System/additive | Time | Pathway or Go-term | Scorea | No. of total genesb | No. of DEGsd | Response genese |
---|---|---|---|---|---|---|
Overlap Zno | ||||||
Ileum/ZnO | 23 days | Mineral absorption | 15.1 | 51 | 4 | SLC39A4, MT1F, HEPH, MT1A |
IPEC-J2/ZnO | 2 h | Mineral absorption | 20.4 | 51 | 5 | HMOX1, S100G, SLC30A1, MT1A |
Jejunum/ZnO | 23 days | PAK pathway | 12.7 | 620 | 9 | CDH2, PLA2G7, FOS, CXCL13, MYLK, PAK1, OSM, TUBA8, GDF6 |
IPEC-J2/ZnO | 2 h | PAK pathway | 15.0 | 731 | 18 | BMP2, CSF2, CXCL2, FOS, GDF15, HBEGF, IL1A, IL6, IL8, JUN, KLF10, MLLT4, NGF, NRG1, SLC2A4, SNAI1, TCF21, ZYX |
Jejunum/ZnO | 23 days | Influenza A | 10.9 | 317 | 6 | FOS, HSPA8, OAS2, RSAD2, HLA-DQA1, DDX58 |
IPEC-J2/ZnO | 2 h | Influenza A | 16.3 | 317 | 12 | DNAJB1, FOS, HLA-DQA1, HSPA1A, HSPA1B, IL1A, IL6, IL8, JUN, SOCS3, TICAM1, TNFAIP3 |
Jejunum/ZnO | 23 days | Cytoskeleton remodelling keratin filaments | 20.9 | 48 | 5 | KRT7, PLEC, TUBA1C, TUBA8, TUBA3C |
Jejunum/ZnO | 23 days | Cytoskeletal signalling | 13.0 | 242 | 6 | ARHGAP35, KRT7, MARK1, PLEC, PAK1, DES |
Jejunum/ZnO | 23 days | Cytoplasmic microtubules | 24.5 | 102 | 7 | DYNC2H1, MARK1, PLEC, TUBA1C, TUBA8, TUBA3C, DES |
IPEC-J2/ZnO | 2 h | Cell adhesion_ECM remodelling | 9.3 | 61 | 4 | HBEGF, IL8, PLAU, SERPINE1 |
Jejunum/ZnO | 23 days | Cell adhesion molecules (CAMs) | 9.7 | 145 | 4 | CD8A, CDH2, VTCN1, HLA-DQA1 |
Jejunum/ZnO | 23 days | Cell adhesion gap junctions | 10.9 | 49 | 3 | TUBA1C, TUBA8, TUBA3C |
IPEC-J2/ZnO | 6 h | Adhesion | 11.0 | 80 | 10 | ADAM9, CLDN1, CTNNB1, CYR61, DOCK1, ITGA5, MPZL1, NEDD9, NOV, SERPINE1 |
Overlap rye | ||||||
IPEC-J2 10 vs. 5%/rye | 2 h | Cell cycle | 11.1 | 538 | 24 | ATM, CASC5, CDC27, CENPF, CEP152, CNTRL, KIF20A, LMNA, MAD1L1, NINL, NIPBL, PCM1, PDS5B, PSMB4, RPS27A, SGOL2, SMC2, SMC3, SMC4, STAG2, SYNE2, TOP2A, TPR, UBB |
Jejunum 10%/rye | 28 days | Cell cycle | 10.1 | 538 | 11 | ARPP19, OPTN, RAB1A, MAD2L1, FZR1, RFWD2, E2F4, NUP35, NUP214, YWHAG, RUVBL1 |
IPEC-J2 10%/rye | 2 h | Cell cycle | 8.3 | 538 | 4 | ATM, CENPF, NIPBL, SYNE2 |
Jejunum 5%/rye | 21 days | Cell cycle | 15.2 | 538 | 17 | ARPP19, CDK2, OPTN, RAB1A, CSNK2B, MAD2L1, CNTRL, PSMD11, CENPE, GINS2, E2F2, MCM10, SGOL1, NUP160, NUP214, SMC1B, RUVBL1 |
Jejunum 10%/rye | 28 days | Cell cycle/checkpoint control | 7.9 | 229 | 6 | ARPP19, MAD2L1, VCP, YWHAG, MKI67, ZBTB17 |
Jejunum 10 vs. 5%/rye | 28 days | Cell cycle/checkpoint control | 8.7 | 229 | 6 | ARPP19, MAD2L1, VCP, MKI67, MLH1, ZBTB17 |
