Table 2.
Transcription factors with over-represented target motifs in the different clusters
| Targets cluster | Motif id | TF Name | Peach genome (v2) gene id | TF Cluster | Predicted TF family | TF Arabidopsis homologous | Transcription Factor Predicted function | Enrichment adjusted p value | |
|---|---|---|---|---|---|---|---|---|---|
| 1 - Dark green | MP00508 | PavAGL15 | Prupe.2G023100 | 7 - red | MADS | AT5G13790 | Agamous-like MADS-box protein AGL15 | 2.8E-05 | (***) |
| MP00605 | PavSEP3 | Prupe.1G223600 | 7 - red | MADS | AT1G24260 | K-box region and MADS-box transcription factor SEP3 / AGL9 | 2.5E-02 | (*) | |
| MP00077 | PavAP3 | Prupe.1G371300 | 9 - purple | MADS | AT3G54340 | K-box region and MADS-box transcription factor family protein AP3 | 2.8E-05 | (***) | |
| MP00609 | PavAG | Prupe.4G070500 | 9 - purple | MADS | AT4G18960 | K-box region and MADS-box transcription factor AG | 2.5E-02 | (*) | |
| 2 - grey | MP00335 | PavGATA15 | Prupe.1G126000 | 4 - light blue | GATA | AT3G06740 | GATA transcription factor 15 | 6.4E-06 | (***) |
| MP00206 | Prupe.3G048600 | 6 - orange | C2H2 | AT3G13810 | Zinc finger protein MAGPIE | 7.8E-03 | (**) | ||
| 3 - pink | MP00302 | PavDREB2C | Prupe.2G256900 | 6 - orange | ERF | AT2G40340 | Dehydration-responsive element-binding protein 2C | 3.2E-03 | (**) |
| MP00605 | PavSEP3 | Prupe.1G223600 | 7 - red | MADS | AT1G24260 | K-box region and MADS-box transcription factor SEP3 / AGL9 | 7.4E-03 | (**) | |
| 4 - light blue | MP00527 | Prupe.1G480400 | 4 - light blue | ERF | AT5G11190 | Ethylene-responsive transcription factor | 5.0E-04 | (***) | |
| MP00394 | PavCDF3 | Prupe.5G194600 | 5 - brown | Dof | AT3G47500 | cycling DOF factor 3 | 3.0E-02 | (*) | |
| MP00302 | PavDREB2C | Prupe.2G256900 | 6 - orange | ERF | AT2G40340 | Dehydration-responsive element-binding protein 2C | 2.7E-03 | (**) | |
| MP00508 | PavAGL15 | Prupe.2G023100 | 7 - red | MADS | AT5G13790 | Agamous-like MADS-box protein AGL15 | 1.7E-02 | (*) | |
| MP00374 | PavERF1 | Prupe.1G037900 | 8 - royal blue | ERF | AT3G23240 | ethylene response factor | 1.6E-05 | (***) | |
| MP00584 | Prupe.6G165700 | 8 - royal blue | ERF | AT5G50080 | Ethylene-responsive transcription factor | 5.2E-03 | (**) | ||
| MP00315 | PavAGL6 | Prupe.2G151000 | 9 - purple | MADS | AT2G45650 | MADS-box transcription factor | 2.8E-02 | (*) | |
| MP00441 | Prupe.4G055600 | 9 - purple | ERF | AT4G18450 | Ethylene-responsive transcription factor | 3.0E-02 | (*) | ||
| 5 - brown | MP00527 | Prupe.1G480400 | 4 - light blue | ERF | AT5G11190 | Ethylene-responsive transcription factor | 9.6E-08 | (***) | |
| MP00302 | PavDREB2C | Prupe.2G256900 | 6 - orange | ERF | AT2G40340 | Dehydration-responsive element-binding protein 2C | 3.7E-09 | (***) | |
| MP00294 | PavABI5 | Prupe.7G112200 | 7 - red | bZIP | AT2G36270 | ABSCISIC ACID-INSENSITIVE 5 | 1.8E-02 | (*) | |
| 6 - orange | MP00402 | PavOBP1 | Prupe.7G142500 | 1 - dark green | Dof | AT3G50410 | OBF-binding protein | 7.2E-03 | (**) |
