Selected Cell
Cell:
Value:
6h results genes
12h results genes
24h results genes
DAVID 6h
DAVID 12h
DAVID 24h
A
B
C
D
E
F
G
H
I
J
1
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3
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5
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30
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40
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50
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Supplementary Table S2. List of down and upregulated genes comparing P. putida KT2440 cultures in solid vs liquid media at 6 hours of incubation. | |||||||||
PP number | DAVID accession number | Symbol | Product | FoldChange | p.adj.Value | ||||
PP_0008 | 1043484 | rnpA | ribonuclease P protein component | 4.96 | 0.00000815 | ||||
PP_0009 | 1043485 | rpmH | 50S ribosomal protein L34 | 6.66 | 0.00000927 | ||||
PP_0023 | 1043502 | NP_742193.1 | hypothetical protein | 2.23 | 0.00048457 | ||||
PP_0068 | 1043549 | def-I | peptide deformylase | 4.73 | 0.00000000 | ||||
PP_0089 | 1043570 | osmC | stress-induced peroxiredoxin | 4.11 | 0.00000014 | ||||
PP_0115 | 1043606 | katE | hydroperoxidase | 3.21 | 0.00008868 | ||||
PP_0135 | 1043635 | NP_742305.1 | hypothetical protein | 7.62 | 0.00000035 | ||||
PP_0136 | 1043636 | NP_742306.1 | hypothetical protein | 3.41 | 0.00092760 | ||||
PP_0157 | 1043670 | gcdR | gcdH transcriptional regulator | 2.54 | 0.00021027 | ||||
PP_0161 | 1043684 | NP_742330.1 | putative transmembrane sensor | -23.00 | 0.00000000 | ||||
PP_0162 | 1043685 | NP_742331.1 | ECF family RNA polymerase sigma-70 factor | -13.42 | 0.00000000 | ||||
PP_0180 | 1043706 | NP_742349.1 | cytochrome c family protein | -2.92 | 0.00020427 | ||||
PP_0213 | 1043755 | gabD-I | succinate-semialdehyde dehydrogenase | -2.23 | 0.00002239 | ||||
PP_0214 | 1043757 | gabT | 5-aminovalerate aminotransferase DavT | -2.09 | 0.00075493 | ||||
PP_0235 | 1043789 | NP_742403.1 | peroxidase | 4.03 | 0.00000000 | ||||
PP_0236 | 1043798 | ssuE | NAD(P)H-dependent FMN reductase subunit | 4.28 | 0.00018864 | ||||
PP_0270 | 1043866 | NP_742437.1 | sensor histidine kinase | -8.20 | 0.00000000 | ||||
PP_0271 | 1043867 | gltR-I | two-component system response regulator | -9.78 | 0.00000000 | ||||
PP_0339 | 1044044 | aceE | pyruvate dehydrogenase E1 component | 2.71 | 0.00000075 | ||||
PP_0350 | 1044057 | NP_742517.1 | ferrichrome-iron receptor | -4.05 | 0.00026270 | ||||
PP_0351 | 1044058 | NP_742518.1 | transmembrane sensor | -14.36 | 0.00000000 | ||||
PP_0352 | 1044059 | NP_742519.1 | ECF family RNA polymerase sigma-70 factor | -12.51 | 0.00000000 | ||||
PP_0369 | 1044078 | NP_742536.2 | diguanylate cyclase | -4.18 | 0.00003866 | ||||
PP_0389 | 1044101 | rpsU | 30S ribosomal protein S21 | 4.44 | 0.00000228 | ||||
PP_0404 | 1044119 | lptD | LPS-assembly protein LptD | 2.66 | 0.00003415 | ||||
PP_0415 | 1044137 | rpe | ribulose-5-phosphate 3-epimerase | 3.02 | 0.00003245 | ||||
PP_0418 | 1044141 | estP | esterase EstP | 2.16 | 0.00053502 | ||||
PP_0440 | 1044182 | tufA | elongation factor Tu-A | 3.67 | 0.00000061 | ||||
PP_0441 | 1044184 | secE | protein translocase subunit SecE | 3.02 | 0.00001712 | ||||
PP_0445 | 1044188 | rplJ | 50S ribosomal protein L10 | 2.75 | 0.00000183 | ||||
PP_0446 | 1044189 | rplL | 50S ribosomal protein L7/L12 | 2.20 | 0.00006480 | ||||
PP_0449 | 1044192 | rpsL | 30S ribosomal protein S12 | 3.50 | 0.00000003 | ||||
PP_0450 | 1044193 | rpsG | 30S ribosomal protein S7 | 2.41 | 0.00015258 | ||||
PP_0451 | 1044195 | fusA | elongation factor G 1 | 2.63 | 0.00000036 | ||||
PP_0452 | 1044196 | tufB | elongation factor Tu-B | 2.72 | 0.00000017 | ||||
PP_0453 | 1044199 | rpsJ | 30S ribosomal protein S10 | 5.40 | 0.00000000 | ||||
PP_0454 | 1044200 | rplC | 50S ribosomal protein L3 | 4.33 | 0.00000998 | ||||
PP_0455 | 1044201 | rplD | 50S ribosomal protein L4 | 2.89 | 0.00025272 | ||||
PP_0456 | 1044202 | rplW | 50S ribosomal protein L23 | 2.79 | 0.00055586 | ||||
PP_0458 | 1044204 | rpsS | 30S ribosomal protein S19 | 2.27 | 0.00022455 | ||||
PP_0459 | 1044206 | rplV | 50S ribosomal protein L22 | 2.37 | 0.00004627 | ||||
PP_0460 | 1044209 | rpsC | 30S ribosomal protein S3 | 2.42 | 0.00023044 | ||||
PP_0461 | 1044210 | rplP | 50S ribosomal protein L16 | 2.16 | 0.00059235 | ||||
PP_0468 | 1044227 | rpsH | 30S ribosomal protein S8 | 3.53 | 0.00000025 | ||||
PP_0469 | 1044228 | rplF | 50S ribosomal protein L6 | 2.69 | 0.00003449 | ||||
PP_0476 | 1044241 | rpsM | 30S ribosomal protein S13 | 3.15 | 0.00001644 | ||||
PP_0477 | 1044242 | rpsK | 30S ribosomal protein S11 | 2.27 | 0.00043908 | ||||
PP_0478 | 1044244 | rpsD | 30S ribosomal protein S4 | 2.25 | 0.00033652 | ||||
PP_0481 | 1044248 | katA | catalase | 45.36 | 0.00000000 | ||||
PP_0482 | 1044249 | bfr-I | bacterioferritin | 4.56 | 0.00000000 | ||||
PP_0486 | 1044256 | NP_742652.1 | GntR family transcriptional regulator | 4.88 | 0.00000002 | ||||
PP_0513 | 1044288 | nrdR | DNA-binding transcriptional repressor NrdR | 4.90 | 0.00023149 | ||||
PP_0516 | 1044291 | ribAB-I | bifunctional 3%2C4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II | 2.70 | 0.00000754 | ||||
PP_0538 | 1044317 | ppa | inorganic pyrophosphatase | 2.61 | 0.00001116 | ||||
PP_0552 | 1044336 | bdhA | 2%2C3-butanediol dehydrogenase | 5.09 | 0.00000000 | ||||
PP_0553 | 1044339 | acoC | acetoin cleaving system dihydrolipoyllysine-residue acetyltransferase | 5.35 | 0.00000000 | ||||
PP_0554 | 1044340 | acoB | acetoin:2%2C6-dichlorophenolindophenol oxidoreductase subunit beta | 5.20 | 0.00000000 | ||||
PP_0555 | 1044342 | acoA | acetoin:2%2C6-dichlorophenolindophenol oxidoreductase subunit alpha | 4.86 | 0.00000000 | ||||
PP_0556 | 1044343 | NP_742719.1 | acetoin catabolism protein | 2.42 | 0.00011583 | ||||
PP_0558 | 1044345 | accC | acetyl-CoA carboxylase biotin carboxylase subunit | 2.35 | 0.00023044 | ||||
PP_0559 | 1044346 | accB | acetyl-CoA carboxylase biotin carboxyl carrier subunit | 4.00 | 0.00000000 | ||||
PP_0560 | 1044348 | aroQ-I | type II 3-dehydroquinate dehydratase | 4.05 | 0.00000008 | ||||
PP_0563 | 1044352 | NP_742726.1 | two-component system response regulator | -3.18 | 0.00000004 | ||||
PP_0570 | 1044360 | yfhM | lipoprotein | 2.97 | 0.00000037 | ||||
PP_0600 | 1044414 | rpsT | 30S ribosomal protein S20 | 6.70 | 0.00002500 | ||||
PP_0622 | 1044439 | bamD | outer membrane protein assembly factor BamD | 3.11 | 0.00033190 | ||||
PP_0654 | 1044477 | mdh | malate dehydrogenase | -2.08 | 0.00038357 | ||||
PP_0657 | 1044481 | NP_742818.1 | amino acid ABC transporter substrate-binding protein | 3.47 | 0.00037589 | ||||
PP_0667 | 1044491 | NP_742828.1 | ECF family RNA polymerase sigma-70 factor | -10.98 | 0.00000000 | ||||
PP_0668 | 1044492 | NP_742829.1 | transmembrane sensor | -20.06 | 0.00000000 | ||||
PP_0674 | 1044500 | ettA | ADP/ATP ratio sensor/translation inhibitor | 3.43 | 0.00004606 | ||||
PP_0685 | 1044511 | NP_742846.1 | hypothetical protein | -40.66 | 0.00000000 | ||||
PP_0688 | 1044516 | rplU | 50S ribosomal protein L21 | 7.67 | 0.00000000 | ||||
PP_0689 | 1044517 | rpmA | 50S ribosomal protein L27 | 4.12 | 0.00000805 | ||||
PP_0700 | 1044530 | NP_742861.1 | transmembrane sensor | -14.06 | 0.00000000 | ||||
PP_0703 | 1044534 | NP_742864.1 | transmembrane sensor | -15.24 | 0.00000000 | ||||
