Supplementary Table 1 Genes Commonly Affected During Transition from a Milk-Based Diet

Supplementary Table 1 Genes commonly affected during transition from a milk-based diet to a diet supplemented with grain or hay in rumen epithelium of dairy calves (n=3 per group). Genes were differentially expressed in the same direction in groups of calves fed milk replacer only (MRO) until day 42 of age, followed by a diet of milk replacer plus commercial calf starter (grain) or hay until day 56 of age relative to calves fed MRO until day 42 of age

Ensembl gene ID / Gene description / Fold change
ENSBTAG00000000634 / Melanophilin / -20.4 / *
ENSBTAG00000018948 / Hypoxia-inducible factor 3-alpha / -10.9 / *
ENSBTAG00000009786 / Scinderin / -8.6 / *
ENSBTAG00000034402 / Angiotensin-converting enzyme 2 / -8.0 / *
ENSBTAG00000021158 / DNA-binding protein SATB1 / -7.6 / *
ENSBTAG00000019210 / Adenylate cyclase 2 (brain) / -6.8 / *
ENSBTAG00000014611 / Sortilin-related receptor, L(DLR class) A repeats containing / -6.7 / *
ENSBTAG00000002348 / Electrogenic sodium bicarbonate cotransporter 1 / -6.5
ENSBTAG00000000185 / Sodium- and chloride-dependent neutral and basic amino acid transporter B(0+) / -6.4 / *
ENSBTAG00000004952 / Major facilitator superfamily domain containing 4 / -6.1
ENSBTAG00000012900 / Transmembrane protein 229B / -6.0
ENSBTAG00000018297 / Pleckstrin homology domain containing, family H (with MyTH4 domain) member 1 / -6.0
ENSBTAG00000006676 / Fin bud initiation factor homolog / -5.9 / *
ENSBTAG00000045925 / Cbp/p300-interacting transactivator 1 / -5.8
ENSBTAG00000012182 / GTP-binding protein Di-Ras3 / -5.5
ENSBTAG00000037804 / IKAROS family zinc finger 2 (Helios) / -5.4 / *
ENSBTAG00000004440 / Solute carrier family 15 member 1 / -5.3
ENSBTAG00000016305 / ATPase type 13A4 / -5.3
ENSBTAG00000017239 / Gamma-aminobutyric acid type B receptor subunit 1 isoform 1 / -5.2 / *
ENSBTAG00000012837 / Collagen, type VI, alpha 6 / -5.1
ENSBTAG00000000795 / Nicotinamide mononucleotide adenylyltransferase 2 / -5.0 / *
ENSBTAG00000020800 / BEN domain containing 7 / -4.9
ENSBTAG00000027444 / Supervillin / -4.9 / *
ENSBTAG00000006686 / Nephronectin / -4.8
ENSBTAG00000008761 / TRAF-type zinc finger domain containing 1 / -4.8 / *
ENSBTAG00000007129 / Protein MRVI1 isoform a / -4.8 / *
ENSBTAG00000014377 / Uncharacterized protein / -4.7 / *
ENSBTAG00000001652 / Solute carrier organic anion transporter family member 3A1 / -4.5
ENSBTAG00000020407 / Metastasis suppressor 1 / -4.4
ENSBTAG00000020597 / Dimethylaniline monooxygenase / -4.3 / *
ENSBTAG00000004574 / 2-hydroxyacylsphingosine 1-beta-galactosyltransferase / -4.2
ENSBTAG00000007850 / Inter-alpha-trypsin inhibitor heavy chain H4 precursor / -4.2
ENSBTAG00000007966 / Tubulin tyrosine ligase-like family, member 3 / -4.2 / *
ENSBTAG00000009150 / Spondin-1 / -4.2
ENSBTAG00000009607 / Glycosyltransferase-like 1B / -4.1 / *
ENSBTAG00000018245 / Excitatory amino acid transporter 1 / -3.9
ENSBTAG00000020159 / Na+/K+ transporting ATPase interacting 1 / -3.9
ENSBTAG00000009495 / Basal cell adhesion molecule / -3.8 / *
ENSBTAG00000011482 / Large neutral amino acids transporter small subunit 4 / -3.8 / *
