Table 1 Top 50 most highly induced bacterial genes in roots vs. matrix
Strain ID|Gene ID | Gene name | Base meana | log2FCb | Adjusted Pc | Functiond |
|---|---|---|---|---|---|
Root1280 | 1676 | 645 | 16.8 | 1.31e-16 | Type-1 fimbrial protein, A | |
Root154 | 1230 | 857 | 16.4 | 6e-13 | Unknown | |
Root1277 | 481 | glmS | 1157 | 16.3 | 4.21e-06 | Glutamine-fructose-6-phosphate amidotransferase |
Root154 | 382 | 838 | 16.1 | 6.35e-30 | TonB-dependent receptor | |
Root70 | 3816 | llpE | 634 | 15.2 | 6.54e-25 | Alpha-beta hydrolase fold-3 domain protein |
Root154 | 1686 | rhlE2 | 326 | 14.6 | 8.7e-08 | DEAD DEAH box helicase |
Root154 | 2017 | 1424 | 14.3 | 6.9e-10 | Mycolic acid cyclopropane synthetase | |
Root154 | 1225 | 1096 | 14.1 | 2.78e-12 | Pili and flagellar-assembly chaperone | |
Root70 | 4176 | purU | 345 | 14.1 | 3.01e-22 | Formyltetrahydrofolate deformylase |
Root154 | 768 | 1251 | 14.1 | 3.56e-08 | Unknown | |
Root1277 | 4059 | Echdc | 257 | 13.9 | 5.93e-05 | Enoyl-CoA hydratase/isomerase |
Root154 | 1227 | 3781 | 13.8 | 4.16e-16 | Unknown | |
Root123D2 | 2583 | rskA | 348 | 13.8 | 6.31e-06 | Anti-sigma-K factor |
Root1277 | 897 | 242 | 13.8 | 7.56e-05 | Predicted periplasmic protein (DUF2271) | |
Root154 | 369 | 181 | 13.6 | 2.12e-06 | Xylose isomerase-like TIM barrel | |
Root70 | 1346 | 215 | 13.4 | 1.77e-05 | Nucleotidyltransferase | |
Root569 | 2962 | pstC | 467 | 13.4 | 3.17e-10 | Polypeptide phosphate ABC transporter subunit |
Root154 | 381 | 2868 | 13.4 | 3.25e-15 | Lactoylglutathione lyase and related lyases | |
Root70 | 3634 | 202 | 13.2 | 2.65e-05 | Drug metabolite transporter superfamily | |
Root1277 | 4057 | 1229 | 13.2 | 7.44e-09 | Amine oxidase flavin-containing A | |
Root154 | 985 | filA | 135 | 13.1 | 3.71e-06 | Membrane-bound metallopeptidase |
Root559 | 706 | 219 | 12.9 | 1.4e-06 | Belongs to the UPF0312 family | |
Root61 | 6 | 166 | 12.8 | 1.09e-06 | Unknown | |
Root685 | 2415 | 608 | 12.8 | 1.54e-07 | Copper chaperone PCu(A)C | |
Root123D2 | 3109 | 192 | 12.6 | 0.0001 | Acetyltransferase (GNAT) domain | |
Root154 | 380 | 91 | 12.6 | 3.3e-06 | PFAM TonB-dependent Receptor | |
Root102 | 1333 | 1413 | 12.6 | 2.35e-05 | Unknown | |
Root102 | 4013 | gabD | 841 | 12.5 | 4.26e-05 | Aldehyde dehydrogenase family |
Root70 | 441 | petB | 754 | 12.4 | 2.61e-07 | Cytochrome b6 |
Root322 | 1078 | ilvA | 238 | 12.3 | 1.5e-06 | Pyridoxal-phosphate dependent enzyme |
Root123D2 | 241 | 674 | 12.3 | 3.66e-07 | Membrane fusion protein (TC 8.A.1) family | |
Root123D2 | 1229 | 154 | 12.2 | 0.0002 | Unknown | |
Root1277 | 2958 | dnaA | 403 | 12.1 | 3.58e-05 | Chromosomal replication initiator protein |
Root172 | 4049 | 559 | 12.1 | 9.61e-05 | von Willebrand factor (vWF) type A domain | |
Root149 | 1190 | 204 | 11.9 | 0.0007 | Uncharacterized protein (DUF2059) | |
Root154 | 4234 | rpsP | 53 | 11.6 | 2.24e-05 | Ribosomal protein bS16 family |
Root322 | 1193 | 155 | 11.5 | 1.93e-05 | Major facilitator Superfamily | |
Root322 | 2730 | 201 | 11.5 | 0.0005 | MFS/sugar transport protein | |
Root149 | 1665 | rplQ | 123 | 11.4 | 0.0002 | Ribosomal protein L17 |
Root670 | 456 | dctA | 883 | 11.4 | 3.32e-07 | Aerobic C4-dicarboxylate transporter |
Root322 | 1563 | 136 | 11.4 | 1.93e-05 | Unknown | |
Root149 | 609 | atpF | 115 | 11.3 | 0.0002 | ATP synthase subunit b |
Root569 | 2421 | aspA | 1685 | 11.3 | 1.13e-14 | Aspartate ammonia-lyase |
Root559 | 1423 | rnpA | 90 | 11.3 | 5.94e-05 | Ribonuclease P protein component |
Root559 | 650 | 99 | 11.2 | 0.0001 | Unknown | |
Root322 | 2077 | yigZ | 136 | 11.2 | 0.0001 | Uncharacterized protein family UPF0029 |
Root61 | 2410 | hmuT | 253 | 11.1 | 5.36e-06 | Periplasmic binding protein |
Root61 | 2017 | 62 | 11.0 | 0.0001 | Domain of unknown function (DUF4407) | |
Root61 | 1037 | 878 | 11.0 | 3.45e-10 | Domain of unknown function (DUF4442) |
