TABLE 2.
Summary statistics of enriched upstream TFs for differentially expressed genes (DEGs) in cca1lhy double mutant (Kamioka et al., 2016).
| TF ID (AGI ID) | xa | nb | Observed (%) | Xc | Nd | Expected (%) | p-Value | Corrected p-aluee | Gene symbols | Gene names |
| AT5G02840 | 267 | 824 | 32.4 | 4,110 | 27,206 | 15.1 | 9.65 × 10–37 | 3.37 × 10–34 | LCL1 | LHY/CCA1-LIKE 1 |
| AT4G01280 | 329 | 824 | 39.9 | 6,654 | 27,206 | 24.5 | 1.75 × 10–23 | 3.05 × 10–21 | ||
| AT5G52660 | 196 | 824 | 23.8 | 3,280 | 27,206 | 12.1 | 1.71 × 10–21 | 1.98 × 10–19 | ||
| AT3G09600 | 374 | 824 | 45.4 | 8,276 | 27,206 | 30.4 | 3.27 × 10–20 | 2.85 × 10–18 | LCL5, RVE8 | LHY-CCA1-LIKE5, REVEILLE 8 |
| AT1G01060 | 479 | 824 | 58.1 | 11,896 | 27,206 | 43.7 | 2.47 × 10–17 | 1.72 × 10–15 | LHY1, LHY | LATE ELONGATED HYPOCOTYL 1, LATE ELONGATED HYPOCOTYL |
| AT3G62420 | 275 | 824 | 33.4 | 5,764 | 27,206 | 21.2 | 1.20 × 10–16 | 6.99 × 10–15 | BZIP53 | BASIC REGION/LEUCINE ZIPPER MOTIF 53 |
| AT4G34590 | 344 | 824 | 41.7 | 7,781 | 27,206 | 28.6 | 1.75 × 10–16 | 8.70 × 10–15 | BZIP11, GBF6, ATB2 | G-BOX BINDING FACTOR 6, NA, ARABIDOPSIS THALIANA BASIC LEUCINE-ZIPPER 11 |
| AT2G46270 | 250 | 824 | 30.3 | 5,255 | 27,206 | 19.3 | 9.54 × 10–15 | 4.16 × 10–13 | GBF3 | G-BOX BINDING FACTOR 3 |
| AT1G18330 | 610 | 824 | 74.0 | 16,878 | 27,206 | 62.0 | 9.71 × 10–14 | 3.76 × 10–12 | RVE7, EPR1 | REVEILLE 7, EARLY-PHYTOCHROME-RESPONSIVE1 |
| AT3G56850 | 194 | 824 | 23.5 | 3,936 | 27,206 | 14.5 | 1.39 × 10–12 | 4.86 × 10–11 | AREB3, DPBF3 | ABA-RESPONSIVE ELEMENT BINDING PROTEIN 3 |
| AT5G17300 | 560 | 824 | 68.0 | 15,403 | 27,206 | 56.6 | 8.36 × 10–12 | 2.65 × 10–10 | RVE1 | REVEILLE 1 |
| AT1G32150 | 297 | 824 | 36.0 | 6,979 | 27,206 | 25.7 | 1.37 × 10–11 | 3.97 × 10–10 | bZIP68, | BASIC REGION/LEUCINE ZIPPER TRANSCRIPTION FACTOR 68 |
| AT2G18160 | 126 | 824 | 15.3 | 2,268 | 27,206 | 8.3 | 1.78 × 10–11 | 4.77 × 10–10 | GBF5, bZIP2, FTM3 | BASIC LEUCINE-ZIPPER 2, G-BOX BINDING FACTOR 5, FLORAL TRANSITION AT THE MERISTEM 3 |
| AT5G15830 | 278 | 824 | 33.7 | 6,440 | 27,206 | 23.7 | 2.02 × 10–11 | 5.03 × 10–10 | bZIP3 | BASIC LEUCINE-ZIPPER 3 |
| AT1G45249 | 119 | 824 | 14.4 | 2,112 | 27,206 | 7.8 | 2.95 × 10–11 | 6.87 × 10–10 | AREB1, ABF2 | ABSCISIC ACID RESPONSIVE ELEMENTS-BINDING FACTOR 2, ABSCISIC ACID RESPONSIVE ELEMENTS-BINDING PROTEIN 1 |
| AT2G36270 | 198 | 824 | 24.0 | 4,188 | 27,206 | 15.4 | 3.38 × 10–11 | 7.38 × 10–10 | GIA1, ABI5 | GROWTH-INSENSITIVITY TO ABA 1, ABA INSENSITIVE 5 |
| AT2G35530 | 97 | 824 | 11.8 | 1,630 | 27,206 | 6.0 | 1.44 × 10–10 | 2.96 × 10–9 | bZIP16, | BASIC REGION/LEUCINE ZIPPER TRANSCRIPTION FACTOR 16 |
| AT3G10113 | 559 | 824 | 67.8 | 15,664 | 27,206 | 57.6 | 5.25 × 10–10 | 1.02 × 10–8 | ||
| AT1G75390 | 127 | 824 | 15.4 | 2,485 | 27,206 | 9.1 | 2.97 × 10–9 | 5.46 × 10–8 | bZIP44 | BASIC LEUCINE-ZIPPER 44 |
| AT3G10800 | 82 | 824 | 10.0 | 1,469 | 27,206 | 5.4 | 7.24 × 10–8 | 1.26 × 10–6 | BZIP28 |
aThe number of genes bound by the specific TF in the test set. bThe number of genes in the test set. cThe number of genes bound by the specific TF in the reference set. dThe number of genes in the reference set. eThe p-value after Bonferroni or Benjamini-Hochberg correction.