PP_0704 | 1044535 | NP_742865.1 | ECF family RNA polymerase sigma-70 factor | -6.02 | 0.00000000 | ||||
PP_0711 | 1044542 | ycaC-I | putative hydrolase | 3.59 | 0.00000000 | ||||
PP_0723 | 1044555 | ispE | 4-diphosphocytidyl-2C-methyl-D-erythritol kinase | 5.81 | 0.00000000 | ||||
PP_0732 | 1044565 | hemA | glutamyl-tRNA reductase | 3.11 | 0.00000591 | ||||
PP_0737 | 1044570 | pagL-I | lipid A 3-O-deacylase | 2.24 | 0.00022052 | ||||
PP_0786 | 1044626 | trxB | thioredoxin reductase | 24.22 | 0.00000000 | ||||
PP_0812 | 1044661 | cyoA | cytochrome bo terminal oxidase subunit II | 6.62 | 0.00000000 | ||||
PP_0817 | 1044669 | alaC | aminotransferase | 4.60 | 0.00000003 | ||||
PP_0832 | 1044690 | queA | S-adenosylmethionine:tRNA ribosyltransferase-isomerase | 3.61 | 0.00022671 | ||||
PP_0838 | 1044698 | suhB | bifunctional inositol monophosphatase/glycerol-2-phosphatase | 4.99 | 0.00000000 | ||||
PP_0843 | 1044705 | iscU | iron-sulfur cluster assembly scaffold protein | -2.05 | 0.00082511 | ||||
PP_0846 | 1044710 | hscA | DnaK-like molecular chaperone | -2.18 | 0.00012767 | ||||
PP_0861 | 1044732 | NP_743022.2 | outer membrane ferric siderophore receptor | -3.37 | 0.00078766 | ||||
PP_0863 | 1044737 | NP_743024.1 | hypothetical protein | -2.99 | 0.00001742 | ||||
PP_0864 | 1044738 | speC | ornithine decarboxylase | 3.88 | 0.00018864 | ||||
PP_0883 | 1044767 | opdP | glycine-glutamate dipeptide porin | 2.89 | 0.00000274 | ||||
PP_0897 | 1044785 | NP_743058.1 | class 1 fumarate hydratase | 5.28 | 0.00000000 | ||||
PP_0913 | 1044812 | NP_743074.1 | hypothetical protein | -5.88 | 0.00000000 | ||||
PP_0915 | 1044816 | sodB | superoxide dismutase | 7.67 | 0.00000000 | ||||
PP_0932 | 1044838 | gatC | aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C | 3.19 | 0.00000185 | ||||
PP_0933 | 1044840 | mreB | cell wall structural actin-like protein MreB | 3.03 | 0.00027088 | ||||
PP_0943 | 1044854 | NP_743104.1 | hypothetical protein | -88.09 | 0.00000000 |
A
B
C
D
E
F
G
H
I
J
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
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254
255
256
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258
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270
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273
274
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293
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300
PP_4371 | 1041972 | atoC | two-component system DNA-binding transcriptional activator AtoC | -7.86 | 0.0000000 | ||||
PP_4372 | 1041790 | fleS | two-component system sensor histidine kinase FleS | -5.65 | 0.0000000 | ||||
PP_4380 | 1042471 | flgL | flagellar hook-associated protein FlgL | -5.97 | 0.0000002 | ||||
PP_4381 | 1042481 | flgK | flagellar hook-associated protein FlgK | -5.43 | 0.0000005 | ||||
PP_4382 | 1042627 | flgJ | peptidoglycan hydrolase FlgJ | -5.10 | 0.0000026 | ||||
PP_4383 | 1042309 | flgI | flagellar P-ring protein | -6.73 | 0.0000001 | ||||
PP_4384 | 1044376 | flgH | flagellar L-ring protein | -7.45 | 0.0000000 | ||||
PP_4385 | 1043820 | flgG | flagellar basal-body rod protein FlgG | -5.62 | 0.0000000 | ||||
PP_4386 | 1041829 | flgF | flagellar basal-body rod protein FlgF | -6.25 | 0.0000000 | ||||
PP_4387 | 1043250 | NP_746501.1 | hypothetical protein | -11.53 | 0.0000000 | ||||
PP_4388 | 1044605 | flgE | flagellar hook protein FlgE | -14.12 | 0.0000000 | ||||
PP_4389 | 1041827 | flgD | flagellar basal-body rod modification protein FlgD | -13.19 | 0.0000000 | ||||
PP_4390 | 1041825 | flgC | flagellar basal-body rod protein FlgC | -11.92 | 0.0000000 | ||||
PP_4391 | 1041605 | flgB | flagellar basal-body rod protein FlgB | -10.05 | 0.0000000 | ||||
PP_4394 | 1042637 | flgA | flagella basal body P-ring formation protein | -3.63 | 0.0001295 | ||||
PP_4406 | 1044033 | NP_746520.1 | hypothetical protein | -18.02 | 0.0000000 | ||||
PP_4407 | 1041721 | NP_746521.1 | gamma-aminobutyrate transporter | -11.62 | 0.0000000 | ||||
PP_4459 | 1042042 | NP_746570.1 | transposase | -4.62 | 0.0000156 | ||||
PP_4468 | 1044276 | NP_746579.1 | Cro/CI family transcriptional regulator | 7.86 | 0.0000005 | ||||
PP_4487 | 1042436 | acsA-I | acetyl-CoA synthetase | 9.03 | 0.0000026 | ||||
PP_4531 | 1046254 | NP_746641.1 | hypothetical protein | 5.52 | 0.0000316 | ||||
PP_4561 | 1046343 | csbD | stress response protein | 4.23 | 0.0002443 | ||||
PP_4614 | 1042558 | NP_746723.1 | hypothetical protein | 4.07 | 0.0004835 | ||||
PP_4714 | 1041880 | rimP | ribosome maturation factor | 5.73 | 0.0000002 | ||||
PP_4715 | 1042365 | tpiA | triose phosphate isomerase | 6.11 | 0.0000000 | ||||
PP_4718 | 1045877 | ftsH | integral membrane ATP-dependent zinc metallopeptidase | 3.01 | 0.0005744 | ||||
PP_4731 | 1042313 | bamE | outer membrane protein assembly factor BamE | 3.70 | 0.0001699 | ||||
PP_4794 | 1042400 | leuS | leucine--tRNA ligase | 3.43 | 0.0006090 | ||||
PP_4797 | 1042983 | NP_746902.1 | hypothetical protein | 14.88 | 0.0000000 | ||||
PP_4818 | 1043073 | prmA | ribosomal protein L11 methyltransferase | 6.65 | 0.0000137 | ||||
PP_4871 | 1045422 | NP_746976.1 | lysine decarboxylase family protein | 6.40 | 0.0000001 | ||||
PP_4877 | 1043837 | rpsF | 30S ribosomal protein S6 | 3.55 | 0.0001410 | ||||
PP_4888 | 1041629 | NP_746991.2 | methyl-accepting chemotaxis transducer | -5.30 | 0.0000041 | ||||
PP_4952 | 1043931 | dbpA | 23S rRNA specific ATP-dependent RNA helicase | 4.79 | 0.0002236 | ||||
PP_4958 | 1044074 | ygjP | metal-dependent hydrolase | -3.37 | 0.0008506 | ||||
PP_4959 | 1042674 | NP_747062.1 | diguanylate cyclase | -4.39 | 0.0001484 | ||||
PP_4974 | 1043904 | nhaP | NhaP-type Na+(K+)/H+ antiporter | 5.91 | 0.0000006 | ||||
PP_4975 | 1042725 | NP_747078.1 | acyl-CoA thioesterase | 10.76 | 0.0000000 | ||||
PP_4994 | 1042505 | NP_747096.1 | hypothetical protein | 4.38 | 0.0007998 | ||||
PP_5020 | 1042670 | NP_747121.1 | methyl-accepting chemotaxis protein | -5.02 | 0.0000055 | ||||
PP_5045 | 1041702 | thiI | tRNA sulfurtransferase | 4.07 | 0.0000450 | ||||
PP_5055 | 1042614 | NP_747156.1 | Sulfurtransferase | 4.88 | 0.0000541 | ||||
PP_5074 | 1041992 | hemE | uroporphyrinogen decarboxylase | 4.22 | 0.0000111 | ||||
PP_5087 | 1043893 | rpmE | 50S ribosomal protein L31 | 7.20 | 0.0000101 | ||||
PP_5092 | 1041784 | NP_747193.1 | NLP/P60 protein | 20.77 | 0.0000000 | ||||
PP_5094 | 1044694 | NP_747195.1 | PLP binding domain-containing protein | 4.10 | 0.0001168 | ||||
PP_5165 | 1042564 | plpB | NLPA lipoprotein | 44.86 | 0.0000000 | ||||
PP_5167 | 1042569 | NP_747268.1 | hypothetical protein | 4.15 | 0.0003740 | ||||
PP_5171 | 1042535 | sbp-II | sulfate ABC transporter substrate-binding protein | 6.38 | 0.0000002 | ||||
PP_5172 | 1042508 | NP_747273.1 | hypothetical protein | 28.08 | 0.0000000 | ||||
PP_5204 | 1043355 | NP_747305.1 | hypothetical protein | 9.13 | 0.0000027 | ||||
PP_5214 | 1042415 | rho | transcription termination factor Rho | 6.22 | 0.0000001 | ||||
PP_5215 | 1042429 | trxA | thioredoxin I | 14.40 | 0.0000000 | ||||
PP_5282 | 1042258 | rpmB | 50S ribosomal protein L28 | 4.62 | 0.0000799 | ||||
PP_5295 | 1042222 | NP_747396.3 | hypothetical protein | 3.81 | 0.0003802 | ||||
PP_5307 | 1042225 | exbD | TonB-gated outer membrane transporter gating inner membrane protein | -7.47 | 0.0000000 | ||||
