Differential expression: Low temperature [Temp4C.vs.Ctrl]

Differentially expressed genes in cells grown at 4°C relative to 18°C (OD600nm=0.4, TYES at 200 rpm).

List of differentially expressed genomic elements (CDS and newly identified RNA elements).
Statistical analysis was performed with the limma package. Genes were considered as differentially expressed with a log2-fold change ⩾ 1 and a false discovery rate ⩽ 0.05.

Reference samples: CS3_a, CS3_c
Test samples: Temp4C_a, Temp4C_c

Locus Tag Name (v2) Feature type Location Clusters Base Expr. Delta Expr. Annotation Chromosome order Clusters order
THC0290_N_0021 intra 27164:27223 + A1256 B421 C125 10.49 -1.07 new transcription segment 42 2382
THC0290_0023 sprC CDS 27296:28729 + A1256 B421 C125 11.64 -1.25 Putative adhesin precursor SprC 44 2381
THC0290_0024 sprD CDS 28731:32459 + A1256 B421 C125 11.25 -1.24 Putative cell surface protein precursor SprD 45 2380
THC0290_0064 CDS 85412:86431 + A1302 B443 C129 11.03 -1.24 Probable transmembrane protein of unknown function 114 2444
THC0290_N_0064 3prime 108949:109046 + A1800 B551 C143 10.24 1.09 new transcription segment 148 3887
THC0290_N_0076 5prime 131417:131569 + A205 B75 C24 11.16 -2.65 new transcription segment 177 256
THC0290_0102 CDS 131570:132853 + A204 B75 C24 11.89 -2.80 Protein of unknown function 178 252
THC0290_N_0077 intra 132854:133118 + A205 B75 C24 10.91 -3.26 new transcription segment 179 257
THC0290_0103 CDS 133119:133640 + A204 B75 C24 11.91 -3.00 Protein of unknown function precursor 180 254
THC0290_0104 CDS 133660:134139 + A204 B75 C24 12.39 -2.79 Probable lipoprotein precursor 181 255
THC0290_0105 CDS 134151:135113 + A204 B75 C24 11.75 -2.99 Protein of unknown function precursor 182 253
THC0290_0106 CDS 135128:136084 + A204 B75 C24 12.16 -2.82 Protein of unknown function precursor 183 251
THC0290_N_0108 3prime 182582:182666 - A793 B241 C67 6.46 1.64 new transcription segment 254 1682
THC0290_0171 CDS 215347:216612 - A1083 B365 C107 13.62 -1.17 Probable cell surface protein (Leucine-rich repeat protein) precursor 299 2066
THC0290_0172 CDS 216630:217619 - A1083 B365 C107 13.59 -1.25 Probable cell surface protein (Leucine-rich repeat protein) precursor 300 2071
THC0290_0173 CDS 217635:218969 - A1083 B365 C107 14.00 -1.23 Probable cell surface protein (Leucine-rich repeat protein) precursor 301 2069
THC0290_0174 CDS 219283:220551 - A1083 B365 C107 13.46 -1.48 Probable cell surface protein (Leucine-rich repeat protein) precursor 302 2072
THC0290_0175 CDS 220567:221559 - A1083 B365 C107 13.67 -1.39 Probable cell surface protein (Leucine-rich repeat protein) 303 2073
THC0290_0176 CDS 221575:222702 - A1083 B365 C107 13.63 -1.24 Probable cell surface protein (Leucine-rich repeat protein) precursor 304 2070
THC0290_N_0139 intra 222703:223027 - A1083 B365 C107 12.22 -1.66 new transcription segment 305 2065
THC0290_0177 CDS 223028:224638 - A1083 B365 C107 14.22 -1.08 Probable cell surface protein (Leucine-rich repeat protein) precursor 306 2059
THC0290_N_0140 repeated_region 224639:224914 - A1083 B365 C107 10.45 -1.21 new transcription segment 307 2061
THC0290_0178 CDS 224965:225888 - A1083 B365 C107 13.34 -1.33 Probable cell surface protein (Leucine-rich repeat protein) precursor 308 2067
THC0290_0181 CDS 228393:229796 - A1083 B365 C107 12.48 -1.53 Probable cell surface protein (Leucine-rich repeat protein) precursor 311 2060
THC0290_N_0142 repeated_region 229797:230072 - A1083 B365 C107 10.53 -1.35 new transcription segment 312 2062
