Skip to main content

Table 2 Pathways/processes and GO-terms overlapping between in vitro and in vivo datasets

From: Enrichment of in vivo transcription data from dietary intervention studies with in vitro data provides improved insight into gene regulation mechanisms in the intestinal mucosa

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

  1. aGeneAnalytics pathways with a high score (>18; corresponding with an FDR-corrected p value ≤0.0001) and medium score (>6.5; corresponding with an FDR-corrected p value ≤0.1) were retrieved. Enriched GO-terms with a p value of <0.05 were retrieved from DAVID, except for IPEC-J2 cells at 6 h. GO-terms with a p value of <0.25 were retrieved. Pathway annotations are from GeneAnalytics (http://geneanalytics.genecards.org).
  2. bNumber of genes; total number of genes in a pathway or number of DEGs loaded in DAVID (for GO-term analysis)
  3. cNumber of DEGs loaded in DAVID (for GO-term analysis)
  4. dNumber of DEGs mapped to a pathway or to a GO-term
  5. eOverlapping genes are italicized. Pathway annotations are from GeneAnalytics (http://geneanalytics.genecards.org).