60 |
| cis | binds | Sp1 | 50 |
| HGF | activates | Na+/H+ exchanger | 48 |
| G-CSF | activated | transcription factor | 36 |
| LIF | inhibited | bFGF | 36 |
| ATP | activates | potassium channel | 33 |
| BDNF | activated | ras | 28 |
| DAG | activated | PKC | 27 |
| G-CSF | activated | p53 | 27 |
| LPS | activates | PKC | 27 |
| tau | activates | protein kinase C | 25 |
| cell surface receptor | activates | adenylyl cyclase | 24 |
| Ca2 | inhibits | adenylyl cyclase | 24 |
| Ca2 | inhibits | glucose transporter | 24 |
| Insulin | activates | receptor tyrosine kinase | 24 |
| ATP | activates | ion channel | 22 |
| ATP | inhibited | GAD | 22 |
| CaM | activates | NOS | 20 |
| JNK | activates | c-Jun | 20 |
| Caldesmon | inhibited | ATPase | 19 |
| Galanin | inhibited | adenylate cyclase | 18 |
| Mos | activated | MEK1 | 18 |
| ATA | activates | receptor tyrosine kinase | 16 |
| Xic | inhibits | Cdk2 | 16 |
| p67 | inhibited | eIF-2 alpha | 15 |
| ACTH | activates | glycerol-3-phosphate acyltransferase | 12 |
| Heat shock protein | Binding | HBI | 12 |
| Insulin | activated | glycogen synthase | 12 |
| TNF alpha | activated | PLA2 | 12 |
| CLK | activates | COX | 10 |
| Interferon | activates | protein kinase C | 10 |
| LPS | inhibited | LPS | 9 |
| 14-3-3 zeta | activated | Raf | 8 |
| PHA | activated | CD4 | 8 |
| Xic | inhibits | cyclin E | 8 |
| TNF | activates | NF-kappa B | 7 |
| acidic fibroblast growth factor | activated | c-Raf | 6 |
| bFGF | activates | MAPKK | 6 |
| Bradykinin | activates | adenylate cyclase | 6 |
| CTX | activates | G-protein | 6 |
| granulocyte colony-stimulating factor | activated | Btk | 6 |
| interleukin 2 receptor beta chain | activates | STAT | 6 |
| I2PP2A | inhibited | PP2A | 6 |
| mAb | inhibited | interleukin-4 | 6 |
| NDF | activates | MAP kinase | 6 |
| NGF | activates | MAP kinase | 6 |
| PDGF B | activated | Na+/H+ exchanger | 6 |
| PMA | inhibited | adenylyl cyclase | 6 |
| somatostatin-14 | inhibits | adenylyl cyclase | 6 |
| TCR | activates | MAP kinase | 6 |
| CAL 3 | inhibited | MLR | 5 |
| CSA | activates | mGluR | 5 |
| IFN alpha | activated | STAT3 | 5 |
| metabotropic glutamate receptor | activates | NOS | 5 |
| CD11a | inhibited | SLP | 4 |
| eclosion hormone | activated | nitric oxide synthase | 4 |
| jun | activated | CRE | 4 |
| mix | activated | BaP | 4 |
| mol | inhibited | ACL | 4 |
| PTS1R | inhibit | peroxisomal protein | 4 |
| TGF beta | inhibits | CFC | 4 |
| TPA | inhibit | GJIC | 4 |
| CREB | binds | CRE | 3 |
| Endothelin | inhibits | phosphoinositide phospholipase C | 3 |
| FGF | activates | MAP kinase | 3 |
| LPS | activated | NF-kappa B | 3 |
| mAb | inhibited | TNF alpha | 3 |
| Antp | activates | tsh | 2 |
| FK506 | inhibited | CTL | 2 |
| GM3 | inhibit | IgE | 2 |
| Hbs | inhibit | ACh | 2 |
| IFN-gamma | inhibited | nerve growth factor | 2 |
| Ki-Ras | activates | MEK | 2 |
| cAMPS | inhibits | cAMP-dependent protein kinase | 1 |
| Double-stranded RNA-dependent protein kinase | activates | NF-kappa B | 1 |
| Gypsy | binds | SUHW | 1 |
| H-7 | inhibited | LTP | 1 |