Differential expression: Presence of fish [FishWater.vs.Water]

Differentially expressed genes in cells maintained during 24h in aquarium containing fish (10 juvenile rainbow trout, 5 g) relative to water (10L of dechlorinated water maintained at 10°C under vigorous aeration).

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: Water_a, Water_c
Test samples: FishWater_a, FishWater_c

Locus Tag Name (v2) Feature type Location Clusters Base Expr. Delta Expr. Annotation Chromosome order Clusters order
THC0290_0009 CDS 8244:9227 - A1710 B546 C143 14.08 -1.39 Band 7 family protein 16 3142
THC0290_0014 CDS 17182:18030 + A646 B183 C44 9.20 1.22 Probable SAM-dependent methyltransferase 25 1408
THC0290_N_0032 intra 55358:55525 + A231 B83 C25 8.92 1.23 new transcription segment 65 303
THC0290_N_0033 3prime 60521:60568 + A691 B195 C50 5.90 4.08 new transcription segment 70 1497
THC0290_N_0125 3prime 201124:201191 - A1850 B569 C149 10.91 -1.67 new transcription segment 278 3948
THC0290_0237 fpp1 CDS 288547:291963 - A1062 B352 C104 11.98 2.02 Psychrophilic metalloprotease Fpp1 precursor 403 2030
THC0290_0267 CDS 324293:325300 + A1486 B509 C142 5.08 -1.66 Hypothetical protein precursor 455 2691
THC0290_0300 CDS 361814:364573 - A1062 B352 C104 12.57 1.47 Probable M36 fungalysin family metalloprotease precursor 505 2029
THC0290_0368 CDS 449469:450680 - A1670 B542 C143 9.78 -1.80 Probable lipoprotein precursor 617 3060
THC0290_0370 phoP CDS 453885:454571 + A1767 B546 C143 11.38 -1.47 Two-component system response regulatory protein involved in phosphate regulation 619 3567
THC0290_0427 CDS 519196:519870 - A1719 B546 C143 11.93 -1.77 Probable transcriptional regulator, TetR family 710 3166
THC0290_N_0326 3prime 553386:553649 - A703 B199 C52 8.83 -1.79 new transcription segment 755 1531
THC0290_N_0331 intra 555263:555363 - A599 B183 C44 10.46 2.41 new transcription segment 759 1009
THC0290_0461 nrdA CDS 557960:560380 - A382 B145 C41 11.87 1.50 Ribonucleoside-diphosphate reductase, alpha subunit 765 490
THC0290_N_0336 3prime 564168:564864 + A1252 B419 C125 9.37 -1.36 new transcription segment 775 2374
THC0290_0517 CDS 634225:634386 - A1765 B546 C143 12.23 -2.88 Hypothetical protein 864 3514
THC0290_N_0374 intra 634627:634806 - A1765 B546 C143 13.71 -2.06 new transcription segment 867 3511
THC0290_0519 CDS 634807:635154 - A1765 B546 C143 12.80 -1.30 Conserved protein of unknown function 869 3504
THC0290_0520 CDS 635151:635951 - A1765 B546 C143 12.84 -1.99 Probable transcriptional regulator 870 3505
THC0290_0557 CDS 679618:679926 - A1356 B468 C136 10.40 -1.32 Putative DNA binding protein 933 2516
THC0290_0582 CDS 708481:710181 - A1103 B371 C109 10.59 1.33 Protein of unknown function containing peptidoglycan binding domain 981 2127
THC0290_0638 CDS 772469:773029 + A1710 B546 C143 9.48 -1.64 RNA polymerase ECF-type sigma factor 1078 3144
THC0290_N_0500 3prime 826538:826787 - A1169 B401 C121 8.86 -2.60 new transcription segment 1161 2204
THC0290_0695 fspA CDS 830831:831442 - A618 B183 C44 14.60 -1.74 Flavobacterial-specific protein antigen FspA precursor 1170 1320
THC0290_0737 CDS 873818:874630 - A1063 B352 C104 11.86 1.59 Protein of unknown function 1241 2032
THC0290_N_0577 3prime 935730:935797 - A1650 B542 C143 8.42 -1.43 new transcription segment 1334 3011
THC0290_N_0619 Rfp43 indep 1009763:1009899 + A1839 B563 C145 5.34 -2.84 new transcription segment 1439 3933
THC0290_0969 CDS 1138406:1138603 + A1751 B546 C143 14.16 -2.00 Protein of unknown function 1632 3335
THC0290_0982 CDS 1153638:1155428 - A696 B197 C51 12.15 2.12 Acyl-CoA dehydrogenase family protein 1655 1505
THC0290_N_0702 intra 1155429:1155590 - A694 B196 C51 10.06 2.32 new transcription segment 1656 1501
THC0290_0983 CDS 1155591:1156772 - A696 B197 C51 11.90 1.86 Acetyl-CoA C-acyltransferase 1657 1506
THC0290_N_0703 intra 1156773:1156906 - A696 B197 C51 12.67 1.56 new transcription segment 1658 1508
THC0290_1024 CDS 1206629:1207081 - A1768 B546 C143 10.96 -1.60 Probable lipoprotein precursor 1723 3628
THC0290_N_0733 3prime 1213317:1213392 + A1762 B546 C143 10.75 -1.90 new transcription segment 1737 3413
THC0290_1304 CDS 1504654:1505688 - A470 B170 C44 6.28 -1.73 Probable transcriptional regulator, AraC family 2125 617
THC0290_1315 CDS 1515410:1516276 + A1104 B371 C109 7.38 1.72 Probable transcriptional regulator, AraC family 2139 2128
