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Table 7 Main Gene Ontologies (GO) identified as enriched in almost all the subspecies for the CDS harboring specific mers

From: Identification of genetic relationships and subspecies signatures in Xylella fastidiosa

GO term1 Description FAS2,3 FAS22,3 MUL2,3 PAU2,3 SAN2,3 SAN22,3
GO:0003824 catalytic activity 473/368 669/912 1.64e-7/7.48e-11 343/498 468/1113 4.79e-5/4.20e-8 358/308 761/935 0.0082/1.18e-4 672/143 1039/796 4.35e-37/3.55e-40 779/86 1627/311 0.0108/1.34e-5 630/229 1016/670 1.05e-7/4.37e-11
GO:0000166 nucleotide binding 138/96 1004/1184 0.0246/1.46e-4 106/128 705/1483 0.0115/7.90e-5 143/90 976/1153 9.99e-4/8.70e-6 240/32 1471/907 2.40e-18/2.18e-20 228/54 1418/845 2.30e-7/3.81e-10
GO:0017076 purine nucleotide binding 109/73 1033/1207 0.0469/3.69e-4 87/95 724/1516 0.0077/3.91e-5 118/70 1001/1173 0.0012/1.25e-5 197/20 1514/919 4.04e-18/4.45e-20 181/44 1465/855 2.08e-5/7.77e-8
GO:0032553 ribonucleotide binding 114/74 1028/1206 0.0246/1.33e-4 89/99 722/1512 0.0086/5.12e-5 121/72 998/1171 0.0011/1.12e-5 203/23 1508/916 2.25e-17/2.67e-19 186/48 1460/851 5.83e-5/2.89e-7
GO:0032555 purine ribonucleotide binding 108/73 1034/1207 0.0469/4.80e-4 87/94 724/1517 0.0060/2.64e-5 117/70 1002/1173 0.0015/1.70e-5 197/19 1514/920 1.07e-18/8.34e-21 181/44 1465/855 2.08e-5/7.77e-8
GO:1901265 nucleoside phosphate binding 138/96 1004/1184 0.0246/1.46e-4 106/128 705/1483 0.0115/7.90e-5 143/90 976/1153 9.99e-4/8.70e-6 240/32 1471/907 2.40e-18/2.18e-20 228/54 1418/845 2.30e-7/3.81e-10
GO:0036094 small molecule binding 153/103 989/1177 0.0077/2.11e-5 114/142 697/1469 0.0142/1.10e-4 155/100 964/1143 8.42e-4/5.87e-6 266/33 1445/906 1.49e-21/6.68e-24 251/62 1395/837 2.30e-7/2.82e-10
GO:0043168 anion binding 140/87 1002/1193 0.0030/4.98e-6 102/125 709/1486 0.0206/2.07e-4 140/88 979/1155 0.0010/9.88e-6 242/27 1469/912 4.32e-21/2.11e-23 226/59 1420/840 7.16e-6/1.77e-8
GO:0097367 carbohydrate derivative binding 117/81 1025/1199 0.0469/4.68e-4 94/104 717/1507 0.0060/2.74e-5 126/73 993/1170 5.43e-4/2.60e-6 209/23 1502/916 2.40e-18/2.31e-20 190/50 1456/849 7.27e-5/3.90e-7
GO:0005488 binding 323/277 819/1003 0.0253/1.61e-4 247/353 564/1258 0.0020/5.52e-6 296/245 823/998 0.0078/1.06e-4 547/140 1164/799 1.14e-20/6.54e-23 502/187 1144/712 3.03e-5/1.25e-7
GO:0008152 metabolic process 465/411 677/869 0.0055/1.26e-5 355/521 456/1090 4.79e-5/4.37e-8 397/331 722/912 5.94e-4/3.44e-6 723/168 988/771 4.40e-36/5.38e-39 644/264 1002/635 1.36e-4/7.91e-7
  1. 1Complete datasets are provided in Additional file 7
  2. 2Top line: number of GO-associated CDSs in the list of CDSs harboring specific mers (query) / number of GO-associated CDSs in the CDSs of reference genome that do not harbor specific mers. Middle line: number of non-annotated (no GOs) CDSs in the list of CDSs harboring specific mers (query) / number of non-annotated (no GOs) CDSs in the CDSs of reference genome that do not harbor specific mers. The addition of the four values in each column correspond to the total number of CDS of the reference genome. The addition of the numerator values corresponds to the number of CDS in the query list. The addition of the denominator values corresponds to the number of CDSs of the reference genome that are not in the list of CDSs harboring specific mers. Bottom line: FDR/ P-value
  3. 3Composition of the groups: FAS (subsp. fastidiosa, 12): ATCC 35879, DSM 10026, CFBP 7969, CFBP 7970, CFBP 8071, CFBP 8082, CFBP 8351, EB92–1, GB514, M23, Stag’s Leap, Temecula1. FAS2 (subsp. fastidiosa, 13): All the members of the group FAS, plus CFBP 8073. MUL (subsp. multiplex, 10): ATCC 35871, BB01, CFBP 8078, CFBP 8416, CFBP 8417, CFBP 8418, Dixon, Griffin-1, M12, Sy-VA. SAN (subsp. sandyi, 1): Ann-1. SAN2 (subsp. sandyi-like, 2): CO33 and CFBP 8356. PAU (subsp. pauca, 18): 32, 3124, 11,399, 6c, 9a5c, CFBP 8072, CoDiRO, COF0324, COF0407, CVC0251, CVC0256, Fb7, Hib4, J1a12, OLS0478, OLS0479, Pr8x, U24D