Supplemental data

Table 1. Proteins for differentially expressed genes identified using Ingenuity software as involved in colorectal cancer. (A) for Caco-K microarray analysis and (B) Caco-H microarray analysis.

A

Category / Process / Significance / Molecules
Cancer / Invasion / 6,82E-04 / AGT, IGF2, PDCD4, PTGS2, TFF1, TFF2, TFF3
Cancer / Invasion / 2,26E-03 / AGT, HAS2, IGF2, NUAK1, PDCD4, PTGS2, TFF1, TFF2, TFF3
Cancer / Colorectal cancer / 6,72E-05 / ACOT7, ACOX2, ACSL5, AIM1, AKR1C1, AKR1C2, AKR1C3, ANXA4, BEX4, CCND2, CEBPD, CLDN3, COL2A1, COL6A3, COLEC12, CRABP2, CTGF, CXCL12, CXCR7, DKK1, EPB41L3, F12, FGFR3, FZD7, GATA6, GDF15, GMNN, GPR177, HMOX1, HTRA1, ITPR3, KLK6, MAP4K4, MSX1, NQO1, NUAK1, PCOLCE, PITX2, PLEK2, PPP2R1B, PTGS2, RAB31, S100A4, SDC1, SLC26A2, TEAD4, TFPI, TNFRSF11B, TUBA4A, TUBB3, ZFP36L2
Cellular Movement / Invasion / 6,82E-04 / AGT, IGF2, PDCD4, PTGS2, TFF1, TFF2, TFF3
Cellular Movement / Invasion / 2,26E-03 / AGT, HAS2, IGF2, NUAK1, PDCD4, PTGS2, TFF1, TFF2, TFF3
Gastrointestinal Disease / Colorectal cancer / 6,72E-05 / ACOT7, ACOX2, ACSL5, AIM1, AKR1C1, AKR1C2, AKR1C3, ANXA4, BEX4, CCND2, CEBPD, CLDN3, COL2A1, COL6A3, COLEC12, CRABP2, CTGF, CXCL12, CXCR7, DKK1, EPB41L3, F12, FGFR3, FZD7, GATA6, GDF15, GMNN, GPR177, HMOX1, HTRA1, ITPR3, KLK6, MAP4K4, MSX1, NQO1, NUAK1, PCOLCE, PITX2, PLEK2, PPP2R1B, PTGS2, RAB31, S100A4, SDC1, SLC26A2, TEAD4, TFPI, TNFRSF11B, TUBA4A, TUBB3, ZFP36L2
Gastrointestinal Disease / Invasion / 6,82E-04 / AGT, IGF2, PDCD4, PTGS2, TFF1, TFF2, TFF3
Gastrointestinal Disease / Invasion / 2,26E-03 / AGT, HAS2, IGF2, NUAK1, PDCD4, PTGS2, TFF1, TFF2, TFF3

