Table 4. Functional classification of genes in cluster 3: early down late up.
Functional classification of genes in cluster 3 (Table 2). The table highlights different gene classes that were enriched in the early down-late up dataset and their corresponding trends of change throughout the time course. Functional annotation was performed using DAVID gene ontology tool. Gene enrichment reflects genes that are highly associated with the indicated functional terms (i.e SNARE interaction, protein transport, protein localization and intracellular transport). It is based on the EASE Score (threshold p-value< 0.1), a modified Fisher Exact statistical test used to measure gene enrichment in annotation terms in the DAVID system. The EASE score for each class is shown as the gene enrichment p-value. Genes are enriched for SNARE interaction, protein trafficking, vesicle mediated transport and regulation of transcription. A number of genes show overlapping functions in vesicle trafficking and protein localization
| SNARE INTERACTION IN VESICULAR TRANSPORT | FOLD CHANGE RELATIVE TO CONTROL | ||||
|---|---|---|---|---|---|
| Enrichment p-value: 0.004060282 | |||||
| Gene symbol | Gene name | 1.5hrs | 3hrs | 6hrs | 12hrs |
| Bet 1l | blocked early in transport 1 homolog (S. cerevisiae) like | −1.31 | −1.10 | −1.14 | −1.08 |
| Gosr1 | golgi SNAP receptor complex member 1 | −1.29 | −1.18 | −1.07 | 1.07 |
| Stx18 | syntaxin 18 | −1.22 | 1.04 | −1.15 | −1.12 |
| PROTEIN TRANSPORT | FOLD CHANGE RELATIVE TO CONTROL | ||||
| Enrichment p-value: 0.030887946 | |||||
| Gene symbol | Gene name | 1.5hrs | 3hrs | 6hrs | 12hrs |
| Rab8b | RAB8B, member RAS oncogene family | −1.38 | −1.35 | −1.06 | 1.07 |
| Rufy1 | RUN and FYVE domain containing 1 | −1.31 | −1.12 | −1.09 | −1.12 |
| Arntl | aryl hydrocarbon receptor nuclear translocator-like | −1.25 | −1.08 | −1.08 | 1.14 |
| Bet1l | blocked early in transport 1 homolog (S. cerevisiae) like | −1.31 | −1.10 | −1.14 | −1.08 |
| Gosr1 | golgi SNAP receptor complex member 1 | −1.29 | −1.18 | −1.07 | 1.07 |
| Myo1c | myosin IC | −1.22 | −1.03 | 1.03 | −1.07 |
| Stam | signal transducing adaptor molecule (SH3 domain and ITAM motif) 1 | −1.20 | −1.14 | −1.10 | −1.12 |
| Stam2 | signal transducing adaptor molecule (SH3 domain and ITAM motif) 2 | −1.23 | −1.02 | −1.18 | −1.20 |
| Zfp280b | similar to suppressor of hairy wing homolog 2; zinc finger protein 280b | −1.35 | −1.15 | −1.09 | 1.35 |
| Slc15a4 | solute carrier family 15, member 4 | −1.30 | −1.35 | −1.19 | −1.00 |
| Stx18 | syntaxin 18 | −1.22 | 1.04 | −1.15 | −1.12 |
| PROTEIN LOCALIZATION | FOLD CHANGE RELATIVE TO CONTROL | ||||
| Enrichment p-value: 0.041166313 | |||||
| Gene symbol | Gene name | 1.5hrs | 3hrs | 6hrs | 12hrs |
| Rab8b | RAB8B, member RAS oncogene family | −1.38 | −1.35 | −1.06 | 1.07 |
| Rufy1 | RUN and FYVE domain containing 1 | −1.31 | −1.12 | −1.09 | −1.12 |
| Arntl | aryl hydrocarbon receptor nuclear translocator-like | −1.25 | −1.08 | −1.08 | 1.14 |
| Bet1l | blocked early in transport 1 homolog (S. cerevisiae) like | −1.31 | −1.10 | −1.14 | −1.08 |
| Gosr1 | golgi SNAP receptor complex member 1 | −1.29 | −1.18 | −1.07 | 1.07 |
| Myo1c | myosin IC | −1.22 | −1.03 | 1.03 | −1.07 |
| Stam | signal transducing adaptor molecule (SH3 domain and ITAM motif) 1 | −1.20 | −1.14 | −1.10 | −1.12 |
| Stam2 | signal transducing adaptor molecule (SH3 domain and ITAM motif) 2 | −1.23 | −1.02 | −1.18 | −1.20 |
| Zfp280b | similar to suppressor of hairy wing homolog 2; zinc finger protein 280b | −1.35 | −1.15 | −1.09 | 1.35 |
