Table S1.
Enrichment cluster scores and P values of DAVID enrichment analysis
| Gene ontology term | Gene IDs | Fold enrichment | P |
| Enrichment Score: 7.333 | |||
| Endoplasmic reticulum part | RAB2B, FKBP9, ERP29, PDIA6, PDIA4, CALU, STT3A, P4HA2, P4HA1, TXNDC5, SEC22B, ASPH, FKBP10, SSR3, RCN2 | 7.88 | 5.13E-09 |
| Endoplasmic reticulum lumen | FKBP9, P4HA2, P4HA1, TXNDC5, ERP29, PDIA6, PDIA4, FKBP10, RCN2, CALU | 16.86 | 6.22E-09 |
| Endoplasmic reticulum | RAB2A, RAB2B, FKBP9, CKAP4, ERP29, PDIA6, PDIA4, SRPRB, ALDH3A2, CALU, SCFD1, STT3A, LEPRE1, P4HA2, P4HA1, TXNDC5, SEC22B, ASPH, FKBP10, RAB21, RCN2, SSR3 | 3.19 | 3.15E-06 |
| Enrichment Score: 7.235 | |||
| Translation | RPSA, CARS, RPL13, SARS, GM8730, AARS, EIF2A, EEF2, RPS2, RPS4X, RPS8, RPS7, RPS3, GM10653, EIF4G2, RPL7, GM6576, RPL18A, EIF3H, RPLP0, RPL21, RPS12, RPL3, EIF3L, TPR | 8.91 | 6.66E-15 |
| Structural constituent of ribosome | RPSA, RPL13, GM8730, RPS2, RPS4X, RPS8, RPS3, RPS7, GM10653, GM6576, RPL18A, RPL7, RPL21, RPLP0, RPS12, RPL3 | 11.62 | 1.78E-10 |
| Ribonucleoprotein complex | RPSA, RPL13, NHP2L1, SNRPD3, GM8730, EEF2, SRPRB, RPS2, RPS4X, RPS8, RPS7, RPS3, GM10653, PA2G4, RPL7, GM6576, RPL18A, RPLP0, SRRM2, RPL21, RPS12, RPL3, SRP72 | 5.52 | 7.52E-10 |
| Ribosome | RPSA, RPL13, GM8730, RPS2, RPS4X, RPS8, RPS3, RPS7, GM10653, GM6576, RPL18A, RPL7, RPL21, RPLP0, RPS12, RPL3 | 8.85 | 4.97E-09 |
| Structural molecule activity | RPSA, RPL13, GM8730, COL3A1, RPS2, RPS4X, COL5A2, RPS8, RPS7, RPS3, GM10653, COPB2, RPL7, GM6576, RPL18A, RPL21, RPLP0, RPS12, COL1A2, RPL3, TUBB6 | 5.29 | 1.30E-08 |
| Small ribosomal subunit | GM10653, RPSA, GM6576, RPS4X, RPS2, RPS3 | 20.93 | 8.47E-05 |
| Non–membrane-bounded organelle | DYNC1LI2, RPL13, NHP2L1, CAPZA2, TCOF1, RPS2, RPS3, MYL9, GM10653, AKT1, PFN2, SORBS3, RPL7, GM6576, RPLP0, RPL3, EIF3L, H2AFY, TUBB6, DDX21, RPSA, TCP1, GM8730, RPS4X, RPS8, FARP1, RPS7, PA2G4, RPL18A, RPL21, RPS12, SRP72, WDR1, MAPRE1 | 2.02 | 8.96E-05 |
| Ribosomal subunit | GM10653, RPSA, RPL7, GM6576, RPS4X, RPS2, RPS3 | 11.04 | 1.97E-04 |
| Enrichment Score: 5.729 | |||
| Endoplasmic reticulum lumen | FKBP9, P4HA2, P4HA1, TXNDC5, ERP29, PDIA6, PDIA4, FKBP10, RCN2, CALU | 16.86 | 6.22E-09 |
| Intracellular organelle lumen | FKBP9, NHP2L1, TCOF1, PDIA6, PDIA4, CALU, GOT2, P4HA2, P4HA1, SRRM2, EIF3L, DDX21, ACADM, ERP29, ACADL, RBBP7, PA2G4, C1QBP, TXNDC5, SRP72, HSPD1, RBM14, FKBP10, MDH2, RCN2 | 2.68 | 1.01E-05 |
| Enrichment Score: 3.707 | |||