ENSBTAG00000040338 / Obscurin-like 1 / -3.8 / *
ENSBTAG00000004645 / ADAMTS-like 3 / -3.7
ENSBTAG00000008248 / Dystrophin / -3.7
ENSBTAG00000010647 / BDNF/NT-3 growth factors receptor / -3.7 / *
ENSBTAG00000011280 / TBK1 binding protein 1 / -3.6
ENSBTAG00000020489 / Sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A / -3.6
ENSBTAG00000031340 / Solute carrier family 6, member 20 / -3.6 / *
ENSBTAG00000009637 / Solute carrier family 12 member 2 / -3.5 / *
ENSBTAG00000010163 / Sodium channel, nonvoltage-gated 1, gamma / -3.4 / *
ENSBTAG00000001843 / WW domain-binding protein 1 / -3.4 / *
ENSBTAG00000009495 / Basal cell adhesion molecule / -3.4 / *
ENSBTAG00000014372 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 / -3.3
ENSBTAG00000005021 / Sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A / -3.3 / *
ENSBTAG00000000738 / Death-associated protein kinase 1 / -3.2
ENSBTAG00000002974 / Dimethylaniline monooxygenase / -3.2
ENSBTAG00000015362 / Bone morphogenetic protein 7 / -3.2
ENSBTAG00000005356 / Suppression of tumorigenicity 5 protein / -3.2 / *
ENSBTAG00000002640 / Kalirin, RhoGEF kinase / -3.1
ENSBTAG00000012629 / Zinc finger protein 362 / -3.1
ENSBTAG00000007449 / Heparan sulfate glucosamine 3-O-sulfotransferase 1 / -3.0
ENSBTAG00000011518 / Retinoic acid receptor beta / -3.0
ENSBTAG00000010360 / Leucine-rich repeats and immunoglobulin-like domains 1 / -2.9 / *
ENSBTAG00000016105 / H2A histone family, member Y / -2.9
ENSBTAG00000019745 / Lipase maturation factor 1 / -2.9
ENSBTAG00000010986 / Potassium voltage-gated channel, KQT-like subfamily, member 1 / -2.8
ENSBTAG00000014269 / Scavenger receptor class B member 1 / -2.8
ENSBTAG00000015251 / Asparagine-linked glycosylation 13 homolog / -2.8
ENSBTAG00000012922 / PHD finger protein 2 / -2.7
ENSBTAG00000019265 / Acylglycerol kinase, mitochondrial / -2.7
ENSBTAG00000034373 / Cadherin-13 precursor / -2.7
ENSBTAG00000005234 / Ly6/PLAUR domain-containing protein 1 / -2.6
ENSBTAG00000007392 / Uterine milk protein / -2.6
ENSBTAG00000011541 / Retinoblastoma-like 1 (p107) / -2.6
ENSBTAG00000001629 / Sex comb on midleg homolog 1 (Drosophila) / -2.5
ENSBTAG00000008948 / P2X purinoceptor / -2.5
ENSBTAG00000012897 / Integrin, alpha 7 / -2.5
ENSBTAG00000013165 / Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 / -2.5
ENSBTAG00000033983 / Dual specificity mitogen-activated protein kinase kinase 1 / -2.5 / *
ENSBTAG00000008527 / Splicing factor, arginine/serine-rich 6 / -2.5 / *
ENSBTAG00000006928 / Ornithine aminotransferase, mitochondrial precursor / -2.5 / *
ENSBTAG00000010125 / Signal transducer and activator of transcription 5B / -2.4
ENSBTAG00000012039 / PHACTR1 phosphatase and actin regulator 1 / -2.4
ENSBTAG00000012519 / Xanthine dehydrogenase/oxidase / -2.4
ENSBTAG00000021444 / Twist-related protein 2 / -2.4
ENSBTAG00000021940 / Coiled-coil domain-containing protein 149 / -2.4
ENSBTAG00000001788 / Podoplanin / -2.3 / *
ENSBTAG00000003721 / Carbohydrate sulfotransferase 1 / -2.3
ENSBTAG00000009496 / Signal transducer and activator of transcription 5A / -2.3
ENSBTAG00000012107 / Solute carrier family 25, member 28 / -2.3
ENSBTAG00000012193 / Tetratricopeptide repeat domain 28 / -2.3