PP_5308 | 1042220 | tonB | TonB energy transducing system subunit TonB | -4.23 | 0.0000800 | ||||
PP_5323 | 1042169 | NP_747424.1 | M23/M37 family peptidase | -3.76 | 0.0003797 | ||||
PP_5336 | 1042159 | purE | 5-(carboxyamino)imidazole ribonucleotide mutase | 6.73 | 0.0000070 | ||||
PP_5409 | 1041649 | glmS | L-glutamine/D-fructose-6-phosphate aminotransferase | 6.06 | 0.0004700 | ||||
PP_5410 | 1042019 | NP_747510.1 | DeoR family transcriptional regulator | 19.75 | 0.0000000 | ||||
PP_5477 | 26969776 | YP_009236951.1 | hypothetical protein | 6.80 | 0.0000200 | ||||
PP_5505 | 26969808 | YP_009236982.1 | transmembrane protein | -10.31 | 0.0000000 | ||||
PP_5524 | 26969828 | YP_009236999.1 | hypothetical protein | 24.99 | 0.0000000 | ||||
PP_5559 | 26969867 | YP_009237033.1 | hypothetical protein | 13.24 | 0.0000000 | ||||
PP_5560 | 26969868 | YP_009237034.1 | hypothetical protein | 6.04 | 0.0000695 | ||||
PP_5566 | 26969873 | YP_009237039.1 | hypothetical protein | 9.56 | 0.0008186 | ||||
PP_5592 | 26969897 | YP_009237061.1 | hypothetical protein | 9.00 | 0.0000000 | ||||
PP_5593 | 26969898 | YP_009237062.1 | hypothetical protein | 17.24 | 0.0000000 | ||||
PP_5594 | 26969899 | YP_009237063.1 | hypothetical protein | 8.31 | 0.0000001 | ||||
PP_5596 | 26969901 | YP_009237065.1 | hypothetical protein | 3.99 | 0.0006339 | ||||
PP_5597 | 26969902 | YP_009237066.1 | hypothetical protein | 6.16 | 0.0001263 | ||||
PP_5645 | 26969954 | YP_009237118.1 | hypothetical protein | -6.40 | 0.0000009 | ||||
PP_5659 | 26969967 | YP_009237130.1 | hypothetical protein | 6.03 | 0.0000188 | ||||
PP_5660 | 26969968 | kdpF | potassium-transporting ATPase subunit F | -8.63 | 0.0000115 | ||||
PP_5710 | 26970031 | YP_009237184.1 | hypothetical protein | -4.07 | 0.0001484 | ||||
NoSymbol | cspA regulatory region | 3.31 | 0.0002640 | ||||||
NoSymbol | gyrA regulatory region | 5.78 | 0.0000025 | ||||||
NoSymbol | tRNA-Glu | 5.89 | 0.0000006 | ||||||
NoSymbol | tRNA-Gly | 6.76 | 0.0000059 | ||||||
NoSymbol | tRNA-Glu | 9.47 | 0.0000156 | ||||||
NoSymbol | tRNA-Gly | 6.07 | 0.0000905 | ||||||
NoSymbol | tRNA-Glu | 4.11 | 0.0004182 | ||||||
NoSymbol | tRNA-Val | 5.26 | 0.0000122 | ||||||
NoSymbol | tRNA-Arg | 3.75 | 0.0002838 | ||||||
NoSymbol | tRNA-Gln | 21.25 | 0.0000004 | ||||||
pck | --- | 7.31 | 0.0000000 | ||||||
NoSymbol | P15 ncRNA | 7.23 | 0.0006726 | ||||||
NoSymbol | P9 ncRNA | 9.46 | 0.0000135 | ||||||
NoSymbol | tRNA-Arg | 9.12 | 0.0000292 | ||||||
NoSymbol | tRNA-Arg | 7.16 | 0.0000001 | ||||||
NoSymbol | tRNA-Arg | 5.73 | 0.0007230 | ||||||
NoSymbol | tRNA-Ser | 4.05 | 0.0000121 | ||||||
NoSymbol | tRNA-Tyr | 6.75 | 0.0000000 | ||||||
NoSymbol | tRNA-Gly | 7.75 | 0.0000000 | ||||||
NoSymbol | tRNA-Thr | 8.22 | 0.0000935 | ||||||
NoSymbol | tRNA-Trp | 7.05 | 0.0000000 | ||||||
NoSymbol | tRNA-Met | 9.87 | 0.0000000 | ||||||
NoSymbol | P24 ncRNA | 7.62 | 0.0000168 | ||||||
NoSymbol | tRNA-Leu | 10.20 | 0.0000000 |
A
B
C
D
E
F
G
H
I
J
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
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100
Supplementary Table S4. List of down and upregulated genes comparing P. putida KT2440 cultures in solid vs liquid media at 24 hours of incubation. | |||||||||
PP number | DAVID accession number | Symbol | Product | FoldChange | p.adj.Value | ||||
PP_0004 | 1043472 | trmF | tRNA uridine 5-carboxymethylaminomethyl modification protein | 2.42 | 0.00046481 | ||||
PP_0007 | 1043483 | yidD | hypothetical protein | 5.99 | 0.00003606 | ||||
PP_0008 | 1043484 | rnpA | ribonuclease P protein component | 10.56 | 0.00000000 | ||||
PP_0009 | 1043485 | rpmH | 50S ribosomal protein L34 | 11.25 | 0.00000000 | ||||
PP_0010 | 1043486 | dnaA | chromosomal replication initiator protein | 3.82 | 0.00001151 | ||||
PP_0026 | 1043505 | NP_742196.1 | cobalt/cadmium/zinc exporter | 2.42 | 0.00036530 | ||||
PP_0061 | 1043542 | glyQ | glycine-tRNA ligase subunit alpha | 4.19 | 0.00000049 | ||||
PP_0067 | 1043548 | fmt | methionyl-tRNA formyltransferase | 10.22 | 0.00000000 | ||||
PP_0068 | 1043549 | def-I | peptide deformylase | 6.94 | 0.00000000 | ||||
PP_0085 | 1043566 | NP_742255.1 | hypothetical protein | 2.96 | 0.00003387 | ||||
PP_0089 | 1043570 | osmC | stress-induced peroxiredoxin | 5.33 | 0.00000000 | ||||
PP_0091 | 1043573 | NP_742261.1 | putative lipoprotein | -3.10 | 0.00000130 | ||||
PP_0092 | 1043574 | NP_742262.1 | putative lipoprotein | 4.08 | 0.00000033 | ||||
PP_0096 | 1043578 | prlC | oligopeptidase A | 3.89 | 0.00000000 | ||||
PP_0113 | 1043604 | metI | ABC transporter permease | 2.91 | 0.00044632 | ||||
PP_0114 | 1043605 | metN | methionine ABC transporter ATP-binding protein | 11.67 | 0.00000000 | ||||
PP_0115 | 1043606 | katE | hydroperoxidase | 4.85 | 0.00000000 | ||||
PP_0122 | 1043615 | NP_742292.1 | hypothetical protein | -2.65 | 0.00012208 | ||||
PP_0144 | 1043652 | NP_742314.1 | insulinase family metalloprotease | 3.17 | 0.00040026 | ||||
PP_0146 | 1043654 | ygdQ | transport protein | 3.00 | 0.00021471 | ||||
PP_0147 | 1043655 | citN | citrate transporter | 6.87 | 0.00000000 | ||||
PP_0148 | 1043656 | NP_742318.1 | hypothetical protein | -3.48 | 0.00000191 | ||||
PP_0149 | 1043657 | NP_742319.1 | hypothetical protein | 2.67 | 0.00037369 | ||||
PP_0156 | 1043668 | pntAA | pyridine nucleotide transhydrogenase subunit alpha | 3.20 | 0.00024838 | ||||
PP_0161 | 1043684 | NP_742330.1 | putative transmembrane sensor | -4.25 | 0.00005944 | ||||
PP_0168 | 1043692 | NP_742337.1 | putative surface adhesion protein | -3.90 | 0.00000000 | ||||
PP_0169 | 1043693 | NP_742338.1 | TauD/TfdA family dioxygenase | 7.61 | 0.00000823 | ||||
PP_0195 | 1043722 | NP_742364.1 | hypothetical protein | -3.12 | 0.00019026 | ||||
PP_0196 | 1043723 | yheS | ABC transporter ATP-binding protein | 3.34 | 0.00013045 | ||||
PP_0199 | 1043726 | qmcA | membrane protease family protein | -3.20 | 0.00000683 | ||||
PP_0200 | 1043728 | nfeD | membrane bound peptidase NefD | -3.50 | 0.00000034 | ||||
PP_0201 | 1043729 | NP_742370.1 | hypothetical protein | -2.82 | 0.00000603 | ||||
PP_0202 | 1043730 | NP_742371.1 | CBS domain-containing protein | 7.70 | 0.00000000 | ||||
PP_0203 | 1043732 | NP_742372.1 | dipeptidase | 2.58 | 0.00062307 | ||||
PP_0204 | 1043733 | NP_742373.1 | GntR family transcriptional regulator | 11.38 | 0.00000000 | ||||
PP_0215 | 1043758 | NP_742383.1 | two-component system response regulator | -2.16 | 0.00080612 | ||||
PP_0216 | 1043759 | NP_742384.2 | sensory box/GGDEF family protein | 4.97 | 0.00000000 | ||||
PP_0218 | 1043761 | NP_742386.1 | sensory box protein | 2.99 | 0.00013509 | ||||
PP_0224 | 1043769 | NP_742392.1 | DszC family monooxygenase | 72.77 | 0.00000000 | ||||
PP_0227 | 1043773 | fliY | cystine-binding protein | 2.74 | 0.00055104 | ||||
PP_0233 | 1043786 | tauA | taurine ABC transporter substrate-binding protein | 33.06 | 0.00000000 | ||||
PP_0234 | 1043787 | oprE | outer-membrane porin E | 5.20 | 0.00000015 | ||||
PP_0235 | 1043789 | NP_742403.1 | peroxidase | 23.03 | 0.00000000 | ||||
PP_0236 | 1043798 | ssuE | NAD(P)H-dependent FMN reductase subunit | 50.49 | 0.00000000 | ||||
PP_0237 | 1043799 | ssuA | aliphatic sulfonatesABC transporter substrate-binding protein | 4.08 | 0.00022293 | ||||
