Table 3.
Prioritized top ranked genes with poor functional descriptions for future experimental investigations. Genes were given scores based on expression patterns identified from i) unique differential expression in a single contrast, ii) tissue/condition specific expression and iii) biologically relevant co-expression modules (each given a score of 2) while hub genes in a co-expression module were given a score of 4. Gene orthologs with similar expression profiles were given additional scores derived from the phylogenetic distance. Total score was calculated as the aggregate of individual scores. Top ranked genes (two per species) are represented here
| Score | ||||||||
|---|---|---|---|---|---|---|---|---|
| Organism | Gene ID | Differential expression | Condition specific expression | Co-expression | Hub gene | Consensus expression | Total | Arabidopsis orthologs |
| A. thaliana Araport11 | AT5G02090 | 2 | 2 | 2 | 0 | 18.73 | 24.73 | AT2G20080 |
| AT2G44010 | 0 | 2 | 2 | 0 | 19.2 | 23.2 | AT4G28840 | |
| B. distachyon | Bradi1g38210 | 0 | 2 | 2 | 0 | 10.7 | 14.7 | AT2G42760 |
| Bradi2g23445 | 0 | 0 | 2 | 0 | 11.69 | 13.69 | AT5G02090; AT2G37750 | |
| C. reinhardtii | Cre02.g078550 | 0 | 2 | 2 | 4 | 0 | 8 | |
| Cre02.g092700 | 0 | 2 | 2 | 4 | 0 | 8 | ||
| E. grandis | Eucgr.F01122 | 0 | 2 | 2 | 0 | 17.12 | 21.12 | |
| Eucgr.B00604 | 0 | 2 | 2 | 0 | 16.57 | 20.57 | AT5G08050 | |
| G. max | Glyma.16G013600 | 0 | 0 | 2 | 0 | 20.84 | 45.68 | AT3G14280 |
| Glyma.13G227500 | 0 | 0 | 2 | 0 | 20.28 | 44.56 | AT1G33055 | |
| K. fedtschenkoi | Kaladp0965s0006 | 2 | 0 | 2 | 0 | 26.23 | 30.23 | AT2G30230; AT1G06980 |
| Kaladp0065s0016 | 0 | 0 | 2 | 0 | 19.79 | 21.79 | AT4G28840; AT2G20080 | |
| M. truncatula | Medtr3g031140 | 0 | 2 | 2 | 0 | 27.28 | 31.28 | AT2G30230; AT1G06980 |
| Medtr2g079300 | 2 | 2 | 2 | 0 | 18.11 | 24.11 | ||
| P. hallii var. filipes | Pahal.3G090000 | 2 | 2 | 2 | 0 | 13.2 | 19.2 | AT5G02160 |
| Pahal.7G305700 | 2 | 2 | 2 | 0 | 12.05 | 18.05 | AT4G21445 | |
| P. hallii var. hallii | PhHAL.5G229300 | 2 | 2 | 2 | 0 | 11.532 | 17.532 | AT5G62770; AT3G27880; AT1G23710; AT1G70420 |
| PhHAL.3G160400 | 0 | 0 | 2 | 0 | 14.55 | 16.55 | ||
| P. patens | Pp3c11_15500 | 2 | 2 | 2 | 4 | 0 | 10 | |
| Pp3c13_2427 | 0 | 2 | 2 | 4 | 0 | 8 | ||
| P. trichocarpa | Potri.018G084100 | 2 | 2 | 2 | 0 | 19.79 | 25.79 | AT4G28840; AT2G20080 |
| Potri.003G193400 | 2 | 0 | 2 | 0 | 20.89 | 24.89 | ||
| P. virgatum | Pavir.5NG404000 | 0 | 0 | 2 | 0 | 13.64 | 15.64 | |
| Pavir.2NG640501 | 0 | 2 | 2 | 0 | 9.72 | 13.72 | AT5G13720 | |
| S. bicolor | Sobic.009G229000 | 0 | 0 | 2 | 4 | 13.35 | 19.35 | AT4G28840; AT2G20080 |
| Sobic.001G118400 | 2 | 2 | 2 | 0 | 10.44 | 16.44 | AT1G73885 | |
| S. bicolorRio | SbRio.08G154700 | 0 | 2 | 2 | 0 | 12.31 | 16.31 | AT5G08050 |
| SbRio.10G134000 | 0 | 2 | 2 | 0 | 12.05 | 16.05 | AT4G01150 | |
| S. angustifolium | Sphfalx02G142200 | 2 | 2 | 2 | 4 | 0 | 10 | |
| Sphfalx11G077900 | 2 | 2 | 0 | 0 | 4.5 | 8.5 | AT3G03341 | |
| S. italica | Seita.9G407600 | 2 | 0 | 2 | 0 | 12.7053 | 16.7053 | AT1G63410; AT3G14260 |
| Seita.9G436900 | 0 | 2 | 2 | 0 | 12.5741 | 16.5741 | AT2G30230; AT1G06980 | |
| S. viridis | Sevir.1G151100 | 2 | 0 | 2 | 0 | 13.2732 | 17.2732 | AT1G12320; AT1G62840; AT3G60780; AT2G45360 |
| Sevir.5G247600 | 0 | 0 | 2 | 0 | 13.2732 | 15.2732 | AT5G62770; AT3G27880; AT1G23710; AT1G70420 | |