THC0290_1316 CDS 1516638:1518572 + A687 B193 C48 10.27 1.64 Probable myosin-crossreactive antigen 2140 1489
THC0290_1318 CDS 1519624:1521210 + A687 B193 C48 9.12 1.25 Probable myosin-crossreactive antigen 2142 1492
THC0290_1319 CDS 1521229:1521756 + A687 B193 C48 8.35 1.55 Protein of unknown function 2143 1490
THC0290_1326 ybcL CDS 1530049:1530588 + A692 B195 C50 12.57 3.84 Probable phospholipid-binding protein precursor YbcL 2151 1498
THC0290_1327 CDS 1530569:1530829 + A692 B195 C50 11.80 4.68 Protein of unknown function 2152 1499
THC0290_1339 CDS 1544648:1545673 + A1876 B578 C149 10.66 1.34 Probable two-component system sensor histidine kinase 2165 3980
THC0290_1502 CDS 1743248:1744315 + A1035 B342 C102 10.81 1.33 Protein of unknown function 2465 1994
THC0290_1507 CDS 1748731:1750641 - A1017 B325 C88 12.17 -2.02 Probable transmembrane protein of unknown function 2473 1972
THC0290_1526 CDS 1774415:1775356 - A1796 B549 C143 11.93 1.88 Protein of unknown function precursor 2501 3879
THC0290_1527 CDS 1775368:1782057 - A1796 B549 C143 12.99 1.64 Protein of unknown function precursor containing a C-terminal secretion signal. Putative adhesin 2502 3880
THC0290_1626 CDS 1887285:1887971 + A765 B228 C63 11.85 -1.68 Probable ABC-type transport system, ATPase component 2690 1650
THC0290_1640 CDS 1901160:1902068 - A1714 B546 C143 12.31 -2.04 Probable transmembrane protein of unknown function 2716 3155
THC0290_N_1109 3prime-PT 1920516:1920593 - A794 B241 C67 6.01 -2.24 new transcription segment 2745 1683
THC0290_1657 glnA CDS 1920647:1922836 - A961 B305 C84 12.82 -2.72 Glutamate--ammonia ligase 2746 1903
THC0290_N_1206 intra 2077689:2077767 - A452 B168 C44 4.87 1.99 new transcription segment 2985 585
THC0290_1824 CDS 2113997:2115304 - A1763 B546 C143 14.37 -1.23 Protein of unknown function 3028 3437
THC0290_1830 CDS 2122074:2123462 + A1765 B546 C143 10.08 -1.23 Protein of unknown function 3035 3496
THC0290_1859 CDS 2159423:2159875 - A1751 B546 C143 13.16 -2.04 Probable peroxiredoxin 3093 3341
THC0290_1863 CDS 2162962:2163354 + A266 B95 C28 12.02 -1.40 Protein of unknown function 3099 349
THC0290_N_1264 3prime 2191301:2191847 + A1869 B577 C149 9.33 1.49 new transcription segment 3137 3971
THC0290_N_1290 intra 2225939:2225999 + A700 B199 C52 7.28 -2.43 new transcription segment 3192 1525
THC0290_1916 CDS 2226196:2227179 + A700 B199 C52 9.82 -2.37 Probable acyl-[acyl-carrier-protein] desaturase 3194 1527
THC0290_N_1291 intra 2227180:2227238 + A700 B199 C52 9.76 -2.34 new transcription segment 3195 1524
THC0290_1917 ccoN/ccoO CDS 2227239:2229419 + A700 B199 C52 10.11 -2.40 Cytochrome c oxidase, cbb3-type, subunit I and II 3196 1521
THC0290_N_1292 intra 2229420:2229495 + A700 B199 C52 10.22 -2.70 new transcription segment 3197 1520
THC0290_1919 ccoP CDS 2229694:2230629 + A700 B199 C52 10.61 -2.37 Cytochrome c oxidase, cbb3-type, subunit III 3199 1522
THC0290_1923 CDS 2233345:2233575 + A698 B198 C52 9.70 -2.85 Protein of unknown function 3204 1512
THC0290_N_1310 3prime 2267237:2267297 - A954 B302 C82 11.00 1.60 new transcription segment 3238 1893
THC0290_N_1312 intra 2268616:2268698 - A791 B240 C67 9.25 2.08 new transcription segment 3242 1680
THC0290_N_1380 intra 2413572:2413639 - A646 B183 C44 5.21 2.72 new transcription segment 3461 1407
THC0290_2101 CDS 2422448:2423926 + A1796 B549 C143 15.16 1.26 SusD/RagB family lipoprotein precursor 3471 3883
THC0290_N_1398 3prime 2443579:2443958 - A1644 B540 C143 9.37 -1.59 new transcription segment 3507 2992
THC0290_N_1402 intra 2451893:2451990 + A453 B168 C44 9.90 1.28 new transcription segment 3519 588
THC0290_N_1415 3prime 2474911:2475654 - A1653 B542 C143 9.37 -2.71 new transcription segment 3551 3020
THC0290_2192 CDS 2535814:2536179 - A600 B183 C44 8.86 1.37 Hypothetical protein precursor 3625 1056
THC0290_2288 CDS 2642593:2643324 + A605 B183 C44 10.08 1.38 Probable membrane-associated phospholipid phosphatase 3773 1230
THC0290_2337 porP CDS 2699227:2700144 - A659 B185 C45 11.10 1.46 Protein of unknown function precursor PorP 3863 1433
THC0290_N_1535 intra 2700145:2700215 - A659 B185 C45 11.81 2.05 new transcription segment 3864 1431
THC0290_2338 claF CDS 2700216:2706242 - A712 B202 C53 12.23 1.48 Protein of unknown function precursor, putative adhesin 3865 1548
THC0290_N_1551 3prime-PT 2730595:2731833 + A1216 B416 C125 8.07 -2.45 new transcription segment 3900 2281