| MP00526 | Prupe.1G390800 | 1 - dark green | ERF | AT5G25190 | Ethylene-responsive transcription factor | 1.3E-02 | (*) | ||
| MP00249 | PavMYB63 | Prupe.4G136300 | 1 - dark green | MYB | AT1G79180 | myb domain protein | 1.3E-02 | (*) | |
| 7 - red | MP00206 | Prupe.3G048600 | 6 - orange | C2H2 | AT3G13810 | Zinc finger protein | 2.0E-04 | (***) | |
| 8 - royal blue | MP00526 | Prupe.1G390800 | 1 - dark green | ERF | AT5G25190 | Ethylene-responsive transcription factor | 3.6E-02 | (*) | |
| MP00581 | PavLOB | Prupe.5G167800 | 4 - light blue | LBD | AT5G63090 | Lateral organ boundaries (LOB) domain family protein | 2.8E-20 | (***) | |
| MP00527 | PavSHN3 | Prupe.1G480400 | 4 - light blue | ERF | AT5G11190 | Ethylene-responsive transcription factor | 5.9E-03 | (**) | |
| MP00624 | PavTCX2 | Prupe.1G019100 | 4 - light blue | CPP | AT4G14770 | TESMIN/TSO1-like CXC 2 | 1.3E-02 | (*) | |
| MP00229 | Prupe.1G551600 | 6 - orange | C2H2 | AT1G72050 | transcription factor IIIA | 1.1E-02 | (*) | ||
| MP00302 | PavDREB2C | Prupe.2G256900 | 6 - orange | ERF | AT2G40340 | Dehydration-responsive element-binding protein 2C | 2.9E-02 | (*) | |
| MP00294 | PavABI5 | Prupe.7G112200 | 7 - red | bZIP | AT2G36270 | ABSCISIC ACID-INSENSITIVE 5 | 4.0E-03 | (**) | |
| MP00080 | PavPI | Prupe.1G489400 | 7 - red | MADS | AT5G20240 | K-box region and MADS-box transcription factor family protein | 4.2E-02 | (*) | |
| MP00186 | PavABF2 | Prupe.1G434500 | 8 - royal blue | bZIP | AT1G45249 | abscisic acid responsive elements-binding factor | 0.0E+ 00 | (***) | |
| 9 - purple | MP00375 | PavMYB14 | Prupe.1G039200 | 5 - brown | MYB | AT2G31180 | Myb-related protein | 7.3E-04 | (***) |
| MP00229 | Prupe.1G551600 | 6 - orange | C2H2 | AT1G72050 | transcription factor IIIA | 8.2E-31 | (***) | ||
| 10 - yellow | MP00272 | PavSVP | Prupe.6G199000 | 1 - dark green | MADS | AT2G22540 | K-box region and MADS-box transcription factor family protein | 7.4E-03 | (**) |
| MP00295 | PavDOF2 | Prupe.6G253300 | 1 - dark green | Dof | AT2G37590 | Dof zinc finger protein | 7.4E-03 | (**) | |
| MP00519 | Prupe.6G354000 | 2 - grey | ERF | AT5G18450 | Dehydration-responsive element-binding protein 2G | 2.3E-02 | (*) | ||
| MP00217 | Prupe.1G310100 | 6 - orange | ERF | AT1G68550 | Ethylene-responsive transcription factor | 1.7E-02 | (*) | ||
| MP00374 | Prupe.1G037900 | 8 - royal blue | ERF | AT3G23240 | Ethylene-responsive transcription factor | 2.6E-02 | (*) | ||
| MP00441 | Prupe.4G055600 | 9 - purple | ERF | AT4G18450 | Ethylene-responsive transcription factor | 2.6E-02 | (*) | ||
We investigated whether some differentially expressed transcription factors specifically targeted motifs in specific clusters. Based on the motif list available for peach was obtained from PlantTFDB [37], overrepresentation of motifs targeted by transcription factors was performed using hypergeometric tests. p-values obtained were corrected using a false discovery rate [38]: (***): adj. p-value <0.001; (**): adj. p-value <0.01; (*): adj. p-value <0.05