THC0290_0182 CDS 230123:231112 - A1083 B365 C107 10.84 -1.07 Probable cell surface protein (Leucine-rich repeat protein) precursor 313 2056
THC0290_0183 CDS 231127:232047 - A1083 B365 C107 12.58 -1.03 Probable cell surface protein (Leucine-rich repeat protein) precursor 314 2057
THC0290_0184 CDS 232062:233117 - A1083 B365 C107 10.84 -1.36 Probable cell surface protein (Leucine-rich repeat protein) precursor 315 2058
THC0290_N_0172 5prime 273673:273853 + A834 B252 C69 8.22 1.23 new transcription segment 382 1741
THC0290_N_0196 intra 315768:315824 + A292 B108 C30 7.41 -1.08 new transcription segment 441 377
THC0290_0264 CDS 322321:323505 + A1756 B546 C143 6.18 -1.40 Transposase IS91 family 450 3360
THC0290_0265 CDS 323507:323950 + A1756 B546 C143 5.85 -1.50 Hypothetical protein 451 3361
THC0290_N_0207 3prime 334509:334577 - A298 B110 C31 6.99 2.28 new transcription segment 469 383
THC0290_0316 CDS 387602:388201 + A1040 B344 C102 12.02 -1.21 Hypothetical protein precursor 528 2001
THC0290_N_0235 3prime 393012:393683 - A127 B53 C18 7.09 -1.72 new transcription segment 538 160
THC0290_0322 CDS 393684:394175 - A1464 B506 C142 9.89 -1.07 Probable transmembrane protein of unknown function 539 2658
THC0290_N_0247 3prime 416229:416973 - A130 B53 C18 7.62 -1.03 new transcription segment 562 164
THC0290_0429 CDS 521589:522020 + A1509 B519 C143 8.41 1.28 Hypothetical transmembrane protein 712 2728
THC0290_N_0309 3prime 522021:522213 + A1509 B519 C143 9.37 1.27 new transcription segment 713 2729
THC0290_N_0310 3prime-PT 522214:522414 + A771 B233 C66 8.69 1.29 new transcription segment 714 1656
THC0290_0500 CDS 605227:607704 - A1093 B367 C107 9.18 -1.01 Probable S8 and S53 subtilisin family serine endopeptidase precursor 836 2113
THC0290_0501 CDS 607701:608105 - A1756 B546 C143 8.87 -1.03 Hypothetical lipoprotein precursor 837 3359
THC0290_N_0366 intra 613818:613961 + A1818 B557 C145 5.69 -1.33 new transcription segment 846 3909
THC0290_N_0394 repeated_region 661670:662043 + A1749 B546 C143 5.71 -1.49 new transcription segment 912 3323
THC0290_N_0443 3prime 741661:741738 - A769 B231 C65 5.97 1.38 new transcription segment 1022 1654
THC0290_N_0465 intra 770297:771152 + A1715 B546 C143 6.74 1.21 new transcription segment 1075 3159
THC0290_0642 CDS 776332:777606 + A1767 B546 C143 7.84 1.01 Protein of unknown function precursor 1082 3568
THC0290_N_0485 3prime 803148:803240 - A1242 B419 C125 9.74 1.17 new transcription segment 1127 2320
THC0290_N_0495 intra 817086:817137 + A1674 B543 C143 8.57 1.25 new transcription segment 1147 3072
THC0290_0681 CDS 817138:819144 + A1674 B543 C143 10.47 1.60 Probable TonB-dependent outer membrane receptor precursor 1148 3071
THC0290_0682 CDS 819184:819525 + A1674 B543 C143 10.34 1.20 Protein of unknown function 1149 3069
THC0290_0684 sulP CDS 819971:821572 + A1674 B543 C143 12.15 1.11 Probable sulfate permease 1152 3076
THC0290_0832 dcp2 CDS 990238:992370 - A1796 B549 C143 9.51 1.20 Peptidyl-dipeptidase precursor Dcp2 1410 3876
THC0290_0900 CDS 1058487:1059572 + A1198 B413 C124 6.08 1.45 Probable membrane fusion efflux lipoprotein precursor 1512 2244
THC0290_0901 CDS 1059740:1062964 + A1198 B413 C124 6.22 1.24 Probable multidrug resistance protein. AcrB/AcrD/AcrF family protein 1514 2245
THC0290_0922 CDS 1082167:1082580 + A1649 B541 C143 9.30 -1.11 Protein of unknown function 1549 3010
THC0290_N_0657 intra 1087045:1087158 + A1085 B365 C107 10.75 -1.24 new transcription segment 1554 2076