| Glutamine family amino acid metabolic process | GOT2, ALDH18A1, GFPT1, PHGDH, ASNS, CAD | 17.24 | 2.29E-05 |
| Amine biosynthetic process | GOT2, ALDH18A1, MAT2A, SRM, PHGDH, ASNS, PSAT1 | 11.85 | 2.55E-05 |
| Cellular amino acid biosynthetic process | GOT2, ALDH18A1, MAT2A, PHGDH, ASNS, PSAT1 | 16.84 | 2.56E-05 |
| Carboxylic acid biosynthetic process | GOT2, PTGES3, ALDH18A1, MAT2A, PHGDH, ASNS, GSTO1, PSAT1 | 7.01 | 1.38E-04 |
| Nitrogen compound biosynthetic process | GOT2, ALDH18A1, MAT2A, SRM, ATP5B, PHGDH, ASNS, CAD, PSAT1 | 3.68 | 2.96E-03 |
| Aspartate family amino acid metabolic process | GOT2, PHGDH, ASNS | 16.84 | 1.33E-02 |
| Enrichment Score: 3.484 | |||
| Pigment granule | RAB2A, LAMP1, ERP29, TMED10, SEC22B, PDIA6, PDIA4, CALU | 11.43 | 5.73E-06 |
| Melanosome | RAB2A, LAMP1, ERP29, TMED10, SEC22B, PDIA6, PDIA4, CALU | 11.43 | 5.73E-06 |
| Cytoplasmic membrane-bounded vesicle | RAB2A, COPZ2, CAPZA2, ERP29, ESD, PDIA6, PDIA4, CALU, COPB2, LAMP1, TMED10, SEC22B, VAMP2, HSPD1, RAB21 | 4.40 | 6.37E-06 |
| Cytoplasmic vesicle | RAB2A, COPZ2, CAPZA2, ERP29, ESD, PDIA6, PDIA4, CALU, COPB2, LAMP1, TMED10, SEC22B, VAMP3, VAMP2, HSPD1, RAB21 | 3.82 | 1.48E-05 |
| Endomembrane system | COPZ2, RAB2B, CAPZA2, CLIC1, MAN2A1, COPB2, STT3A, TMED10, SEC22B, VAMP2, ASPH, TPR, RAB21, SSR3 | 3.18 | 3.97E-04 |
| Cytoplasmic vesicle membrane | COPZ2, COPB2, CAPZA2, TMED10, VAMP2, RAB21 | 8.37 | 7.12E-04 |
| Golgi apparatus part | COPZ2, COPB2, RAB2B, MAN2A1, TMED10, SEC22B, VAMP2, RAB21 | 4.28 | 2.54E-03 |
| Golgi apparatus | COPZ2, RAB2A, COPB2, RAB2B, MAN2A1, SCFD1, ARF4, TMED10, SEC22B, VAMP2, MAPRE1, RAB21 | 2.14 | 2.30E-02 |
| Enrichment Score: 3.081 | |||
| Protein folding | FKBP9, CCT5, TCP1, FKBP5, FKBP4, AARS, HSPD1, FKBP10 | 7.78 | 7.14E-05 |
| Peptidyl-prolyl cis-trans isomerase activity | FKBP9, FKBP5, FKBP4, FKBP10 | 14.33 | 2.61E-03 |
| Enrichment Score: 2.076 | |||
| Endomembrane system | COPZ2, RAB2B, CAPZA2, CLIC1, MAN2A1, COPB2, STT3A, TMED10, SEC22B, VAMP2, ASPH, TPR, RAB21, SSR3 | 3.18 | 3.97E-04 |
| Nuclear envelope-ER network | RAB2B, STT3A, SEC22B, ASPH, SSR3 | 3.79 | 4.18E-02 |
| Enrichment Score: 1.969 | |||
| Procollagen-proline dioxygenase activity | LEPRE1, P4HA2, P4HA1 | 53.73 | 1.27E-03 |
| Peptidyl-proline dioxygenase activity | LEPRE1, P4HA2, P4HA1 | 53.73 | 1.27E-03 |
| Oxidoreductase activity (paired donors) | LEPRE1, P4HA2, P4HA1, ASPH | 16.71 | 1.67E-03 |
| l-ascorbic acid binding | LEPRE1, P4HA2, P4HA1 | 18.80 | 1.07E-02 |