ENSBTAG00000005478 / POZ (BTB) and AT hook containing zinc finger 1 / -2.3 / *
ENSBTAG00000004344 / Long-chain-fatty-acid--CoA ligase 1 / -2.2
ENSBTAG00000007841 / Wilms tumor 1 interacting protein / -2.2
ENSBTAG00000008550 / GTPase, IMAP family member 7 / -2.2
ENSBTAG00000004990 / Neogenin 1 / -2.1
ENSBTAG00000011748 / Sphingomyelin synthase 1 / -2.1
ENSBTAG00000016568 / LUC7-like / -2.1 / *
ENSBTAG00000002148 / RAB3D, member RAS oncogene family / -2.0
ENSBTAG00000006330 / RNA-binding protein 5 / -2.0
ENSBTAG00000009665 / Utrophin / -2.0 / *
ENSBTAG00000027151 / Rho GTPase activating protein 26 / -2.0
ENSBTAG00000001204 / KIAA1462 homolog / -1.9
ENSBTAG00000007074 / Zinc finger protein 389 / -1.9
ENSBTAG00000010395 / Dedicator of cytokinesis 9 / -1.9
ENSBTAG00000013281 / Spermatogenesis associated 21 / -1.9
ENSBTAG00000014698 / Caspase recruitment domain-containing protein 11 / -1.9
ENSBTAG00000019611 / Membrane associated guanylate kinase, WW and PDZ domain containing 3 / -1.9
ENSBTAG00000019807 / COL27A1 protein / -1.9
ENSBTAG00000045520 / Proenkephalin-B preproprotein / -1.9
ENSBTAG00000014390 / Myotubularin-related protein 9 / -1.8
ENSBTAG00000016933 / Interleukin-27 receptor subunit alpha / -1.8
ENSBTAG00000019204 / Reticulon-3 / -1.8
ENSBTAG00000020149 / Ribonuclease H2 subunit B / -1.8
ENSBTAG00000014093 / Isocitrate dehydrogenase / -1.7
ENSBTAG00000017957 / Spermatogenesis associated 24 / -1.7
ENSBTAG00000027612 / Protein phosphatase methylesterase 1 / -1.7
ENSBTAG00000014697 / SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 / -1.6
ENSBTAG00000006759 / Succinyl-CoA ligase / 1.5
ENSBTAG00000004120 / HemK methyltransferase family member 1 / 1.6
ENSBTAG00000006806 / Keratin, type I cytoskeletal 17 / 1.6
ENSBTAG00000007399 / Lysosomal-associated membrane protein 2 isoform 1 / 1.6
ENSBTAG00000008625 / Pleckstrin homology domain-containing family F member 1 / 1.6
ENSBTAG00000010923 / Ras-related protein Rab-9A / 1.6
ENSBTAG00000011239 / Signal peptidase complex catalytic subunit SEC11A / 1.6
ENSBTAG00000011285 / TRM1-like protein / 1.6
ENSBTAG00000014060 / U6 snRNA-associated Sm-like protein LSm6 / 1.6
ENSBTAG00000017832 / PDK3 protein / 1.6
ENSBTAG00000020865 / Protein pellino homolog 1 / 1.6
ENSBTAG00000024107 / Inositol polyphosphate-5-phosphatase, 75kDa / 1.6
ENSBTAG00000025593 / Coiled-coil domain containing 32 / 1.6
ENSBTAG00000043956 / Ubiquitin-conjugating enzyme E2 E3 / 1.6
ENSBTAG00000044000 / Primase, DNA, polypeptide 1 (49kDa) / 1.6
ENSBTAG00000000632 / RAD54 homolog B (S. cerevisiae) / 1.7
ENSBTAG00000004675 / Zinc finger protein 18 / 1.7
ENSBTAG00000006715 / F-box only protein 8 / 1.7
ENSBTAG00000006818 / Transmembrane protein 185A / 1.7
ENSBTAG00000006837 / Ubiquitin-like modifier-activating enzyme 6 / 1.7
ENSBTAG00000006957 / Solute carrier family 2, facilitated glucose transporter member 8 / 1.7
ENSBTAG00000007013 / TOM1-like protein 1 / 1.7
ENSBTAG00000007303 / Double-strand-break repair protein rad21 homolog / 1.7
ENSBTAG00000007394 / 60S ribosomal protein L22-like 1 / 1.7
ENSBTAG00000009508 / UPF0466 protein C22orf32 homolog, mitochondrial / 1.7
ENSBTAG00000010731 / Cyclin-dependent kinase 4 inhibitor D / 1.7
ENSBTAG00000013901 / Phosphatidylserine synthase 1 / 1.7