PP_0245 | 1043816 | yhgF | transcriptional accessory protein | 3.94 | 0.00015384 | ||||
PP_0250 | 1043825 | hslR | heat shock protein Hsp15 | -2.99 | 0.00001677 | ||||
PP_0257 | 1043838 | fdhD | protein sulfur transferase | 3.36 | 0.00000762 | ||||
PP_0283 | 1043898 | aotP | arginine/ornithine ABC transporter ATP-binding protein AotP | 2.87 | 0.00013133 | ||||
PP_0294 | 1043981 | cbcV | choline/betaine/carnitine ABC transporter ATP binding protein | -3.71 | 0.00000003 | ||||
PP_0296 | 1043984 | cbcX | choline/betaine/carnitine ABC transporter substrate-binding protein | -2.41 | 0.00063327 | ||||
PP_0298 | 1043988 | gbdR | AraC family transcriptional regulator | -2.81 | 0.00001865 | ||||
PP_0308 | 1044001 | NP_742475.1 | dipeptidase | -2.76 | 0.00050783 | ||||
PP_0310 | 1044003 | dgcA | dimethylglycine dehydrogenase subunit | -3.71 | 0.00000049 | ||||
PP_0318 | 1044013 | NP_742485.1 | hypothetical protein | 6.77 | 0.00000000 | ||||
PP_0325 | 1044023 | soxA | sarcosine oxidase subunit alpha | -3.14 | 0.00004049 | ||||
PP_0327 | 1044026 | purU-I | formyltetrahydrofolate deformylase | -3.13 | 0.00020784 | ||||
PP_0330 | 1044029 | NP_742497.2 | hypothetical protein | 3.14 | 0.00000688 | ||||
PP_0339 | 1044044 | aceE | pyruvate dehydrogenase E1 component | 3.38 | 0.00000801 | ||||
PP_0352 | 1044059 | NP_742519.1 | ECF family RNA polymerase sigma-70 factor | 2.66 | 0.00079287 | ||||
PP_0389 | 1044101 | rpsU | 30S ribosomal protein S21 | 9.04 | 0.00000000 | ||||
PP_0404 | 1044119 | lptD | LPS-assembly protein LptD | 3.43 | 0.00000058 | ||||
PP_0405 | 1044120 | NP_742571.1 | hypothetical protein | -2.59 | 0.00045275 | ||||
PP_0406 | 1044121 | NP_742572.1 | nucleotidyltransferase family protein | -3.59 | 0.00000284 | ||||
PP_0407 | 1044124 | djlA | DnaJ-like protein DjlA | -4.04 | 0.00000002 | ||||
PP_0415 | 1044137 | rpe | ribulose-5-phosphate 3-epimerase | 3.10 | 0.00002240 | ||||
PP_0435 | 1044168 | NP_742601.1 | M23/M37 family peptidase | 2.49 | 0.00009781 | ||||
PP_0440 | 1044182 | tufA | elongation factor Tu-A | 8.19 | 0.00000000 | ||||
PP_0441 | 1044184 | secE | protein translocase subunit SecE | 5.62 | 0.00000000 | ||||
PP_0442 | 1044185 | nusG | transcription antipausing factor NusG | 2.75 | 0.00006797 | ||||
PP_0445 | 1044188 | rplJ | 50S ribosomal protein L10 | 2.55 | 0.00099181 | ||||
PP_0449 | 1044192 | rpsL | 30S ribosomal protein S12 | 4.68 | 0.00000000 | ||||
PP_0450 | 1044193 | rpsG | 30S ribosomal protein S7 | 3.55 | 0.00000075 | ||||
PP_0453 | 1044199 | rpsJ | 30S ribosomal protein S10 | 7.83 | 0.00000000 | ||||
PP_0454 | 1044200 | rplC | 50S ribosomal protein L3 | 7.88 | 0.00000000 | ||||
PP_0468 | 1044227 | rpsH | 30S ribosomal protein S8 | 7.98 | 0.00000000 | ||||
PP_0469 | 1044228 | rplF | 50S ribosomal protein L6 | 6.51 | 0.00000000 | ||||
PP_0470 | 1044230 | rplR | 50S ribosomal protein L18 | 2.72 | 0.00040611 | ||||
PP_0476 | 1044241 | rpsM | 30S ribosomal protein S13 | 7.59 | 0.00000000 | ||||
PP_0477 | 1044242 | rpsK | 30S ribosomal protein S11 | 4.32 | 0.00000000 | ||||
PP_0481 | 1044248 | katA | catalase | 593.45 | 0.00000000 | ||||
PP_0482 | 1044249 | bfr-I | bacterioferritin | 2.41 | 0.00027373 | ||||
PP_0486 | 1044256 | NP_742652.1 | GntR family transcriptional regulator | 4.17 | 0.00001714 | ||||
PP_0500 | 1044272 | NP_742664.1 | dTDP-4-rhamnose reductase-like protein | 5.14 | 0.00000001 | ||||
PP_0512 | 1044287 | NP_742675.2 | hypothetical protein | -4.31 | 0.00000001 | ||||
PP_0513 | 1044288 | nrdR | DNA-binding transcriptional repressor NrdR | 5.11 | 0.00002502 | ||||
PP_0516 | 1044291 | ribAB-I | bifunctional 3%2C4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II | 2.89 | 0.00011510 | ||||
PP_0527 | 1044303 | dxs | 1-deoxyxylulose-5-phosphate synthase | 2.64 | 0.00015877 | ||||
PP_0529 | 1044305 | xseB | exodeoxyribonuclease 7 small subunit | 5.26 | 0.00040704 | ||||
PP_0536 | 1044315 | NP_742699.1 | hypothetical protein | -3.00 | 0.00005888 | ||||
PP_0538 | 1044317 | ppa | inorganic pyrophosphatase | 5.04 | 0.00000002 | ||||
PP_0545 | 1044329 | aldB-I | aldehyde dehydrogenase | -2.70 | 0.00019173 | ||||
PP_0546 | 1044330 | NP_742709.2 | sigma-54 dependent transcriptional regulator | -3.20 | 0.00000084 | ||||
PP_0550 | 1044334 | NP_742713.1 | hypothetical protein | -2.84 | 0.00000865 | ||||
PP_0552 | 1044336 | bdhA | 2%2C3-butanediol dehydrogenase | 2.52 | 0.00027543 | ||||
PP_0553 | 1044339 | acoC | acetoin cleaving system dihydrolipoyllysine-residue acetyltransferase | 6.93 | 0.00000000 | ||||
PP_0554 | 1044340 | acoB | acetoin:2%2C6-dichlorophenolindophenol oxidoreductase subunit beta | 6.24 | 0.00000012 | ||||
PP_0555 | 1044342 | acoA | acetoin:2%2C6-dichlorophenolindophenol oxidoreductase subunit alpha | 8.43 | 0.00000000 |
A
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D
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27
28
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33
34
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Supplementary Table S5. DAVID Functional analysis results for 6 hours comparison | ||||||||||
Category | Term | Genes (DAVID accession numbers) | List Total | Pop Hits | Pop Total | Count | % | P-Value | Benjamini | -log10(PValue) |
GOTERM_MF_DIRECT | GO:0003735 structural constituent of ribosome | 1044200, 1044517, 1044199, 1044204, 1044516, 1044227, 1044202, 1044228, 1044201, 1042258, 1044244, 1044241, 1044206, 1044242, 1044209, 1044192, 1044193, 1045775, 1043485, 1043991, 1043893, 1044189, 1044188, 1043891, 1044210, 1044101, 1044414, 1043837 | 323 | 54 | 3273 | 28 | 6 | 3.8E-14 | 9.1E-12 | 13.420216403383188 |
GOTERM_BP_DIRECT | GO:0006412 translation | 1044200, 1044517, 1044199, 1044204, 1044516, 1044227, 1044202, 1044228, 1044201, 1042258, 1044244, 1044241, 1044206, 1044242, 1044209, 1044192, 1044193, 1045775, 1043485, 1043991, 1043549, 1043893, 1044189, 1044188, 1043891, 1044210, 1044838, 1044101, 1044414, 1043837 | 248 | 62 | 2269 | 30 | 6.5 | 3.9E-13 | 6.0E-11 | 12.4089353929735 |
GOTERM_CC_DIRECT | GO:0005840 ribosome | 1044200, 1043991, 1044517, 1044199, 1043893, 1044189, 1044188, 1044516, 1043891, 1044227, 1044202, 1044228, 1044201, 1042258, 1044241, 1044242, 1044210, 1044101, 1044414, 1045775, 1043485, 1043837 | 218 | 42 | 2035 | 22 | 4.7 | 1.1E-10 | 3.5E-9 | 9.958607314841775 |
KEGG_PATHWAY | ppu00190: Oxidative phosphorylation | 1042262, 1044317, 1044661, 1042266, 1042396, 1042277, 1042269, 1042285, 1041621, 1042273, 1042274, 1042283, 1042025, 1042426, 1045401, 1042014, 1042613, 1042016, 1042018, 1042421, 1041990, 1045265, 1042260, 1046071, 1042005 | 187 | 51 | 1575 | 25 | 5.4 | 1.8E-10 | 1.5E-8 | 9.744727494896694 |
GOTERM_MF_DIRECT | GO:0019843 rRNA binding | 1044200, 1043991, 1043893, 1044204, 1044516, 1044227, 1044202, 1044228, 1044201, 1044244, 1044206, 1044241, 1044242, 1044210, 1044209, 1044192, 1044193, 1044414, 1043837 | 323 | 35 | 3273 | 19 | 4.1 | 4.5E-10 | 5.4E-8 | 9.346787486224656 |
KEGG_PATHWAY | ppu00020: Citrate cycle (TCA cycle) | 1044044, 1044342, 1044340, 1042396, 1044785, 1044339, 1042406, 1042423, 1042414, 1042426, 1042413, 1042613, 1045338, 1042422, 1044855, 1042421, 1042391, 1044477 | 187 | 32 | 1575 | 18 | 3.9 | 9.7E-9 | 4.0E-7 | 8.013228265733755 |
