Table 3.
Microarrays and signaling pathways
| Pathway/cascade/function | Key molecule(s) identifieda | Reference |
|---|---|---|
| MAPK signaling | ||
| GPCR/MAPK | Small GTPase/apoptosis signaling genes | MAPK Chang et al. [137] |
| NFκB/MAPK/ERK | PI3 K/Akt/mTOR | Mendes et al. [138] |
| MAPK/JNK | Mitochondrial function related genes | Cízková et al. [139] |
| Other signaling | ||
| Angiogenesis signaling | HIF-1α-dependent genes | Copple et al. [140] |
| Nuclear receptor signaling | PPARγ-associated genes | Lee et al. [141] |
| ErbB/HER signaling | Scaffolding adaptors | Nakaoka et al. 2007 [142] |
| Ubiquitin/proteasome signaling | NF-κB/IκB signaling genes | Granese et al. [143] |
| Chromatin/epigenetic regulation | ||
| Histone modification | Hdac1 (histone deacetylase) | Reichmann et al. [144] |
| Heterochromatin | HP1-regulated genes | Lee et al. [145] |
| DNA methylation | SCARA5 (scavenger receptor) | Khamas et al. [146] |
| Apoptosis | ||
| Infectious response | NF-κB/p53/RB/JUN/apoptosis genes | Faherty et al. [147] |
| Virus induced apoptosis | p53/caspase-1 | Nasirudeen and Liu [148] |
| Death receptor signaling | FAS-mediated apoptosis genes | Wang et al. [149] |
| Autophagy | ||
| Starvation stress | Autophagy-related genes | Burgess et al. [150] |
| PI3 K/Akt/FOXO/mTOR | Glutamine synthetase | van der Vos et al. [151] |
| Cellular metabolism | ||
| Insulin receptor signaling | Metabolic process-related genes | Bolukbasi et al. [152] |
| AMPK signaling | AMPK activators | Solskov et al. [153] |
| Translational control | ||
| eIF2 signaling | tRNA processing genes | Saikia et al. [154] |
| eIF4/p70S6 K signaling | eIF4 factors | Villas-Bôas et al. [155] |
| mTOR signaling | TGF-β/MNK1/SMAD2 | Grzmil et al. [156] |
| Cell cycle/DNA damage | ||
| G1/S checkpoint | EIF2 activator | Stockwell et al. [157] |
| G2/M DNA damage checkpoint | RB/E2F/ECT2 | Eguchi et al. [158] |
| Cytoskeletal regulation and adhesion | ||
| Actin dynamics | PKCδ/cofilin | Wada-Kiyama et al. [159] |
| Microtubule dynamics | Formin1 | Simon-Areces et al. [160] |
| Adherens junction dynamics | Diabetes-related genes | Caramori et al. [161] |
| Immunology and inflammation | ||
| Inflammatory response | miR-155/Jak/STAT | Kutty et al. [162] |
| Cytokine receptor signaling | TLR/IL-1R | Abend et al. [163] |
| T-cell activation | NF-κB/Rel | Chang et al. [164] |
| TLR-sinduced inflammation | TLR4-responsive genes | Yang et al. [165] |
| B-cell receptor signaling | Cytokines | Franke et al. [166] |
| Rheumatoid arthritis | T-cell receptors | Kim et al. [167] |
| Neuroscience | ||
| Alzheimer’s disease | Neurological disease-related genes | Walker et al. [168] |
| Parkinson’s disease | FOXO1 | Dumitriu et al. [169] |
| Development and differentiation | ||
| Wnt/β-catenin signaling | Wnt-associated genes | Nguyen et al. [170] |
| Notch signaling | RB family genes | Viatour et al. [171] |
| Hedgehog signaling | Eyeless/hedgehog-regulated genes | Nfonsam et al. [172] |
| TGF-β signaling | Corneal dystrophy-associated genes | Choi et al. [173] |
Classification of pathways/cascades/functions was based on that by Cell Signaling Technology (http://www.cellsignal.com/). A representative case is listed for each category
AMPK AMP-activated protein kinase, eIF eukaryotic initiation factor, FOXO forkhead box O, GPCR G-protein-coupled receptor, IGF-1 insulin-like growth factor-1, IL-1R interleukin-1 receptor, JNK c-Jun N-terminal kinase, MAPK mitogen-activated protein kinase, mTOR mammalian target of rapamycin, PI3 K phosphatidylinositol 3-kinase, PPARγ peroxisome proliferator-activated receptor γ, RB retinoblastoma, TLR Toll-like receptor
aProteins and/or cellular factors identified by microarray assay and subsequent characterization, such as RT-PCR and Western blotting