Table 1.
Top 40 up- and down-regulated host genes in attenuated passage based on the log2FoldChange and padj value.
| Gene_id | Gene_name | Gene_description | Attenuated (average RPKM*) | Virulent (Average RPKM*) | log2FoldChange | padj |
|---|---|---|---|---|---|---|
| ENSBTAG00000020524 | UPK3BL1 | Bos taurus uroplakin 3B-like (UPK3BL1), mRNA. [Source:RefSeq mRNA;Acc:NM_001168011] | 25.5484371 | 0.3468303 | 6.20492255 | 0.00010761 |
| ENSBTAG00000000376 | P2RX3 | purinergic receptor P2X 3 [Source:VGNC Symbol;Acc:VGNC:32519] | 37.0572054 | 0.6936606 | 5.83671086 | 1.40E-05 |
| ENSBTAG00000003030 | KCNQ2 | potassium voltage-gated channel subfamily Q member 2 [Source:VGNC Symbol;Acc:VGNC:30487] | 9.85363751 | 0 | 5.79271357 | 0.003043 |
| ENSBTAG00000006806 | KRT17 | keratin 17 [Source:VGNC Symbol;Acc:VGNC:50398] | 56.5290977 | 1.22118738 | 5.46777552 | 1.27E-08 |
| ENSBTAG00000012630 | PAMR1 | peptidase domain containing associated with muscle regeneration 1 [Source:VGNC Symbol;Acc:VGNC:32562] | 10.1895288 | 0.30529685 | 4.87936486 | 0.01556863 |
| ENSBTAG00000018395 | KIAA1217 | KIAA1217 [Source:VGNC Symbol;Acc:VGNC:30566] | 18.4306952 | 0.61059369 | 4.85316467 | 0.00212362 |
| ENSBTAG00000048591 | THBD | thrombomodulin [Source:HGNC Symbol;Acc:HGNC:11784] | 16.6750819 | 0.61059369 | 4.71007582 | 0.00360285 |
| ENSBTAG00000008944 | CRB1 | Bos taurus crumbs 1, cell polarity complex component (CRB1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192482] | 171.441218 | 7.37485138 | 4.53543835 | 2.45E-27 |
| ENSBTAG00000002661 | ISLR2 | immunoglobulin superfamily containing leucine rich repeat 2 [Source:VGNC Symbol;Acc:VGNC:30299] | 284.796605 | 12.7310177 | 4.47289549 | 5.13E-41 |
| ENSBTAG00000004261 | SPON2 | spondin 2 [Source:VGNC Symbol;Acc:VGNC:35228] | 98.5821353 | 5.22738488 | 4.25252666 | 7.42E-15 |
| ENSBTAG00000003777 | TIE1 | Bos taurus tyrosine kinase with immunoglobulin like and EGF like domains 1 (TIE1), mRNA. [Source:RefSeq mRNA;Acc:NM_173965] | 11.9451421 | 0.65212714 | 4.2094648 | 0.01658889 |
| ENSBTAG00000005404 | MSC | musculin [Source:VGNC Symbol;Acc:VGNC:31691] | 26.5104467 | 1.57839235 | 4.05093325 | 0.00034497 |
| ENSBTAG00000050719 | − | calcium-dependent phospholipase A2 PLA2G2D1 [Source:NCBI gene;Acc:494318] | 10.864386 | 0.6936606 | 4.04658787 | 0.03146184 |
| ENSBTAG00000054512 | IGSF1 | Bos taurus immunoglobulin superfamily member 1 (IGSF1), mRNA. [Source:RefSeq mRNA;Acc:NM_001105048] | 9.91758328 | 0.66250877 | 3.93311066 | 0.03703225 |
| ENSBTAG00000025634 | FMN1 | formin 1 [Source:HGNC Symbol;Acc:HGNC:3768] | 17.0322943 | 1.30425429 | 3.72041477 | 0.00404415 |
| ENSBTAG00000008832 | CCL1 | C–C motif chemokine ligand 1 [Source:VGNC Symbol;Acc:VGNC:26943] | 114.442319 | 9.05707389 | 3.66458396 | 1.12E-16 |
| ENSBTAG00000007421 | CDH5 | cadherin 5 [Source:NCBI gene;Acc:414735] | 31.246492 | 2.52544167 | 3.61207206 | 8.13E-05 |
| ENSBTAG00000037553 | KRT33A | Bos taurus keratin 33A (KRT33A), mRNA. [Source:RefSeq mRNA;Acc:NM_001099099] | 227.067215 | 18.905438 | 3.58304894 | 2.45E-27 |
| ENSBTAG00000017060 | ITGB2 | integrin subunit beta 2 [Source:VGNC Symbol;Acc:VGNC:30327] | 22.5558378 | 1.94599286 | 3.54144292 | 0.00091222 |
| ENSBTAG00000002739 | PDE1C | phosphodiesterase 1C [Source:VGNC Symbol;Acc:VGNC:32673] | 15.0138893 | 1.34578774 | − 3.52040797 | 0.01313049 |