KEGG_PATHWAY | ppu01120: Microbial metabolism in diverse environments | 1044346, 1042253, 1044345, 1044342, 1046257, 1044340, 1042396, 1043939, 1042406, 1045402, 1042613, 1046926, 1042391, 1046726, 1042092, 1046807, 1046808, 1046845, 1042860, 1045004, 1042365, 1044785, 1042525, 1044339, 1046512, 1046613, 1046612, 1044855, 1044477, 1046812, 1044366, 1046818, 1041814, 1044137, 1045925, 1041590, 1044222, 1046507, 1044904, 1042423, 1042426, 1046180, 1042422, 1042421, 1043755, 1047015, 1045930, 1044044, 1041755, 1042490, 1044648, 1041851, 1044929, 1046932, 1042414, 1042413, 1045338, 1041608, 1041607, 1043023, 1047012 | 187 | 262 | 1575 | 61 | 13.1 | 1.4E-8 | 3.8E-7 | 7.853871964321761 |
KEGG_PATHWAY | ppu03010: Ribosome | 1044200, 1044517, 1044199, 1044204, 1044516, 1044227, 1044202, 1044228, 1044201, 1042258, 1044244, 1044241, 1044206, 1044242, 1044209, 1044192, 1044193, 1045775, 1043485, 1043991, 1043893, 1044189, 1044188, 1043891, 1044210, 1044101, 1044414, 1043837 | 187 | 76 | 1575 | 28 | 6 | 2.5E-8 | 5.1E-7 | 7.602059991327962 |
GOTERM_BP_DIRECT | GO:0006352 DNA-templated transcription, initiation | 1043685, 1042732, 1043876, 1041651, 1046334, 1044941, 1044059, 1042166, 1042476, 1045054, 1044535, 1042506, 1044491 | 248 | 21 | 2269 | 13 | 2.8 | 2.6E-7 | 2.0E-5 | 6.585026652029182 |
GOTERM_MF_DIRECT | GO:0016987 sigma factor activity | 1043685, 1042732, 1043876, 1041651, 1046334, 1044941, 1044059, 1042166, 1042476, 1045054, 1044535, 1042506, 1044491 | 323 | 25 | 3273 | 13 | 2.8 | 1.1E-6 | 8.6E-5 | 5.958607314841775 |
GOTERM_MF_DIRECT | GO:0046933 proton-transporting ATP synthase activity, rotational mechanism | 1042025, 1042014, 1042016, 1042018, 1045265, 1042005, 1046071 | 323 | 7 | 3273 | 7 | 1.5 | 5.6E-6 | 3.3E-4 | 5.251811972993799 |
GOTERM_MF_DIRECT | GO:0008137 NADH dehydrogenase (ubiquinone) activity | 1042262, 1045401, 1042269, 1042285, 1041621, 1042260, 1042273, 1042283 | 323 | 10 | 3273 | 8 | 1.7 | 7.7E-6 | 3.7E-4 | 5.113509274827518 |
GOTERM_BP_DIRECT | GO:0015986 ATP synthesis coupled proton transport | 1042025, 1042014, 1041990, 1042018, 1045265, 1042005, 1046071 | 248 | 7 | 2269 | 7 | 1.5 | 1.0E-5 | 5.1E-4 | 5 |
KEGG_PATHWAY | ppu01130: Biosynthesis of antibiotics | 1044346, 1044345, 1044342, 1044340, 1046257, 1042396, 1045534, 1044248, 1044348, 1045533, 1042406, 1042613, 1042391, 1046726, 1042092, 1042860, 1045004, 1042365, 1044785, 1044339, 1044855, 1044477, 1044327, 1047007, 1045513, 1044137, 1041814, 1044224, 1041649, 1046542, 1046744, 1044904, 1042423, 1042426, 1042422, 1042421, 1044044, 1043224, 1044931, 1044932, 1041851, 1046932, 1042414, 1043606, 1042413, 1044738, 1045338, 1041607, 1043023, 1044555 | 187 | 235 | 1575 | 50 | 10.8 | 1.0E-5 | 1.7E-4 | 5 |
KEGG_PATHWAY | ppu00364: Fluorobenzoate degradation | 1046812, 1046807, 1046808, 1046845, 1045930, 1046818, 1046512 | 187 | 7 | 1575 | 7 | 1.5 | 1.6E-5 | 2.2E-4 | 4.795880017344074 |
KEGG_PATHWAY | ppu01200: Carbon metabolism | 1044346, 1042253, 1044345, 1044342, 1044340, 1042396, 1044137, 1041814, 1044248, 1042406, 1042423, 1044904, 1042426, 1042613, 1042422, 1042421, 1042391, 1044044, 1042860, 1045004, 1042490, 1042365, 1044785, 1044339, 1044929, 1043606, 1042414, 1042413, 1045338, 1043023, 1044855, 1044477 | 187 | 127 | 1575 | 32 | 6.9 | 2.6E-5 | 3.0E-4 | 4.585026652029182 |
GOTERM_BP_DIRECT | GO:0006099 tricarboxylic acid cycle | 1042414, 1042423, 1042413, 1042426, 1042396, 1042613, 1045338, 1042422, 1044855, 1042421, 1044477 | 248 | 22 | 2269 | 11 | 2.4 | 3.9E-5 | 0.0015 | 4.4089353929735005 |
KEGG_PATHWAY | ppu01100: Metabolic pathways | 1044346, 1042253, 1044345, 1044342, 1043982, 1046257, 1044340, 1044348, 1042402, 1042406, 1045402, 1045401, 1045604, 1046807, 1046808, 1042262, 1046845, 1045219, 1042860, 1045004, 1042266, 1042365, 1042269, 1042525, 1044339, 1044855, 1042260, 1046812, 1044366, 1046818, 1041702, 1041814, 1044137, 1045925, 1044224, 1044698, 1041590, 1044222, 1042423, 1042426, 1042422, 1042421, 1043755, 1045265, 1043757, 1044565, 1045930, 1044044, 1044291, 1041616, 1044930, 1043224, 1044148, 1041802, 1042490, 1044931, 1044932, 1044929, 1042414, 1044738, 1042413, 1046171, 1041608, 1041607, 1043023, 1041990, 1044555, 1043164, 1042396, 1043939, 1041621, 1045534, 1045533, 1042014, 1042613, 1043805, 1042016, 1046726, 1042018, 1042391, 1042092, 1044785, 1046512, 1042025, 1046613, 1046612, 1044477, 1044327, 1047007, 1045513, 1042277, 1042273, 1042274, 1041649, 1046542, 1046744, 1041844, 1043798, 1044904, 1042130, 1047015, 1044661, 1042285, 1042283, 1044838, 1041851, 1046932, 1045338, 1045133, 1045586, 1047012, 1046071, 1042005 | 187 | 755 | 1575 | 113 | 24.3 | 2.4E-4 | 0.0024 | 3.6197887582883936 |
KEGG_PATHWAY | ppu00362: Benzoate degradation | 1046807, 1046812, 1046808, 1046845, 1045930, 1042860, 1041755, 1046818, 1043939, 1045925, 1046512, 1046932, 1046613, 1046612 | 187 | 39 | 1575 | 14 | 3 | 2.9E-4 | 0.0026 | 3.5376020021010435 |
KEGG_PATHWAY | ppu01220: Degradation of aromatic compounds | 1046812, 1046807, 1046808, 1046845, 1045930, 1046818, 1046726, 1043939, 1045925, 1046512 | 187 | 22 | 1575 | 10 | 2.2 | 4.7E-4 | 0.0038 | 3.3279021420642825 |
GOTERM_CC_DIRECT | GO:0045261 proton-transporting ATP synthase complex, catalytic core F(1) | 1042025, 1042014, 1042016, 1042018, 1042005 | 218 | 5 | 2035 | 5 | 1.1 | 5.8E-4 | 0.0092 | 3.2365720064370627 |
GOTERM_MF_DIRECT | GO:0000049 tRNA binding | 1044199, 1046544, 1041702, 1044241, 1044192, 1045214, 1044193, 1043484, 1044210 | 323 | 22 | 3273 | 9 | 1.9 | 7.5E-4 | 0.029 | 3.1249387366082995 |
GOTERM_MF_DIRECT | GO:0048038 quinone binding | 1042262, 1042266, 1042277, 1042269, 1042285, 1041621, 1042260 | 323 | 14 | 3273 | 7 | 1.5 | 0.0013 | 0.044 | 2.886056647693163 |
GOTERM_MF_DIRECT | GO:0004601 peroxidase activity | 1043789, 1045103, 1045608, 1046468, 1045549, 1043570 | 323 | 10 | 3273 | 6 | 1.3 | 0.0015 | 0.044 | 2.823908740944318 |
GOTERM_CC_DIRECT | GO:0015935 small ribosomal subunit | 1044204, 1044244, 1044192, 1044193, 1044209 | 218 | 7 | 2035 | 5 | 1.1 | 0.0034 | 0.036 | 2.4685210829577446 |
GOTERM_CC_DIRECT | GO:0045263 proton-transporting ATP synthase complex, coupling factor F(o) | 1042004, 1041990, 1045265, 1046071 | 218 | 4 | 2035 | 4 | 0.9 | 0.0044 | 0.035 | 2.356547323513812 |
GOTERM_MF_DIRECT | GO:0051920 peroxiredoxin activity | 1043789, 1045103, 1045608, 1046468, 1045549 | 323 | 8 | 3273 | 5 | 1.1 | 0.0047 | 0.12 | 2.3279021420642825 |
KEGG_PATHWAY | ppu00620: Pyruvate metabolism | 1044346, 1044345, 1044044, 1044342, 1042860, 1044340, 1044785, 1046419, 1044339, 1043023, 1044855, 1042391, 1044477 | 187 | 46 | 1575 | 13 | 2.8 | 0.0053 | 0.039 | 2.275724130399211 |
GOTERM_MF_DIRECT | GO:0003746 translation elongation factor activity | 1045850, 1044182, 1043241, 1044195, 1044196 | 323 | 9 | 3273 | 5 | 1.1 | 0.0078 | 0.17 | 2.107905397309519 |
GOTERM_MF_DIRECT | GO:0031177 phosphopantetheine binding | 1044150, 1042489, 1042600, 1042549 | 323 | 5 | 3273 | 4 | 0.9 | 0.0081 | 0.16 | 2.09151498112135 |
GOTERM_BP_DIRECT | GO:0009058 biosynthetic process | 1046744, 1043224, 1041995, 1042489, 1044669, 1042513, 1043501 | 248 | 18 | 2269 | 7 | 1.5 | 0.0094 | 0.25 | 2.0268721464003012 |