ENSBTAG00000014931 / Myeloid leukemia factor 2 / 1.7
ENSBTAG00000017729 / Nuclear receptor subfamily 2 group C member 1 / 1.7
ENSBTAG00000019929 / Integrin alpha-V / 1.7
ENSBTAG00000020924 / F-box/WD repeat-containing protein 9 / 1.7
ENSBTAG00000021575 / Bromodomain-containing protein 7 / 1.7
ENSBTAG00000021883 / AP-3 complex subunit mu-1 / 1.7
ENSBTAG00000030690 / Ras association and DIL domains / 1.7
ENSBTAG00000047434 / Translin-associated factor X / 1.7
ENSBTAG00000000019 / Serine incorporator 1 / 1.8
ENSBTAG00000000212 / NAD kinase / 1.8
ENSBTAG00000000240 / A-kinase anchor protein 7 / 1.8
ENSBTAG00000001393 / Metal-response element-binding transcription factor 2 / 1.8
ENSBTAG00000002175 / SRSF protein kinase 2 / 1.8
ENSBTAG00000003483 / Nudix (nucleoside diphosphate linked moiety X)-type motif 18 / 1.8
ENSBTAG00000003904 / GPN-loop GTPase 1 / 1.8
ENSBTAG00000005843 / Oligoribonuclease, mitochondrial / 1.8
ENSBTAG00000009374 / Poly (ADP-ribose) polymerase 2 / 1.8
ENSBTAG00000010015 / NmrA-like family domain-containing protein 1 / 1.8
ENSBTAG00000010118 / Histone acetyltransferase type B catalytic subunit / 1.8
ENSBTAG00000010581 / Membrane associated guanylate kinase, WW and PDZ domain containing 1 / 1.8
ENSBTAG00000011957 / cAMP-responsive element-binding protein-like 2 / 1.8
ENSBTAG00000012447 / Serine/threonine-protein phosphatase PP1-beta catalytic subunit / 1.8
ENSBTAG00000012746 / Kelch domain-containing protein 3 / 1.8
ENSBTAG00000012860 / PDZ domain-containing protein 11 / 1.8
ENSBTAG00000012940 / Transmembrane protein 25 / 1.8
ENSBTAG00000013869 / SH3 domain-binding protein 4 / 1.8
ENSBTAG00000014691 / Brefeldin A-inhibited guanine nucleotide-exchange protein 1 / 1.8
ENSBTAG00000015522 / 28S ribosomal protein S31, mitochondrial / 1.8
ENSBTAG00000015556 / NEDD8-activating enzyme E1 catalytic subunit / 1.8
ENSBTAG00000015776 / Hippocampus abundant transcript 1 / 1.8
ENSBTAG00000016266 / Succinate dehydrogenase / 1.8
ENSBTAG00000017263 / Max-interacting protein 1 / 1.8
ENSBTAG00000018097 / Poly(A)-specific ribonuclease PARN / 1.8
ENSBTAG00000018278 / ATP synthase subunit O, mitochondrial / 1.8
ENSBTAG00000018542 / Cytochrome c oxidase subunit 5B, mitochondrial / 1.8
ENSBTAG00000019096 / Cytochrome b-c1 complex subunit 1, mitochondrial precursor / 1.8
ENSBTAG00000021678 / High affinity copper uptake protein 1 / 1.8
ENSBTAG00000022069 / Ataxin 2 / 1.8
ENSBTAG00000025099 / RING finger protein 145 / 1.8
ENSBTAG00000031012 / GPI-anchor transamidase / 1.8
ENSBTAG00000037377 / Abhydrolase domain-containing protein 14B / 1.8
ENSBTAG00000046220 / Uncharacterized protein / 1.8
ENSBTAG00000000251 / Delta-aminolevulinic acid dehydratase / 1.9
ENSBTAG00000000312 / Glutamate / 1.9
ENSBTAG00000000712 / F-box/WD repeat-containing protein 2 / 1.9
ENSBTAG00000002125 / Guanine nucleotide-binding protein G(olf) subunit alpha / 1.9
ENSBTAG00000002500 / F-box/LRR-repeat protein 15 / 1.9
ENSBTAG00000003232 / Ras-related protein Rab-7L1 / 1.9
ENSBTAG00000003469 / Protein Churchill / 1.9
ENSBTAG00000003635 / Solute carrier family 35, member C2 / 1.9
ENSBTAG00000004381 / Tumor-associated calcium signal transducer 2 / 1.9