| Vitamin binding | GOT2, LEPRE1, P4HA2, P4HA1, PSAT1 | 5.18 | 1.55E-02 |
| Carboxylic acid binding | LEPRE1, P4HA2, P4HA1, CAD | 5.90 | 2.97E-02 |
| Enrichment Score: 1.946 | |||
| tRNA aminoacylation for protein translation | CARS, SARS, AARS, TPR | 10.74 | 5.93E-03 |
| tRNA aminoacylation | CARS, SARS, AARS, TPR | 10.74 | 5.93E-03 |
| Amino acid activation | CARS, SARS, AARS, TPR | 10.74 | 5.93E-03 |
| Ligase activity (aminoacyl-tRNA) | CARS, SARS, AARS, TPR | 10.45 | 6.41E-03 |
| Enrichment Score: 1.903 | |||
| Endomembrane system | COPZ2, RAB2B, CAPZA2, CLIC1, MAN2A1, COPB2, STT3A, TMED10, SEC22B, VAMP2, ASPH, TPR, RAB21, SSR3 | 3.18 | 3.97E-04 |
| Golgi apparatus part | COPZ2, COPB2, RAB2B, MAN2A1, TMED10, SEC22B, VAMP2, RAB21 | 4.28 | 2.54E-03 |
| Golgi membrane | COPZ2, COPB2, RAB2B, MAN2A1, SEC22B, RAB21 | 5.32 | 5.23E-03 |
| Protein transport | RAB2A, COPZ2, RAB2B, ERP29, COPB2, SCFD1, ARF4, TMED10, SEC22B, SRP72, TPR, RAB21, SSR3 | 2.47 | 5.91E-03 |
| Protein localization | RAB2A, COPZ2, RAB2B, ERP29, COPB2, SCFD1, ARF4, TMED10, SEC22B, SRP72, TPR, GNB2L1, RAB21, SSR3 | 2.30 | 7.19E-03 |
| Vesicle-mediated transport | COPZ2, RAB2A, COPB2, RAB2B, SCFD1, ARF4, TMED10, SEC22B, VAMP3, VAMP2 | 2.65 | 1.26E-02 |
| Golgi apparatus | COPZ2, RAB2A, COPB2, RAB2B, MAN2A1, SCFD1, ARF4, TMED10, SEC22B, VAMP2, MAPRE1, RAB21 | 2.14 | 2.30E-02 |
| Intracellular protein transport | COPZ2, RAB2A, COPB2, TMED10, SRP72, TPR, SSR3 | 3.13 | 2.37E-02 |
| Enrichment Score: 1.597 | |||
| Cofactor binding | GOT2, ACADM, PHGDH, ACADL, PSAT1, IDH3A, MDH1 | 3.88 | 9.02E-03 |
| Coenzyme binding | ACADM, PHGDH, ACADL, IDH3A, MDH1 | 3.92 | 3.80E-02 |
| NAD or NADH binding | PHGDH, IDH3A, MDH1 | 8.55 | 4.72E-02 |
| Enrichment Score: 1.596 | |||
| Nucleotide binding | DYNC1LI2, ALDH18A1, ATP5B, FKBP4, ASNS, CAD, AKT1, UBE2D3, TUBB6, DDX21, TPR, RAB21, RAB2A, RAB2B, CARS, TCP1, ACADM, MAT2A, SARS, AARS, EEF2, SRPRB, ACADL, IDH3A, CCT5, ARF4, PHGDH, HSPD1, RBM14, MDH1 | 1.72 | 2.56E-03 |
| Purine nucleotide binding | DYNC1LI2, ALDH18A1, ATP5B, FKBP4, ASNS, CAD, AKT1, UBE2D3, TUBB6, DDX21, TPR, RAB21, RAB2A, RAB2B, CARS, TCP1, ACADM, MAT2A, SARS, AARS, EEF2, SRPRB, ACADL, CCT5, ARF4, HSPD1 | 1.74 | 5.06E-03 |
| Ribonucleotide binding | RAB2A, RAB2B, TCP1, CARS, DYNC1LI2, ALDH18A1, MAT2A, SARS, ATP5B, FKBP4, AARS, ASNS, CAD, EEF2, SRPRB, AKT1, UBE2D3, CCT5, ARF4, TUBB6, DDX21, HSPD1, TPR, RAB21 | 1.68 | 1.20E-02 |
| Enrichment Score: 1.591 | |||