IPEC-J2 10 vs. 5%/rye | 2 h | Cell cycle/checkpoint control | 13.1 | 229 | 15 | ATM, CDC27, CEND1, FOSB, LMNA, NHEJ1, PCM1, RAD50, RAN, SMC2, SMC3, SMC4, SMG1, STAG2, TPT1 |
IPEC-J2 10 vs. 5%/rye | 2 h | Biosynthesis of the N-glycan precursor (dolichol–LLO) and transfer to a nascent protein | 46.3 | 696 | 51 | ACTB, EEF1A1, EEF1A2, EEF1G, FAU, GFPT1, LMAN1, LMNA, MBOAT4, MUC4, SLC25A6, SLC30A7, TUBA1B, RPL19, RPL5, including 36 RPL and RPS variants |
Jejunum 10 vs. 5%/rye | 28 days | Biosynthesis of the N-glycan precursor (dolichol–LLO) and transfer to a nascent protein | 6.9 | 696 | 10 | ALG14, COQ2, RPL37, SRP9, ST3GAL4, LDHD, IGFBP1, PIGA, F2, ZBTB17 |
Jejunum 5%/rye | 21 days | Biosynthesis of the N-glycan precursor (dolichol–LLO) and transfer to a nascent protein | 15.6 | 696 | 20 | ARFGAP1, CTSG, GCNT3, EIF4B, ALG14, COQ2, RPL37, RPL19, RPL5, SRP9, ST3GAL4, LDHD, MUC17, PFDN1, TPP1, INHA, IGFBP1, ATP6AP2, SPHK1, F2 |
IPEC-J2 5%/rye | 2 h | Biosynthesis of the N-glycan precursor (dolichol–LLO) and transfer to a nascent protein | 87.5 | 696 | 39 | ACTB, EEF1A1, EEF1G, MUC13, STS, TUBA1B, RPL19, RPL5, including 32 RPL and RPS variants |
Rye; related in vivo pathways | ||||||
Jejunum 10 vs. 5%/rye | 28 days | Signalling by BMP | 6.8 | 48 | 3 | NUP214, TOB1, ZFYVE16 |
Jejunum 10 vs. 5%/rye | 21 days | Ovarian infertility genes | 21.0 | 32 | 4 | ESR2, INHA, NR5A1, ZP3 |
Jejunum 10 vs. 5%/rye | 21 days | Ca-dependent events | 9.6 | 247 | 4 | CYP11A1, NR5A1, OPRM1, STAR |
Overlap amoxicillin | ||||||
Jejunum/amox | 14 days | CC_FAT/GO:0015630 ~ microtubule cytoskeleton | 0.016 | 31c | 5 | IFT20, MID1IP1, STMN1, MAP7D1, TACC1 |
IPEC-J2/amox | 6 h | CC_FAT/GO:0015630 ~ microtubule cytoskeleton | 0.241 | 707c | 21 | APC2, NIN, IFT80, FLOT1, ALMS1, MID1IP1, MID1, MARK1, TUBGCP3, KIF1B, RCC2, DYNLL1, CEP350, CLIC5, KIFAP3, TBCC, TUBA4A, STRBP, NDRG2, KATNAL1, TUBB3 |
Jejunum/amox | 14 days | CC_FAT/GO:0005856 ~ cytoskeleton | 0.009 | 31c | 8 | ARPC1A, IFT20, MYL12A, MID1IP1, STMN1, HNRNPH1, MAP7D1, TACC1 |
Amoxicillin; related in vivo pathways | ||||||
Jejunum/amox | 14 days | Aurora B signalling | 10.2 | 39 | 2 | TACC1, STMN1 |
Jejunum/amox | 6 h | Validated targets of C-MYC transcriptional repression | 17.9 | 62 | 11 | CCND1, CDKN1B, CEBPD, CLU, DDIT3, DKK1, NDRG1, NDRG2, RBL1, S100A7, ZBTB17 |
Jejunum/amox | 6 h | Cell cycle/checkpoint control | 11.9 | 229 | 18 | BRD2, CCND1, CDC25A, CDKN1B, CSNK1A1, DDIT4, FOSB, KAT5, NBN, NEK7, PLK3, RBBP8, RCC2, SMG1, TFAP2C, TP53BP1, YWHAG, ZBTB17 |