ENSBTAG00000005184 / TP53 target 5 / 1.9
ENSBTAG00000006075 / Succinyl-CoA ligase / 1.9
ENSBTAG00000006950 / COP9 signalosome complex subunit 4 / 1.9
ENSBTAG00000007578 / Hypothetical protein LOC532603 / 1.9
ENSBTAG00000007942 / PAP associated domain containing 5 / 1.9
ENSBTAG00000009137 / Protein NKG7 / 1.9
ENSBTAG00000009232 / Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha isoform / 1.9
ENSBTAG00000011623 / Vacuole membrane protein 1 / 1.9
ENSBTAG00000011837 / ATPase ASNA1 / 1.9
ENSBTAG00000012262 / F-box only protein 10 / 1.9
ENSBTAG00000012844 / E3 ubiquitin-protein ligase LRSAM1 / 1.9
ENSBTAG00000012857 / Cyclin M2 / 1.9
ENSBTAG00000013007 / Hypothetical protein LOC516545 / 1.9 / *
ENSBTAG00000013611 / Sodium channel and clathrin linker 1 / 1.9
ENSBTAG00000014644 / tRNA-dihydrouridine synthase 2-like / 1.9
ENSBTAG00000014675 / Pentatricopeptide repeat-containing protein 2 / 1.9
ENSBTAG00000015807 / Galactose-1-phosphate uridylyltransferase / 1.9
ENSBTAG00000015853 / Succinate dehydrogenase cytochrome b560 subunit, mitochondrial / 1.9
ENSBTAG00000016254 / Histone deacetylase 5 / 1.9
ENSBTAG00000016527 / Hypothetical protein LOC510161 / 1.9
ENSBTAG00000017184 / Transcriptional regulator Kaiso / 1.9
ENSBTAG00000018283 / 3-ketoacyl-CoA thiolase, peroxisomal / 1.9
ENSBTAG00000019183 / Fuzzy homolog (Drosophila) / 1.9
ENSBTAG00000019542 / 39S ribosomal protein L39, mitochondrial / 1.9
ENSBTAG00000019589 / Hypothetical protein LOC518967 / 1.9
ENSBTAG00000020980 / Catalase / 1.9
ENSBTAG00000026243 / Hypothetical protein LOC617968 / 1.9
ENSBTAG00000038842 / NEDD8 precursor / 1.9
ENSBTAG00000043951 / Inositol(myo)-1(or 4)-monophosphatase 2 / 1.9
ENSBTAG00000046552 / Gamma-glutamylaminecyclotransferase / 1.9
ENSBTAG00000014700 / Cytoplasmic dynein 1 light intermediate chain 1 / 2.0 / *
ENSBTAG00000000010 / Ubiquitin-like protein 7 / 2.0
ENSBTAG00000001854 / Anamorsin / 2.0
ENSBTAG00000002049 / Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial / 2.0
ENSBTAG00000002298 / Cytoskeleton-associated protein 2-like / 2.0
ENSBTAG00000002542 / Lysine-rich coiled-coil protein 1 / 2.0
ENSBTAG00000002714 / Guanine nucleotide-binding protein G(i) subunit alpha-1 / 2.0
ENSBTAG00000004064 / 3'(2'),5'-bisphosphate nucleotidase 1 / 2.0
ENSBTAG00000005416 / Peptidylprolyl isomerase (cyclophilin)-like 3 / 2.0
ENSBTAG00000005475 / Hypothetical protein LOC510320 / 2.0
ENSBTAG00000005744 / Para-hydroxybenzoate--polyprenyltransferase, mitochondrial precursor / 2.0
ENSBTAG00000005865 / Mitogen-activated protein kinase 6 / 2.0
ENSBTAG00000007003 / Thymidylate synthase / 2.0
ENSBTAG00000007654 / Carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 7 / 2.0
ENSBTAG00000008646 / tRNA methyltransferase 112 homolog / 2.0
ENSBTAG00000008683 / L-lactate dehydrogenase A chain / 2.0
ENSBTAG00000008953 / Antigen peptide transporter 1 / 2.0
ENSBTAG00000010009 / Transmembrane and coiled-coil domain-containing protein 1 / 2.0
ENSBTAG00000010387 / Protein FAM188A / 2.0
ENSBTAG00000012069 / Transmembrane and coiled-coil domain-containing protein C6orf129 homolog / 2.0
ENSBTAG00000012656 / Putative transcription factor Ovo-like 1 / 2.0
ENSBTAG00000012946 / Heat shock factor protein 2 / 2.0