| Organelle membrane | COPZ2, RAB2B, ALDH18A1, ATP5B, CAPZA2, ALDH3A2, GOT2, COPB2, MAN2A1, STT3A, TMED10, SEC22B, SLC25A1, VAMP2, HSPD1, ASPH, RAB21, MDH2, SSR3 | 2.85 | 8.52E-05 |
| Mitochondrial matrix | GOT2, ACADM, C1QBP, HSPD1, ACADL, MDH2 | 4.47 | 1.07E-02 |
| Mitochondrial part | GOT2, ACADM, ALDH18A1, C1QBP, ATP5B, SLC25A1, HSPD1, ACADL, ALDH3A2, MDH2 | 2.32 | 2.71E-02 |
| Mitochondrial inner membrane | GOT2, ALDH18A1, ATP5B, SLC25A1, HSPD1, ALDH3A2, MDH2 | 2.87 | 3.40E-02 |
| Enrichment Score: 1.458 | |||
| Collagen | COL3A1, COL1A2, LOX, COL5A2 | 25.56 | 4.64E-04 |
| Collagen fibril organization | P4HA1, COL3A1, LOX, COL5A2 | 23.53 | 6.01E-04 |
| SMAD binding | COL3A1, COL1A2, COL5A2 | 18.80 | 1.07E-02 |
| Extracellular matrix structural constituent | COL3A1, COL1A2, COL5A2 | 12.54 | 2.33E-02 |
| Enrichment Score: 1.404 | |||
| Energy derivation by oxidation | PTGES3, AKT1, IDH3A, MDH2, MDH1 | 6.30 | 7.95E-03 |
| Tricarboxylic acid cycle | IDH3A, MDH2, MDH1 | 16.11 | 1.45E-02 |
| Acetyl-CoA catabolic process | IDH3A, MDH2, MDH1 | 15.44 | 1.57E-02 |
| Aerobic respiration | IDH3A, MDH2, MDH1 | 13.73 | 1.96E-02 |
| Coenzyme catabolic process | IDH3A, MDH2, MDH1 | 12.78 | 2.25E-02 |
| Acetyl-CoA metabolic process | IDH3A, MDH2, MDH1 | 11.95 | 2.55E-02 |
| Cofactor catabolic process | IDH3A, MDH2, MDH1 | 11.58 | 2.70E-02 |
| Enrichment Score: 1.363 | |||
| Energy derivation | PTGES3, AKT1, IDH3A, MDH2, MDH1 | 6.30 | 7.95E-03 |
| Hexose metabolic process | PTGES3, AKT1, MAN2A1, MDH2, MDH1 | 3.65 | 4.70E-02 |
| Enrichment Score: 1.332 | |||
| Vesicle-mediated transport | COPZ2, RAB2A, COPB2, RAB2B, SCFD1, ARF4, TMED10, SEC22B, VAMP3, VAMP2 | 2.65 | 1.26E-02 |
| Exocytosis | SCFD1, TMED10, VAMP3, VAMP2 | 4.49 | 5.85E-02 |
| Enrichment Score: 1.109 | |||
| GTP binding | RAB2A, RAB2B, FKBP4, ARF4, TUBB6, EEF2, SRPRB, RAB21 | 2.83 | 2.21E-02 |
| Guanyl nucleotide binding | RAB2A, RAB2B, FKBP4, ARF4, TUBB6, EEF2, SRPRB, RAB21 | 2.76 | 2.49E-02 |
| Guanyl ribonucleotide binding | RAB2A, RAB2B, FKBP4, ARF4, TUBB6, EEF2, SRPRB, RAB21 | 2.76 | 2.49E-02 |
| Enrichment Score: 0.089 | |||
| Regulation of translation | AKT1, EIF4G2, PA2G4, EIF2A | 4.94 | 4.64E-02 |
DAVID functional annotation clustering analysis for candidate proteins whose abundance significantly changes at CT18 vs. CT30 and is significantly increased in Bmal1−/− cells compared with WT cells at both CT18 and CT30. Gene ontology terms with P < 0.05 shown. See Fig. 6C for diagrammatic presentation of results.