| ENSBTAG00000006686 | NPNT | nephronectin [Source:VGNC Symbol;Acc:VGNC:32209] | 6.81535641 | 68.6539285 | − 3.3327037 | 2.22E-09 |
| ENSBTAG00000042166 | RF00410 | − | 1.68557075 | 17.2356305 | − 3.341479 | 0.01078732 |
| ENSBTAG00000006855 | TDRD1 | tudor domain containing 1 [Source:VGNC Symbol;Acc:VGNC:35715] | 3.05655381 | 32.6042682 | − 3.4157894 | 4.53E − 05 |
| ENSBTAG00000003398 | KCNG1 | potassium voltage-gated channel modifier subfamily G member 1 [Source:VGNC Symbol;Acc:VGNC:30442] | 61.5126929 | 666.608932 | − 3.4385742 | 2.36E-44 |
| ENSBTAG00000005370 | TMTC1 | Bos taurus transmembrane and tetratricopeptide repeat containing 1 (TMTC1), mRNA. [Source:RefSeq mRNA;Acc:NM_001192761] | 4.40013653 | 57.4349605 | − 3.7038803 | 1.50E-08 |
| ENSBTAG00000042696 | RF00071 | small nucleolar RNA, C/D box 73A [Source:HGNC Symbol;Acc:HGNC:10235] | 2.38781081 | 32.1493473 | − 3.7487039 | 0.00147441 |
| ENSBTAG00000005425 | GATA4 | GATA binding protein 4 [Source:VGNC Symbol;Acc:VGNC:29268] | 0.67787935 | 9.54307417 | − 3.8148273 | 0.04964 |
| ENSBTAG00000053497 | GNLY | granulysin [Source:NCBI gene;Acc:404173] | 2.04887114 | 28.7995165 | − 3.8210854 | 0.00013213 |
| ENSBTAG00000009341 | CCDC146 | Bos taurus coiled-coil domain containing 146 (CCDC146), mRNA. [Source:RefSeq mRNA;Acc:NM_001205487] | 1.01377939 | 14.6271358 | − 3.8396071 | 0.0153719 |
| ENSBTAG00000009302 | RCAN2 | Bos taurus regulator of calcineurin 2 (RCAN2), transcript variant 2, mRNA. [Source:RefSeq mRNA;Acc:NM_001015632] | 1.01073103 | 15.3083605 | − 3.9136064 | 0.00772622 |
| ENSBTAG00000046107 | TTBK1 | tau tubulin kinase 1 [Source:HGNC Symbol;Acc:HGNC:19140] | 1.69165875 | 26.4921376 | − 3.965986 | 0.00012693 |
| ENSBTAG00000010111 | TCF7L1 | transcription factor 7 like 1 [Source:NCBI gene;Acc:515303] | 2.06104713 | 32.20969 | − 3.9795809 | 7.21E-05 |
| ENSBTAG00000012368 | IL21 | interleukin 21 [Source:VGNC Symbol;Acc:VGNC:30141] | 1.34358271 | 21.6281861 | − 3.9958212 | 0.00108001 |
| ENSBTAG00000024675 | CYSLTR1 | Bos taurus cysteinyl leukotriene receptor 1 (CYSLTR1), mRNA. [Source:RefSeq mRNA;Acc:NM_001099726] | 0.99855504 | 16.4111412 | − 4.0180996 | 0.00870421 |
| ENSBTAG00000001068 | ZCWPW1 | zinc finger CW-type and PWWP domain containing 1 [Source:VGNC Symbol;Acc:VGNC:37125] | 0.68701571 | 11.4433525 | − 4.0661589 | 0.02374012 |
| ENSBTAG00000048565 | BASP1 | Bos taurus brain abundant membrane attached signal protein 1 (BASP1), mRNA. [Source:RefSeq mRNA;Acc:NM_174780] | 1.36185543 | 23.6780022 | − 4.120178 | 0.00037734 |
| ENSBTAG00000015094 | VNN1 | Bos taurus vanin 1 (VNN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001024556] | 1.02900375 | 17.8296211 | − 4.1234276 | 0.00314342 |
| ENSBTAG00000007589 | SMAD9 | Bos taurus SMAD family member 9 (SMAD9), mRNA. [Source:RefSeq mRNA;Acc:NM_001076928] | 0.33285168 | 8.39456512 | − 4.5214841 | 0.03301325 |
| ENSBTAG00000003791 | LPAR3 | Bos taurus lysophosphatidic acid receptor 3 (LPAR3), mRNA. [Source:RefSeq mRNA;Acc:NM_001192741] | 0.34807603 | 18.2533247 | − 5.6437392 | 0.0009192 |
| ENSBTAG00000002135 | CD69 | Bos taurus CD69 molecule (CD69), mRNA. [Source:RefSeq mRNA;Acc:NM_174014] | 0 | 12.6541583 | − 6.0743754 | 0.00080407 |
| ENSBTAG00000025659 | ZNF618 | zinc finger protein 618 [Source:VGNC Symbol;Acc:VGNC:37314] | 0.33893968 | 34.9199228 | − 6.5764645 | 2.81E-05 |
*RPKM = reads Per Kilobase of transcript, per Million mapped reads.