| Slc15a4 | solute carrier family 15, member 4 | −1.30 | −1.35 | −1.19 | −1.00 |
| Stx18 | syntaxin 18 | −1.22 | 1.04 | −1.15 | −1.12 |
| INTRACELLULAR TRANSPORT | FOLD CHANGE RELATIVE TO CONTROL | ||||
| Enrichment p-value: 0.086073852 | |||||
| Gene symbol | Gene name | 1.5hrs | 3hrs | 6hrs | 12hrs |
| Ankrd54 | ankyrin repeat domain 54 | −1.27 | −1.23 | −1.19 | 1.09 |
| Arntl | aryl hydrocarbon receptor nuclear translocator-like | −1.25 | −1.08 | −1.08 | 1.14 |
| Bet1l | blocked early in transport 1 homolog (S. cerevisiae) like | −1.31 | −1.10 | −1.14 | −1.08 |
| Gosr1 | golgi SNAP receptor complex member 1 | −1.29 | −1.18 | −1.07 | 1.07 |
| Golga 5 | golgi autoantlgen, golgin subfamily a, 5 | −1.61 | −1.21 | −1.42 | −1.35 |
| Stam | signal transducing adaptor molecule (SH3 domain and ITAM motif) 1 | −1.20 | −1.14 | −1.10 | −1.12 |
| Stam2 | signal transducing adaptor molecule (SH3 domain and ITAM motif) 2 | −1.23 | −1.02 | −1.18 | −1.20 |
| Zfp280b | similar to suppressor of hairy wing homolog 2; zinc finger protein 280b | −1.35 | −1.15 | −1.09 | 1.35 |
| Stx18 | syntaxin 18 | −1.22 | 1.04 | −1.15 | −1.12 |
| Stxbp5l | syntaxin binding protein 5-like | −1.29 | −1.40 | −1.08 | 1.04 |
| Nostrin | nitric oxide synthase trafficker | −1.25 | −1.14 | −1.12 | 1.24 |
| REGULATION OF TRANSCRIPTION | FOLD CHANGE RELATIVE TO CONTROL | ||||
| Enrichment p-value: 1.50E-05 | |||||
| Gene symbol | Gene name | 1.5hrs | 3hrs | 6hrs | 12hrs |
| Cir1 | CBF1 interacting corepressor | −1.39 | −1.27 | −1.13 | 1.11 |
| Gpbp1l1 | GC-rich promoter binding protein 1-like 1; similar to GC-rich promoter binding protein 1-like 1 | −1.49 | −1.45 | −1.12 | −1.14 |
| Smarcal1 | Swi/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1 | −1.32 | −1.19 | −1.02 | 1.14 |
| Ahr | Aryl hydrocarbon receptor | −1.30 | −1.47 | −1.08 | −1.04 |
| Arnt | Aryl hydrocarbon receptor nuclear translocator | −1.27 | −1.23 | −1.04 | 1.08 |
| Arntl | Aryl hydrocarbon receptor nuclear translocator-like | −1.25 | −1.08 | −1.08 | 1.14 |
| Atxn3 | Ataxin 3 | −1.36 | −1.30 | −1.13 | −1.13 |
| Gtf2a1 | General transcription factor IIA, 1 | −1.21 | −1.12 | −1.02 | −1.17 |
| Med 26 | Mediator complex subunit 26 | −1.21 | −1.10 | −1.14 | 1.22 |
| LOC499124 | Mouse zinc finger protein 14-like | −1.21 | −1.21 | −1.03 | 1.04 |
| Prmt6 | Protein arginine methyltransferase 6 | −1.42 | −1.33 | −1.15 | 1.16 |
| Ppp1r10 | Protein phosphatase 1, regulatory subunit 10 | −1.29 | −1.19 | −1.09 | 1.36 |
| Sra1 | Steroid receptor RNA activator 1 | −1.35 | −1.05 | −1.19 | −1.17 |
| Tfam | Transcription factor A, mitochondrial | −1.37 | −1.26 | −1.15 | 1.02 |
| Tfdp2 | Transcription factor Dp-2 (E2F dimerization partner 2) | −1.71 | −1.55 | −1.04 | −1.07 |
| Uimc1 | Ubiquitin interaction motif containing 1 | −1.37 | −1.27 | −1.09 | −1.07 |
| Vsx2 | Visual system homeobox 2 | −1.24 | −1.20 | −1.15 | −1.00 |
| Zc3h8 | Zinc finger CCCH type containing 8 | −1.53 | −1.48 | −1.19 | 1.06 |
| Zfp112 | Zinc finger protein 112 | −1.27 | −1.34 | −1.15 | 1.13 |
| Zfp128 | Zinc finger protein 128 | −1.39 | −1.20 | −1.19 | 1.19 |
| Znf287 | Zinc finger protein 287 | −1.26 | −1.33 | −1.09 | 1.23 |
| Zfp426l2 | Zinc finger protein 426-like 2 | −1.35 | −1.26 | −1.07 | −1.12 |
| Zfp472 | Zinc finger protein 472 | −1.34 | −1.22 | −1.11 | −1.00 |
| Zfp68 | Zinc finger protein 68 | −1.35 | −1.43 | −1.15 | 1.08 |
| Zfp786 | Zinc finger protein 786 | −1.26 | −1.25 | −1.05 | −1.00 |
| Zfp84 | Zinc finger protein 84 | −1.41 | −1.39 | −1.19 | 1.08 |
| Zfp90 | Zinc finger protein 90 | −1.35 | −1.34 | −1.10 | 1.03 |