THC0290_N_0669 3prime 1106163:1106281 + A130 B53 C18 8.58 -1.17 new transcription segment 1580 165
THC0290_0949 CDS 1121975:1122373 - A1520 B521 C143 8.39 2.37 Protein of unknown function 1601 2752
THC0290_1016 kdpF CDS 1196475:1196552 + A1628 B539 C143 4.64 1.42 Potassium-transporting ATPase F subunit 1712 2941
THC0290_1017 kdpA CDS 1196669:1198390 + A1628 B539 C143 4.89 1.14 Potassium-transporting ATPase A subunit 1713 2942
THC0290_1018 kdpB CDS 1198491:1200524 + A1628 B539 C143 5.26 1.05 Potassium-transporting ATPase B subunit 1714 2943
THC0290_1044 mutY CDS 1220495:1221526 + A332 B123 C34 8.33 -1.08 A/G-specific adenine glycosylase 1753 432
THC0290_1054 CDS 1231465:1232691 - A1765 B546 C143 7.89 -1.21 Protein of unknown function precursor containing a C-terminal secretion signal 1769 3479
THC0290_1085 CDS 1265923:1266828 + A1243 B419 C125 8.72 -1.14 Probable lipoprotein precursor 1812 2322
THC0290_1150 CDS 1338848:1339387 + A1747 B546 C143 5.11 1.26 Probable transcriptional regulator, AraC family 1908 3267
THC0290_1201 CDS 1384990:1385493 + A1765 B546 C143 7.58 1.17 Hypothetical lipoprotein precursor 1961 3467
THC0290_1202 CDS 1385642:1386292 + A1742 B546 C143 6.67 1.38 Protein of unknown function precursor 1962 3222
THC0290_1203 CDS 1386310:1386462 + A1311 B450 C132 6.40 1.80 Conserved exported protein of unknown function 1963 2453
THC0290_1204 CDS 1386496:1386726 + A1768 B546 C143 8.75 1.84 Hypothetical protein 1964 3689
THC0290_1226 CDS 1420150:1420488 - A1767 B546 C143 7.88 1.20 Hypothetical protein precursor 2006 3569
THC0290_1233 CDS 1426680:1427324 + A1294 B437 C127 8.11 1.84 Probable peroxiredoxin 2015 2435
THC0290_1239 CDS 1430503:1432671 - A688 B193 C48 7.35 1.15 Cytochrome c oxidase family protein 2021 1494
THC0290_1263 CDS 1462672:1464006 - A801 B244 C67 11.36 1.14 Probable ATP-dependent RNA helicase, DEAD/DEAH box family 2058 1695
THC0290_1280 CDS 1477371:1479464 + A498 B175 C44 9.87 1.02 Probable phosphoglycerol transferase 2083 665
THC0290_N_0843 Rfp58 indep 1500231:1500590 + A1779 B546 C143 5.15 -1.79 new transcription segment 2121 3811
THC0290_N_0910 3prime-PT 1651904:1652210 - A1745 B546 C143 7.85 1.03 new transcription segment 2318 3240
THC0290_N_0937 5prime 1681345:1681454 - A1762 B546 C143 5.20 -1.00 new transcription segment 2368 3420
THC0290_N_0978 5prime 1732259:1732334 - A1762 B546 C143 7.53 -1.06 new transcription segment 2452 3417
THC0290_N_1003 intra 1788164:1788342 - A924 B287 C78 8.48 1.09 new transcription segment 2516 1858
THC0290_1595 CDS 1851066:1852952 + A1762 B546 C143 9.59 -1.01 Protein of unknown function precursor, putative adhesin 2631 3405
THC0290_N_1058 intra 1852953:1853067 + A1762 B546 C143 7.63 -1.01 new transcription segment 2632 3406
THC0290_1634 CDS 1896238:1896348 + A1760 B546 C143 10.03 1.25 Hypothetical protein 2705 3372
THC0290_N_1109 3prime-PT 1920516:1920593 - A794 B241 C67 7.44 1.37 new transcription segment 2745 1683
THC0290_1675 CDS 1943090:1944706 - A1055 B348 C104 8.86 -2.26 Probable asparagine synthetase [glutamine-hydrolyzing] 2775 2022
THC0290_N_1142 Rfp75 indep 1963759:1963927 - A1769 B546 C143 7.25 -1.31 new transcription segment 2808 3743
THC0290_1705 CDS 1978255:1979847 + A608 B183 C44 10.16 1.25 Probable type I modification methyltransferase 2833 1262
THC0290_1706 CDS 1979849:1980568 + A608 B183 C44 10.01 1.26 Hypothetical protein 2834 1263
THC0290_1707 CDS 1980570:1981727 + A532 B180 C44 9.90 1.21 Probable type I restriction-modification system, DNA specificity domain protein 2835 724