KEGG_PATHWAY | ppu01110: Biosynthesis of secondary metabolites | 1044346, 1042253, 1044345, 1044342, 1044340, 1046257, 1042396, 1045534, 1044248, 1044348, 1045533, 1042402, 1042406, 1042613, 1042391, 1046726, 1042092, 1042860, 1045004, 1042365, 1044785, 1044339, 1044855, 1044477, 1044327, 1047007, 1045513, 1044137, 1041814, 1044224, 1046542, 1044904, 1042423, 1042426, 1042422, 1042421, 1044565, 1044044, 1044291, 1043224, 1044148, 1044931, 1044932, 1041851, 1046932, 1043606, 1042414, 1042413, 1044738, 1045338, 1043023, 1044555 | 187 | 334 | 1575 | 52 | 11.2 | 0.019 | 0.12 | 1.721246399047171 |
GOTERM_BP_DIRECT | GO:0042773 ATP synthesis coupled electron transport | 1042269, 1042285, 1042273, 1042283 | 248 | 6 | 2269 | 4 | 0.9 | 0.02 | 0.4 | 1.6989700043360185 |
KEGG_PATHWAY | ppu00622: Xylene degradation | 1046807, 1046808, 1046845, 1046818 | 187 | 6 | 1575 | 4 | 0.9 | 0.025 | 0.15 | 1.6020599913279623 |
GOTERM_MF_DIRECT | GO:0018623 benzoate 1,2-dioxygenase activity | 1046807, 1046808, 1046845 | 323 | 3 | 3273 | 3 | 0.6 | 0.027 | 0.42 | 1.5686362358410126 |
GOTERM_MF_DIRECT | GO:0008177 succinate dehydrogenase (ubiquinone) activity | 1042426, 1042396, 1042421 | 323 | 3 | 3273 | 3 | 0.6 | 0.027 | 0.42 | 1.5686362358410126 |
GOTERM_MF_DIRECT | GO:0046961 proton-transporting ATPase activity, rotational mechanism | 1042025, 1042014, 1042016 | 323 | 3 | 3273 | 3 | 0.6 | 0.027 | 0.42 | 1.5686362358410126 |
GOTERM_CC_DIRECT | GO:0005623 cell | 1044249, 1042429, 1043789, 1045103, 1045608, 1045026, 1045609, 1042391 | 218 | 29 | 2035 | 8 | 1.7 | 0.029 | 0.17 | 1.5376020021010437 |
GOTERM_BP_DIRECT | GO:0015991 ATP hydrolysis coupled proton transport | 1042014, 1041990, 1042005 | 248 | 3 | 2269 | 3 | 0.6 | 0.033 | 0.52 | 1.4814860601221123 |
KEGG_PATHWAY | ppu00361: Chlorocyclohexane and chlorobenzene degradation | 1046812, 1045930, 1046512 | 187 | 3 | 1575 | 3 | 0.6 | 0.038 | 0.2 | 1.4202164033831897 |
KEGG_PATHWAY | ppu00623: Toluene degradation | 1046812, 1045930, 1046512 | 187 | 3 | 1575 | 3 | 0.6 | 0.038 | 0.2 | 1.4202164033831897 |
KEGG_PATHWAY | ppu00650: Butanoate metabolism | 1044336, 1046932, 1042860, 1047007, 1042426, 1042396, 1042613, 1042421, 1043755, 1043757 | 187 | 41 | 1575 | 10 | 2.2 | 0.045 | 0.22 | 1.346787486224656 |
GOTERM_MF_DIRECT | GO:0008199 ferric iron binding | 1046812, 1044249, 1045930, 1045026 | 323 | 9 | 3273 | 4 | 0.9 | 0.051 | 0.62 | 1.2924298239020635 |
GOTERM_MF_DIRECT | GO:0003989 acetyl-CoA carboxylase activity | 1044346, 1044345, 1043023 | 323 | 4 | 3273 | 3 | 0.6 | 0.051 | 0.59 | 1.2924298239020635 |
KEGG_PATHWAY | ppu00350: Tyrosine metabolism | 1046171, 1041608, 1046726, 1041590, 1043755, 1044222 | 187 | 18 | 1575 | 6 | 1.3 | 0.052 | 0.24 | 1.2839966563652008 |
GOTERM_BP_DIRECT | GO:0009072 aromatic amino acid family metabolic process | 1046171, 1041608, 1044222 | 248 | 4 | 2269 | 3 | 0.6 | 0.061 | 0.7 | 1.2146701649892329 |
KEGG_PATHWAY | ppu00640: Propanoate metabolism | 1044346, 1044345, 1046932, 1042406, 1042860, 1042414, 1045338, 1043023 | 187 | 31 | 1575 | 8 | 1.7 | 0.064 | 0.27 | 1.1938200260161127 |
KEGG_PATHWAY | ppu00310: Lysine degradation | 1046932, 1042860, 1042423, 1042413, 1043755, 1043757 | 187 | 20 | 1575 | 6 | 1.3 | 0.077 | 0.31 | 1.113509274827518 |
KEGG_PATHWAY | ppu00010: Glycolysis / Gluconeogenesis | 1044044, 1044342, 1045004, 1044904, 1044340, 1042365, 1046726, 1042391, 1044339 | 187 | 40 | 1575 | 9 | 1.9 | 0.09 | 0.33 | 1.0457574905606752 |
KEGG_PATHWAY | ppu03018: RNA degradation | 1042415, 1045958, 1044904, 1043228, 1043177 | 187 | 15 | 1575 | 5 | 1.1 | 0.091 | 0.32 | 1.0409586076789064 |
GOTERM_MF_DIRECT | GO:0005506 iron ion binding | 1046807, 1046487, 1042262, 1041989, 1046803, 1042530, 1042277, 1041590, 1044732, 1044705, 1046507, 1044057 | 323 | 72 | 3273 | 12 | 2.6 | 0.091 | 0.78 | 1.0409586076789064 |
GOTERM_MF_DIRECT | GO:0046872 metal ion binding | 1044327, 1044345, 1044137, 1041814, 1044248, 1042274, 1045402, 1042613, 1046180, 1046808, 1043549, 1043893, 1044370, 1045006, 1044148, 1042863, 1042269, 1045214, 1046419, 1044839, 1044816, 1043606, 1046171, 1045338, 1044859 | 323 | 185 | 3273 | 25 | 5.4 | 0.092 | 0.77 | 1.0362121726544447 |
GOTERM_MF_DIRECT | GO:0051536 iron-sulfur cluster binding | 1046188, 1042462, 1042396, 1044705, 1042092 | 323 | 18 | 3273 | 5 | 1.1 | 0.093 | 0.75 | 1.0315170514460648 |
GOTERM_BP_DIRECT | GO:0019545 arginine catabolic process to succinate | 1041844, 1043982, 1043805 | 248 | 5 | 2269 | 3 | 0.6 | 0.095 | 0.82 | 1.0222763947111522 |
A
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Supplementary Table S6. DAVID functional analysis results for 12 hours comparison | ||||||||||
Category | Term | Genes (DAVID accession numbers) | List Total | Pop Hits | Pop Total | Count | % | P-Value | Benjamini | -log10(PValue) |
KEGG_PATHWAY | ppu02040: Flagellar assembly | 1042637, 1044605, 1041605, 1043101, 1041829, 1041827, 1042454, 1042481, 1045242, 1041836, 1045701, 1045714, 1041825, 1042471, 1042309, 1043820, 1044376, 1046146, 1041797, 1042947 | 103 | 35 | 1575 | 20 | 7.3 | 8.5E-15 | 4.7E-13 | 14.0705811 |
GOTERM_CC_DIRECT | GO:0031514 motile cilium | 1042637, 1044605, 1041605, 1043101, 1041829, 1045204, 1041827, 1045202, 1042454, 1042481, 1045242, 1041836, 1045701, 1045714, 1041825, 1042471, 1044726, 1043820, 1046146, 1042947 | 139 | 37 | 2035 | 20 | 7.3 | 1.2E-13 | 3.0E-12 | 12.9208188 |
GOTERM_BP_DIRECT | GO:0071973 bacterial-type flagellum-dependent cell motility | 1044605, 1041605, 1041829, 1042454, 1042481, 1041836, 1045714, 1041825, 1042471, 1042309, 1043820, 1044376, 1041797, 1042947 | 139 | 20 | 2269 | 14 | 5.1 | 4.8E-12 | 5.5E-10 | 11.3187588 |
GOTERM_CC_DIRECT | GO:0005840 ribosome | 1044200, 1044517, 1044199, 1043893, 1043891, 1044516, 1044227, 1044228, 1042258, 1044101, 1044414, 1045775, 1043837, 1043485 | 139 | 42 | 2035 | 14 | 5.1 | 1.7E-6 | 2.2E-5 | 5.76955108 |
GOTERM_MF_DIRECT | GO:0003735 structural constituent of ribosome | 1044200, 1044517, 1044199, 1043893, 1043891, 1044516, 1044227, 1044228, 1042258, 1044101, 1044414, 1045775, 1043837, 1043485 | 170 | 54 | 3273 | 14 | 5.1 | 2.0E-6 | 2.9E-4 | 5.69897 |
GOTERM_BP_DIRECT | GO:0006412 translation | 1044200, 1043549, 1044517, 1044199, 1043893, 1044516, 1043891, 1044227, 1044228, 1042258, 1044838, 1044101, 1044414, 1045775, 1043837, 1043485 | 139 | 62 | 2269 | 16 | 5.8 | 2.1E-6 | 1.2E-4 | 5.67778071 |
GOTERM_MF_DIRECT | GO:0003774 motor activity | 1042454, 1041836, 1045714, 1044376, 1041797, 1042947 | 170 | 7 | 3273 | 6 | 2.2 | 6.7E-6 | 4.8E-4 | 5.1739252 |
GOTERM_CC_DIRECT | GO:0009425 bacterial-type flagellum basal body | 1041836, 1044605, 1045714, 1043101, 1041797, 1042947 | 139 | 11 | 2035 | 6 | 2.2 | 4.4E-4 | 0.0038 | 3.35654732 |
GOTERM_MF_DIRECT | GO:0008556 potassium-transporting ATPase activity | 26969968, 1042357, 1042354, 1042353 | 170 | 4 | 3273 | 4 | 1.5 | 5.2E-4 | 0.025 | 3.28399666 |
KEGG_PATHWAY | ppu03010: Ribosome | 1044200, 1044517, 1044199, 1043893, 1043891, 1044516, 1044227, 1044228, 1042258, 1044101, 1044414, 1045775, 1043837, 1043485 | 103 | 76 | 1575 | 14 | 5.1 | 8.1E-4 | 0.022 | 3.09151498 |
GOTERM_MF_DIRECT | GO:0019843 rRNA binding | 1044200, 1046554, 1043893, 1044516, 1044227, 1044228, 1044414, 1043837 | 170 | 35 | 3273 | 8 | 2.9 | 0.0017 | 0.059 | 2.76955108 |
GOTERM_MF_DIRECT | GO:0005524 ATP binding | 1045260, 1044327, 1046235, 1042357, 1044343, 1042354, 1045513, 1046544, 1041702, 1044224, 1041626, 1045202, 1044925, 1044288, 1042400, 1045877, 1046273, 1044394, 1045153, 1043228, 1043542, 1044838, 1046910, 1042415, 1043931, 1043605, 1041790, 1045154, 1042436, 1041607, 1046459, 1041972, 1045113, 1044555 | 170 | 405 | 3273 | 34 | 12.4 | 0.0042 | 0.11 | 2.37675071 |
