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. Author manuscript; available in PMC: 2013 Jun 1.
Published in final edited form as: Mol Oral Microbiol. 2012 Mar 28;27(3):202–219. doi: 10.1111/j.2041-1014.2012.00643.x

Table 2.

60 most highly upregulated genes in V2948 when compared to the parental W83 strain.

locus* common_name M† Fld‡ t P repeat§
PG1484 hypothetical protein 2.099982 4.287042 26.382838 0.000000 (2.7E-11) 12
PG1482 conjugative transposon protein TraF 2.093370 4.267439 22.848107 0.000000 (1.3E-10) 12
PG1483 conjugative transposon protein TraE 1.947643 3.857439 32.154368 0.000000 (3.1E-12) 12
PG1474 conjugative transposon protein TraO 1.937859 3.831366 40.145591 0.000000 (2.7E-13) 12
PG0606 hypothetical protein 1.930285 3.811305 8.643301 0.000003 12
PG1480 conjugative transposon protein TraI 1.743379 3.348184 14.201320 0.000000 (2.0E-08) 12
PG1476 conjugative transposon protein TraM 1.678199 3.200283 38.684244 0.000000 (4.2E-13) 12
PG1475 conjugative transposon protein TraN 1.672028 3.186622 8.500293 0.000004 12
PG1534 conserved domain protein 1.609411 3.051272 10.727336 0.000039 11
PG1974 hypothetical protein 1.583181 2.996297 49.457197 0.000000 (2.8E-14) 12
PG1477 hypothetical protein 1.573150 2.975536 9.623705 0.000001 12
PG1479 conjugative transposon protein TraJ 1.555254 2.938855 23.738661 0.000000 (8.4E-11) 12
PG1481 conjugative transposon protein TraG 1.540755 2.909468 34.855289 0.000000 (1.3E-12) 12
PG1478 conjugative transposon protein TraK 1.482257 2.793854 23.184716 0.000000 (1.1E-10) 12
PG1683 conserved hypothetical protein 1.433670 2.701330 39.828657 0.000000 (3.0E-13) 12
PG1010 ABC transporter, ATP-binding protein 1.374896 2.593492 52.412469 0.000000 (1.5E-14) 12
PG1745 phosphoribulokinase family protein 1.370986 2.586472 22.364335 0.000000 (1.6E-10) 12
PG1473 conjugative transposon protein TraQ 1.352018 2.552689 23.740666 0.000000 (3.9E-10) 11
PG1494 conserved hypothetical protein 1.291271 2.447436 18.081931 0.000000 (1.6E-09) 12
PG1684 Hypothetical protein 1.218886 2.327670 126.990104 0.000000 (9.0E-19) 12
PG1497 DNA-binding protein, histone-like family 1.166672 2.244932 12.700840 0.000000 (6.5E-08) 12
PG1535 transcriptional regulator, putative 1.154254 2.225693 34.191452 0.000000 (1.6E-12) 12
PG0906 lipoprotein, putative 1.145365 2.212022 27.472915 0.000000 (1.7E-11) 12
PG1007 transcriptional regulator, GntR family 1.101514 2.145798 28.705630 0.000000 (1.1E-11) 12
PG1663 ABC transporter, ATP-binding protein 1.085281 2.121788 31.306825 0.000000 (4.2E-12) 12
PG1960 ribosomal protein L28 1.074119 2.105436 24.181677 0.000000 (6.9E-11) 12
PG1119 flavodoxin, putative 1.041524 2.058401 54.008493 0.000000 (1.1E-14) 12
PG1496 Hypothetical protein 1.039165 2.055038 10.057285 0.000001 12
PG0656 ribosomal protein L34 0.949020 1.930561 22.713565 0.000000 (1.4E-10) 12
PG1664 ABC transporter, permease protein, putative 0.942746 1.922183 24.905838 0.000000 (5.0E-11) 12
PG0607 Hypothetical protein 0.934248 1.910894 26.892089 0.000000 (2.2E-11) 12
PG1826 conserved domain protein 0.901095 1.867483 104.112734 0.000000 (1.0E-18) 12
PG1008 Hypothetical protein 0.895692 1.860502 29.357205 0.000000 (8.4E-12) 12
PG1009 Hypothetical protein 0.885176 1.846990 42.007912 0.000000 (1.7E-13) 12
PG1959 ribosomal protein L33 0.875783 1.835004 27.945881 0.000000 (1.4E-11) 12
PG0121 DNA-binding protein HU 0.872345 1.830637 12.626815 0.000000 (6.9E-08) 12
PG1890 lipoprotein, putative 0.860410 1.815555 12.624885 0.000000 (6.9E-08) 12
PG1435 Integrase 0.858677 1.813375 6.251841 0.000062 12
PG1662 Hypothetical protein 0.852168 1.805212 6.034404 0.000085 12
PG1432 Sensor histidine kinase 0.839072 1.788899 8.275893 0.000009 12
PG1609 methylmalonyl-CoA decarboxylase, gamma s. 0.834169 1.782830 9.434488 0.000001 12
PG0536 Hypothetical protein 0.812835 1.756660 18.157552 0.000000 (1.5E-09) 12
PG0928 response regulator 0.812297 1.756005 15.231637 0.000000 (9.7E-09) 12
PG0520 chaperonin, 60 kDa 0.810891 1.754295 11.133896 0.000000 (2.5E-07) 12
PG0609 Hypothetical protein 0.797196 1.737720 4.029668 0.002401 11
PG1004 prolyl oligopeptidase family protein 0.796070 1.736364 30.484226 0.000000 (5.6E-12) 12
PG1676 phosphoenolpyruvate carboxykinase (ATP) 0.787653 1.726264 38.083595 0.000000 (4.9E-13) 12
PG1634 Hypothetical protein 0.787164 1.725679 10.500075 0.000000 (4.5E-07) 12
PG1786 Hypothetical protein 0.786857 1.725312 13.041755 0.000000 (4.9E-08) 12
PG1586 batE protein 0.784310 1.722269 35.544134 0.000000 (1.0E-12) 12
PG1267 Hypothetical protein 0.777617 1.714297 12.905965 0.000000 (5.5E-08) 12
PG0192 Cationic outer membrane protein OmpH 0.775456 1.711731 15.072637 0.000000 (1.1E-08) 12
PG0292 chromate transport protein, putative 0.774012 1.710018 38.544254 0.000000 (4.3E-13) 12
PG0521 chaperonin, 10 kDa 0.771302 1.706810 12.126001 0.000000 (1.0E-07) 12
PG2212 Hypothetical protein 0.771003 1.706456 7.927241 0.000007 12
PG0350 internalin-related protein 0.770678 1.706072 33.152570 0.000000 (2.2E-12) 12
PG0681 Hypothetical protein 0.769667 1.704876 12.227690 0.000000 (9.6E-08) 12
PG0293 secretion activator protein, putative 0.763501 1.697605 23.413056 0.000000 (9.8E-11) 12
PG1005 lipoprotein, putative 0.760033 1.693529 25.405906 0.000000 (4.0E-11) 12
PG0138 malonyl CoA-acyl carrier protein transacylase 0.746919 1.678205 17.931087 0.000000 (1.7E-09) 12
*

Gene ID according to JCVI (formerly TIGR)

†

M = log (aerobic conditions/ anaerobic conditions)

‡

Fld = fold change (ratio of transcript abundance in V2948/W83)

§

Repeats = number of spots used for the analysis