THC0290_1708 CDS 1981738:1982421 + A532 B180 C44 9.29 1.00 Hypothetical protein 2836 725
THC0290_N_1160 3prime 1993681:1993757 - A943 B298 C82 6.87 1.50 new transcription segment 2854 1882
THC0290_tRNA_0033 tRNA 2003330:2003404 - A1769 B546 C143 10.66 -1.75 transfer RNA-Glu 2865 3759
THC0290_tRNA_0034 tRNA 2003436:2003507 - A1769 B546 C143 10.29 -1.74 transfer RNA-Glu 2866 3760
THC0290_N_1181 3prime 2033750:2034014 + A1833 B563 C145 6.89 -1.06 new transcription segment 2907 3926
THC0290_1773 CDS 2056140:2056589 - A1392 B478 C139 10.64 1.12 Probable transmembrane protein of unknown function, putative anti ECF-type sigma factor 2954 2565
THC0290_1779 bluB/cobT CDS 2061863:2063539 - A314 B119 C33 8.54 1.03 Bifunctional protein : cob(II)yrinic acid a,c-diamide reductase and nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase 2962 399
THC0290_1786 CDS 2068911:2069726 + A1795 B549 C143 8.54 1.04 Probable transmembrane protein of unknown function 2972 3869
THC0290_1851 rhlE CDS 2150658:2152004 + A798 B244 C67 11.02 1.12 Putative ATP-dependent RNA helicase RhlE 3077 1687
THC0290_N_1250 3prime 2163355:2164120 + A662 B186 C46 7.89 -1.19 new transcription segment 3101 1436
THC0290_1873 cphA CDS 2175189:2177813 + A1056 B349 C104 9.29 1.18 Cyanophycin synthetase 3120 2023
THC0290_1905 CDS 2215006:2215296 + A1614 B535 C143 11.07 -1.11 Protein of unknown function 3175 2913
THC0290_N_1297 repeated_region 2239621:2239993 - A847 B256 C70 8.75 1.02 new transcription segment 3210 1767
THC0290_1973 degP/Q CDS 2300158:2301543 + A1587 B532 C143 12.12 -2.32 Protease DegP/Q precursor 3297 2859
THC0290_N_1336 intra 2301544:2301764 + A1587 B532 C143 9.93 -2.29 new transcription segment 3298 2860
THC0290_2100 CDS 2419224:2422433 + A1796 B549 C143 11.76 1.09 SusC/RagA family TonB-dependent receptor precursor, Omp121 family 3470 3882
THC0290_2124 CDS 2445446:2446414 + A1773 B546 C143 7.48 -1.25 Probable transmembrane protein of unknown function 3512 3797
THC0290_2125 CDS 2446389:2446838 + A1849 B569 C149 7.48 -1.06 Protein of unknown function 3513 3947
THC0290_N_1401 3prime 2446839:2447017 + A1307 B446 C130 4.72 -1.01 new transcription segment 3516 2449
THC0290_N_1414 5prime 2473389:2473464 + A1749 B546 C143 9.75 -1.65 new transcription segment 3549 3324
THC0290_2157 CDS 2491341:2491841 + A483 B172 C44 10.34 -1.19 Protein of unknown function 3573 640
THC0290_N_1422 intra 2491842:2492026 + A483 B172 C44 11.43 -1.43 new transcription segment 3574 641
THC0290_2189 CDS 2527116:2532788 + A1061 B352 C104 9.21 1.00 Probable lipoprotein precursor 3620 2028
THC0290_2192 CDS 2535814:2536179 - A600 B183 C44 10.55 1.09 Hypothetical protein precursor 3625 1056
THC0290_N_1443 3prime-PT 2542291:2542585 + A540 B180 C44 8.93 1.17 new transcription segment 3631 752
THC0290_2201 CDS 2547111:2550026 + A1081 B364 C107 7.94 -1.07 Protein of unknown function precursor, putative adhesin 3644 2054
THC0290_N_1452 intra 2550027:2550445 + A1082 B364 C107 7.17 -1.21 new transcription segment 3645 2055
THC0290_2214 CDS 2570599:2571780 - A558 B183 C44 9.71 -1.05 Glycosyl transferase, group 2 family protein 3668 815
THC0290_N_1483 3prime 2620163:2620219 - A299 B110 C31 7.05 1.65 new transcription segment 3737 384
THC0290_N_1523 3prime 2681617:2681861 - A1816 B557 C145 7.36 -1.25 new transcription segment 3837 3907
THC0290_2370 CDS 2741784:2742041 - A1768 B546 C143 11.04 -1.06 Addiction module toxin, Txe/YoeB family 3919 3692