GOTERM_MF_DIRECT | GO:0005198 structural molecule activity | 1042481, 1042471, 1042309, 1041797 | 170 | 8 | 3273 | 4 | 1.5 | 0.0062 | 0.14 | 2.20760831 |
GOTERM_BP_DIRECT | GO:0044781 bacterial-type flagellum organization | 1042637, 1043101, 1045204, 1041827 | 139 | 7 | 2269 | 4 | 1.5 | 0.0064 | 0.22 | 2.19382003 |
GOTERM_MF_DIRECT | GO:0004601 peroxidase activity | 1043789, 1045103, 1045608, 1043570 | 170 | 10 | 3273 | 4 | 1.5 | 0.012 | 0.23 | 1.92081875 |
GOTERM_CC_DIRECT | GO:0030694 bacterial-type flagellum basal body, rod | 1041825, 1041605, 1041829 | 139 | 3 | 2035 | 3 | 1.1 | 0.013 | 0.082 | 1.88605665 |
KEGG_PATHWAY | ppu00020: Citrate cycle (TCA cycle) | 1043665, 1044342, 1044340, 1042422, 1044855, 1046547, 1044339 | 103 | 32 | 1575 | 7 | 2.6 | 0.015 | 0.24 | 1.82390874 |
KEGG_PATHWAY | ppu01130: Biosynthesis of antibiotics | 1044327, 1044342, 1046257, 1044340, 1043224, 1045513, 1042365, 1044224, 1046547, 1044248, 1044348, 1041649, 1044339, 1046542, 1043665, 1044925, 1042436, 1042422, 1044855, 1041607, 1042159, 1044879, 1045317, 1044555 | 103 | 235 | 1575 | 24 | 8.8 | 0.022 | 0.27 | 1.65757732 |
GOTERM_BP_DIRECT | GO:0006935 chemotaxis | 1041836, 1045714, 1045448, 1041629, 1043822, 1042947, 1043780 | 139 | 37 | 2269 | 7 | 2.6 | 0.022 | 0.47 | 1.65757732 |
KEGG_PATHWAY | ppu00620: Pyruvate metabolism | 1043665, 1044925, 1044342, 1044340, 1042436, 1044855, 1046419, 1044339 | 103 | 46 | 1575 | 8 | 2.9 | 0.026 | 0.25 | 1.58502665 |
GOTERM_BP_DIRECT | GO:0045454 cell redox homeostasis | 1042429, 1043789, 1045007, 1045103, 1045608, 1045609 | 139 | 30 | 2269 | 6 | 2.2 | 0.032 | 0.53 | 1.49485002 |
GOTERM_MF_DIRECT | GO:0016987 sigma factor activity | 1043685, 1042166, 1045054, 1046334, 1044726 | 170 | 25 | 3273 | 5 | 1.8 | 0.037 | 0.49 | 1.43179828 |
GOTERM_CC_DIRECT | GO:0005623 cell | 1042429, 1043789, 1045103, 1045608, 1045026, 1045609 | 139 | 29 | 2035 | 6 | 2.2 | 0.042 | 0.2 | 1.37675071 |
GOTERM_BP_DIRECT | GO:0006189 'de novo' IMP biosynthetic process | 1044327, 1044224, 1042159, 1046542 | 139 | 14 | 2269 | 4 | 1.5 | 0.049 | 0.62 | 1.30980392 |
GOTERM_MF_DIRECT | GO:0051920 peroxiredoxin activity | 1043789, 1045103, 1045608 | 170 | 8 | 3273 | 3 | 1.1 | 0.06 | 0.63 | 1.22184875 |
KEGG_PATHWAY | ppu02030: Bacterial chemotaxis | 1041836, 1045714, 1045448, 1042670, 1043822, 1042947, 1043780 | 103 | 46 | 1575 | 7 | 2.6 | 0.072 | 0.5 | 1.1426675 |
GOTERM_MF_DIRECT | GO:0003746 translation elongation factor activity | 1045850, 1044182, 1043241 | 170 | 9 | 3273 | 3 | 1.1 | 0.075 | 0.67 | 1.12493874 |
GOTERM_BP_DIRECT | GO:0044780 bacterial-type flagellum assembly | 1042481, 1045242, 1042627 | 139 | 9 | 2269 | 3 | 1.1 | 0.1 | 0.82 | 1 |
A
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Supplementary Table S7. DAVID functional analysis results for 24 hours comparison | ||||||||||
Category | Term | Genes (DAVID accession numbers) | List Total | Pop Hits | Pop Total | Count | % | P-Value | Benjamini | -log10(PValue) |
KEGG_PATHWAY | ppu02040: Flagellar assembly | 1044605, 1042637, 1043042, 1041605, 1043101, 1041829, 1041827, 1043501, 1042454, 1042481, 1045242, 1041836, 1045701, 1045714, 1041825, 1042471, 1042309, 1043820, 1044376, 1046146, 1041797, 1042947 | 269 | 35 | 1575 | 22 | 3 | 8.3E-9 | 8.0E-7 | 8.08092191 |
GOTERM_CC_DIRECT | GO:0031514 motile cilium | 1042637, 1044605, 1043042, 1041605, 1043101, 1041829, 1045204, 1041827, 1045202, 1042454, 1042481, 1045242, 1041836, 1045701, 1045714, 1041825, 1042471, 1044726, 1043820, 1046146, 1042947 | 306 | 37 | 2035 | 21 | 2.9 | 2.6E-8 | 1.1E-6 | 7.58502665 |
GOTERM_BP_DIRECT | GO:0071973 bacterial-type flagellum-dependent cell motility | 1044605, 1041605, 1041829, 1043501, 1042454, 1042481, 1041836, 1045714, 1041825, 1042471, 1042309, 1043820, 1044376, 1041797, 1042947 | 355 | 20 | 2269 | 15 | 2 | 6.3E-8 | 1.5E-5 | 7.20065945 |
GOTERM_CC_DIRECT | GO:0005840 ribosome | 1044200, 1044517, 1044199, 1043893, 1044188, 1044516, 1043891, 1044227, 1044228, 1044230, 1042258, 1044241, 1041596, 1044242, 1044101, 1045770, 1042057, 1044414, 1045775, 1043485, 1043837 | 306 | 42 | 2035 | 21 | 2.9 | 4.0E-7 | 8.9E-6 | 6.39794001 |
GOTERM_MF_DIRECT | GO:0003735 structural constituent of ribosome | 1044200, 1044517, 1044199, 1043893, 1044188, 1044516, 1043891, 1044227, 1044228, 1044230, 1042258, 1041596, 1044241, 1044242, 1044101, 1044192, 1044193, 1042057, 1044414, 1045775, 1043485, 1043837, 1045137 | 459 | 54 | 3273 | 23 | 3.1 | 1.0E-6 | 3.4E-4 | 6 |
GOTERM_BP_DIRECT | GO:0006412 translation | 1044200, 1044517, 1044199, 1044516, 1044227, 1044228, 1042258, 1044241, 1041596, 1044242, 1044192, 1044193, 1042057, 1045775, 1043485, 1043549, 1043893, 1043891, 1044188, 1044230, 1044838, 1044835, 1044101, 1044414, 1043837, 1045137 | 355 | 62 | 2269 | 26 | 3.5 | 1.7E-6 | 2.1E-4 | 5.76955108 |
GOTERM_CC_DIRECT | GO:0005737 cytoplasm | 1045634, 1045842, 1044343, 1042815, 1046257, 1044305, 1042359, 1044580, 1044776, 1041626, 1045671, 1045672, 1041726, 1045635, 1045845, 1043486, 1044726, 1042960, 1042055, 1043631, 1044722, 1042400, 1042723, 1045007, 1042365, 1044626, 1045214, 1043241, 1046554, 1045159, 1046556, 1042024, 1043356, 1045491, 1044327, 1043172, 1044366, 1041912, 1045513, 1046544, 1041702, 1044943, 1044224, 1044947, 1043278, 1045921, 1042427, 1044690, 1044749, 1041880, 1042422, 1046087, 1043073, 1044317, 1044930, 1043228, 1043542, 1042841, 1041658, 1043501, 1043472, 1045333, 1042185, 1045885, 1042381, 1042885, 1046100, 1045889, 1041992, 1045888, 1044182, 1045133, 1046075, 1045278, 1044553, 1043838, 1043780 | 306 | 345 | 2035 | 77 | 10.5 | 7.6E-5 | 0.0011 | 4.11918641 |
KEGG_PATHWAY | ppu01130: Biosynthesis of antibiotics | 1044346, 1044345, 1044342, 1046257, 1044340, 1044303, 1043987, 1045534, 1044248, 1045080, 1044348, 1045533, 1044925, 1042613, 1042960, 1042391, 1044722, 1042159, 1041966, 1042365, 1044785, 1044234, 1044339, 1044914, 1045159, 1045317, 1044477, 1044327, 1043230, 1041911, 1047007, 1042276, 1045513, 1041814, 1044137, 1044224, 1046547, 1041646, 1046542, 1046744, 1043271, 1044904, 1042426, 1042422, 1045508, 1044044, 1043224, 1045333, 1046932, 1045885, 1043606, 1044870, 1046100, 1044738, 1045338, 1041607, 1043023, 1044879, 1044553, 1044555 | 269 | 235 | 1575 | 60 | 8.2 | 4.0E-4 | 0.019 | 3.39794001 |
GOTERM_MF_DIRECT | GO:0019843 rRNA binding | 1044200, 1043893, 1044516, 1044227, 1044228, 1044230, 1044241, 1044242, 1046554, 1044192, 1044193, 1044414, 1042057, 1043837 | 459 | 35 | 3273 | 14 | 1.9 | 5.2E-4 | 0.083 | 3.28399666 |
GOTERM_MF_DIRECT | GO:0003774 motor activity | 1042454, 1041836, 1045714, 1044376, 1041797, 1042947 | 459 | 7 | 3273 | 6 | 0.8 | 8.7E-4 | 0.092 | 3.06048075 |
GOTERM_MF_DIRECT | GO:0000049 tRNA binding | 1044199, 1041701, 1045889, 1046544, 1041702, 1044241, 1044192, 1045214, 1044193, 1043484 | 459 | 22 | 3273 | 10 | 1.4 | 0.0017 | 0.14 | 2.76955108 |
KEGG_PATHWAY | ppu01200: Carbon metabolism | 1044346, 1042253, 1044345, 1044342, 1041911, 1044340, 1041814, 1043987, 1044137, 1046547, 1044248, 1041646, 1045080, 1045894, 1044925, 1044904, 1042426, 1042613, 1042422, 1042391, 1044044, 1045045, 1042365, 1045046, 1044785, 1044339, 1044914, 1045885, 1043606, 1045719, 1045338, 1043023, 1044879, 1044553, 1044477 | 269 | 127 | 1575 | 35 | 4.8 | 0.0026 | 0.08 | 2.58502665 |
GOTERM_MF_DIRECT | GO:0046872 metal ion binding | 1045634, 1044327, 1044345, 1044580, 1041814, 1044137, 1046547, 1044248, 1044918, 1041700, 1041726, 1042966, 1045402, 1045143, 1043652, 1042613, 1046180, 1045597, 1043549, 1043893, 1042681, 1045006, 1043578, 1044148, 1043263, 1045230, 1044787, 1045214, 1046419, 1045049, 1041698, 1044839, 1042002, 1044873, 1045865, 1044816, 1043606, 1044870, 1045338, 1046453 | 459 | 185 | 3273 | 40 | 5.4 | 0.0043 | 0.25 | 2.36653154 |
KEGG_PATHWAY | ppu03010: Ribosome | 1044200, 1044517, 1044199, 1043893, 1044188, 1044516, 1043891, 1044227, 1044228, 1044230, 1042258, 1041596, 1044241, 1044242, 1044101, 1044192, 1044193, 1042057, 1044414, 1045775, 1043485, 1043837, 1045137 | 269 | 76 | 1575 | 23 | 3.1 | 0.0056 | 0.13 | 2.25181197 |
KEGG_PATHWAY | ppu01110: Biosynthesis of secondary metabolites | 1044346, 1042253, 1044345, 1044342, 1046257, 1044340, 1044514, 1044303, 1044580, 1043987, 1044248, 1045534, 1045080, 1044348, 1045533, 1044925, 1045143, 1044583, 1042613, 1042960, 1042391, 1042113, 1044722, 1042159, 1041966, 1043422, 1045009, 1042365, 1044785, 1044234, 1045952, 1044339, 1044914, 1045159, 1045317, 1042120, 1044477, 1044329, 1044327, 1043230, 1047007, 1046895, 1045513, 1042276, 1041814, 1044137, 1044224, 1046547, 1041646, 1046542, 1044886, 1043271, 1044904, 1042426, 1042422, 1041981, 1044565, 1045508, 1044044, 1044291, 1043224, 1044148, 1042185, 1046932, 1045885, 1043606, 1044870, 1044738, 1045338, 1041992, 1043023, 1044879, 1044553, 1044555 | 269 | 334 | 1575 | 74 | 10.1 | 0.0059 | 0.11 | 2.22914799 |
GOTERM_CC_DIRECT | GO:0005623 cell | 1044249, 1042429, 1043789, 1041936, 1045103, 1045608, 1044754, 1045609, 1042391, 1046746, 1046822 | 306 | 29 | 2035 | 11 | 1.5 | 0.007 | 0.074 | 2.15490196 |
KEGG_PATHWAY | ppu00061: Fatty acid biosynthesis | 1044346, 1044925, 1044345, 1042381, 1045719, 1044943, 1043023, 1046532, 1043164 | 269 | 19 | 1575 | 9 | 1.2 | 0.0086 | 0.13 | 2.06550155 |
GOTERM_MF_DIRECT | GO:0003989 acetyl-CoA carboxylase activity | 1044346, 1044925, 1044345, 1043023 | 459 | 4 | 3273 | 4 | 0.5 | 0.0098 | 0.42 | 2.00877392 |
GOTERM_MF_DIRECT | GO:0008556 potassium-transporting ATPase activity | 26969968, 1042357, 1042354, 1042353 | 459 | 4 | 3273 | 4 | 0.5 | 0.0098 | 0.42 | 2.00877392 |
KEGG_PATHWAY | ppu00020: Citrate cycle (TCA cycle) | 1044044, 1044342, 1044340, 1042426, 1042613, 1045338, 1042422, 1042391, 1046547, 1044785, 1044477, 1044339 | 269 | 32 | 1575 | 12 | 1.6 | 0.013 | 0.16 | 1.88605665 |
GOTERM_BP_DIRECT | GO:0006633 fatty acid biosynthetic process | 1044346, 1044925, 1042381, 1046895, 1045719, 1044943, 1043023, 1046532 | 355 | 18 | 2269 | 8 | 1.1 | 0.014 | 0.69 | 1.85387196 |
GOTERM_CC_DIRECT | GO:0009425 bacterial-type flagellum basal body | 1041836, 1044605, 1045714, 1043101, 1041797, 1042947 | 306 | 11 | 2035 | 6 | 0.8 | 0.016 | 0.13 | 1.79588002 |
GOTERM_BP_DIRECT | GO:0009073 aromatic amino acid family biosynthetic process | 1043230, 1043271, 1045317, 1045534, 1045533, 1044348 | 355 | 12 | 2269 | 6 | 0.8 | 0.028 | 0.82 | 1.55284197 |
GOTERM_BP_DIRECT | GO:0045454 cell redox homeostasis | 1042429, 1043789, 1045007, 1045103, 1045608, 1044754, 1045609, 1042391, 1046746, 1046822 | 355 | 30 | 2269 | 10 | 1.4 | 0.034 | 0.81 | 1.46852108 |
KEGG_PATHWAY | ppu00620: Pyruvate metabolism | 1044346, 1044329, 1044345, 1044044, 1044342, 1044340, 1044785, 1046419, 1045080, 1044339, 1044925, 1043023, 1042391, 1044477 | 269 | 46 | 1575 | 14 | 1.9 | 0.037 | 0.37 | 1.43179828 |
GOTERM_MF_DIRECT | GO:0050660 flavin adenine dinucleotide binding | 1046873, 1046280, 1045007, 1042864, 1041701, 1046955, 1046822, 1045081, 1043472, 1043769, 1042179, 1045609, 1042391, 1041966, 1046746 | 459 | 61 | 3273 | 15 | 2 | 0.038 | 0.85 | 1.4202164 |
KEGG_PATHWAY | ppu00230: Purine metabolism | 1044327, 1042681, 1044930, 1043069, 1042276, 1045513, 1044148, 1046955, 1046956, 1041802, 1044224, 1044234, 1046542, 1045865, 1044583, 1041607, 1042159, 1046453, 1044553, 1044386 | 269 | 77 | 1575 | 20 | 2.7 | 0.051 | 0.43 | 1.29242982 |
GOTERM_MF_DIRECT | GO:0033727 aldehyde dehydrogenase (FAD-independent) activity | 1046955, 1046956, 1046453 | 459 | 3 | 3273 | 3 | 0.4 | 0.053 | 0.9 | 1.27572413 |
GOTERM_BP_DIRECT | GO:0006979 response to oxidative stress | 1045143, 1043606, 1045608, 1044248, 1044616, 1043570 | 355 | 14 | 2269 | 6 | 0.8 | 0.054 | 0.89 | 1.26760624 |
GOTERM_BP_DIRECT | GO:0006189 'de novo' IMP biosynthetic process | 1044327, 1044026, 1044224, 1042159, 1044234, 1046542 | 355 | 14 | 2269 | 6 | 0.8 | 0.054 | 0.89 | 1.26760624 |
KEGG_PATHWAY | ppu01212: Fatty acid metabolism | 1044346, 1044925, 1044345, 1046932, 1042381, 1045719, 1044943, 1043023, 1046532, 1045080, 1043164 | 269 | 35 | 1575 | 11 | 1.5 | 0.06 | 0.45 | 1.22184875 |
GOTERM_CC_DIRECT | GO:0009317 acetyl-CoA carboxylase complex | 1044346, 1044925, 1043023 | 306 | 3 | 2035 | 3 | 0.4 | 0.061 | 0.37 | 1.21467016 |
GOTERM_CC_DIRECT | GO:0030694 bacterial-type flagellum basal body, rod | 1041825, 1041605, 1041829 | 306 | 3 | 2035 | 3 | 0.4 | 0.061 | 0.37 | 1.21467016 |
GOTERM_BP_DIRECT | GO:0042744 hydrogen peroxide catabolic process | 1045143, 1043606, 1044248 | 355 | 3 | 2269 | 3 | 0.4 | 0.065 | 0.9 | 1.18708664 |
GOTERM_BP_DIRECT | GO:0000902 cell morphogenesis | 1043443, 1045333, 1044840 | 355 | 3 | 2269 | 3 | 0.4 | 0.065 | 0.9 | 1.18708664 |
GOTERM_BP_DIRECT | GO:0044781 bacterial-type flagellum organization | 1042637, 1043101, 1045204, 1041827 | 355 | 7 | 2269 | 4 | 0.5 | 0.081 | 0.92 | 1.09151498 |
KEGG_PATHWAY | ppu00500: Starch and sucrose metabolism | 1042139, 1046744, 1045885, 1042276, 1042130, 1042113, 1042120 | 269 | 19 | 1575 | 7 | 1 | 0.088 | 0.55 | 1.05551733 |
GOTERM_MF_DIRECT | GO:0005198 structural molecule activity | 1042481, 1042471, 1042309, 1041797 | 459 | 8 | 3273 | 4 | 0.5 | 0.089 | 0.97 | 1.05060999 |
GOTERM_MF_DIRECT | GO:0030976 thiamine pyrophosphate binding | 1045508, 1047007, 1044303, 1041966 | 459 | 8 | 3273 | 4 | 0.5 | 0.089 | 0.97 | 1.05060999 |
GOTERM_MF_DIRECT | GO:0005524 ATP binding | 1045634, 1043885, 1044345, 1043981, 1042357, 1043843, 1044343, 1042815, 1042354, 1041626, 1044776, 1042512, 1045202, 1044918, 1041726, 1044925, 1044288, 1043444, 1043486, 1042307, 1042055, 1042400, 1045877, 1042993, 1044330, 1045214, 1043898, 1046910, 1045159, 1042335, 1043723, 1041972, 1043356, 1045113, 1045260, 1046235, 1044327, 1045263, 1044366, 1046544, 1045513, 1041702, 1044224, 1044984, 1045921, 1041946, 1043228, 1043542, 1043403, 1044500, 1041658, 1043501, 1044838, 1044874, 1044837, 1042415, 1043931, 1044835, 1043605, 1041790, 1045889, 1041607, 1043023, 1045133, 1046075, 1044553, 1044555 | 459 | 405 | 3273 | 67 | 9.1 | 0.09 | 0.96 | 1.04575749 |
GOTERM_MF_DIRECT | GO:0043022 ribosome binding | 1046554, 1045850, 1045770 | 459 | 4 | 3273 | 3 | 0.4 | 0.097 | 0.95 | 1.01322827 |
GOTERM_MF_DIRECT | GO:0015418 quaternary-ammonium-compound-transporting ATPase activity | 1043981, 1043984, 1043435 | 459 | 4 | 3273 | 3 | 0.4 | 0.097 | 0.95 | 1.01322827 |
GOTERM_MF_DIRECT | GO:0004096 catalase activity | 1045143, 1043606, 1044248 | 459 | 4 | 3273 | 3 | 0.4 | 0.097 | 0.95 | 1.01322827 |