B

Category / Process / Significance / Molecules
Cancer / Invasion / 3,14E-04 / AGT, IGF2, KLF4, PTGS2, TFF1, TFF2, TFF3, TMSB4X
Cancer / Invasion / 5,02E-04 / AGT, HAS2, IGF2, KLF4, NRG1, NUAK1, PTGS2, TFF1, TFF2, TFF3, TMSB4X
Cancer / Colorectal cancer / 6,48E-14 / ACOT7, ACOX2, ACSL5, ACTA2 (includes EG:59), AKR1C1, AKR1C2, AKR1C3, ANK3, ANXA4, APOC1, ARHGDIA, BUB1 (includes EG:699), C1ORF121, C9ORF167, CCL2, CCND2, CEBPD, CLDN3, COL2A1, COL4A1, COL4A2, COL6A3, CRABP2, DCC1, DHFR, DKK1, DLG7, DUSP6, EMP1, EMX2, F12, F2R, FGFR3, FOXF2, GATA6, GDF15, GJA1, GLRX2, GPR177, HMGB2, HOXC6, HTRA1, ID2, IGFBP7, INSIG1, IRS1, JAG1, KCNJ2, MCM4, MCM10, MME, MSX1, NCAPG (includes EG:64151), NEK6, NQO1, NRN1, NUAK1, PBK, PDLIM3, PLAT, POLD1, PRNP, PTGS2, PTMA, QPCT (includes EG:25797), RAB31, RGS4, S100A4, SDC1, SLC16A3, SLC26A2, SLC5A3, SPP1, SRPX, STMN2, TEAD4, TGFBR3, TNFRSF11B, TRIP13, TUBA4A, TUBB3, ZFP36L2
Cancer / Cell movement / 3,06E-05 / ARHGEF4, CDH1, CDX1, CDX2, F2, IGF2, IGFBP4, ITGB4, KLF4, MST1, PLEKHC1, PXN, ST6GAL1, TFF2, TMSB4X
Cancer / Development / 1,34E-05 / ABTB1, AGT, AREG, BCL2L1, BIRC5, CCND1, CDH1, CDX1, CDX2, COL18A1, CTSD, EDN1, ENC1, GREM1, IGF2, KLF4, LGALS1, NOS2A, NRG1, RB1, TACSTD1, TMSB4X
Cancer / Migration / 1,59E-03 / ARHGEF4, CDX1, CDX2, IGF2, IGFBP4, ITGB4, KLF4, MST1, PXN, ST6GAL1
Cancer / Growth / 1,95E-05 / ABTB1, AGT, AREG, BCL2L1, BIRC5, CCND1, CDH1, CDX1, CDX2, COL18A1, CTSD, EDN1, ENC1, IGF2, KLF4, LGALS1, NOS2A, NRG1, RB1, TACSTD1, TMSB4X
Cancer / Colon cancer / 7,63E-04 / ACOT7, ANXA4, APOC1, ARHGDIA, C1ORF121, CLDN3, COL2A1, DCC1, DHFR, F12, GDF15, GJA1, GLRX2, INSIG1, MCM4, MCM10, NQO1, POLD1, PTGS2, PTMA, SLC26A2, SPP1, TEAD4, TRIP13, TUBA4A, TUBB3
Cancer / Colon carcinoma / 1,22E-03 / ACOT7, ANXA4, ARHGDIA, C1ORF121, DCC1, DHFR, F12, GJA1, GLRX2, INSIG1, MCM4, MCM10, NQO1, POLD1, PTMA, TEAD4, TRIP13, TUBA4A, TUBB3
Cancer / Colorectal carcinoma / 1,33E-03 / ACOT7, ANXA4, ARHGDIA, C1ORF121, CDX2, COBLL1, DCC1, DHFR, F12, GJA1, GLRX2, INSIG1, MCM4, MCM10, MGMT, NQO1, POLD1, PTGS2, PTMA, TACSTD1, TEAD4, TOP2A, TRIP13, TUBA1A, TUBA4A, TUBB3, TUBB2C
Cancer / Colon tumor / 1,68E-03 / ACOT7, ANXA4, ARHGDIA, C1ORF121, DCC1, DHFR, F12, GDF15, GJA1, GLRX2, INSIG1, MCM4, MCM10, NQO1, POLD1, PTMA, TEAD4, TRIP13, TUBA4A, TUBB3
Cancer / Colorectal tumor / 1,68E-03 / ACOT7, ANXA4, ARHGDIA, C1ORF121, DCC1, DHFR, F12, GDF15, GJA1, GLRX2, INSIG1, MCM4, MCM10, NQO1, POLD1, PTMA, TEAD4, TRIP13, TUBA4A, TUBB3
Cellular Movement / Cell movement / 3,06E-05 / ARHGEF4, CDH1, CDX1, CDX2, F2, IGF2, IGFBP4, ITGB4, KLF4, MST1, PLEKHC1, PXN, ST6GAL1, TFF2, TMSB4X
Cellular Movement / Invasion / 3,14E-04 / AGT, IGF2, KLF4, PTGS2, TFF1, TFF2, TFF3, TMSB4X
Cellular Movement / Invasion / 5,02E-04 / AGT, HAS2, IGF2, KLF4, NRG1, NUAK1, PTGS2, TFF1, TFF2, TFF3, TMSB4X
Cellular Movement / Migration / 1,59E-03 / ARHGEF4, CDX1, CDX2, IGF2, IGFBP4, ITGB4, KLF4, MST1, PXN, ST6GAL1
Cellular Growth and Proliferation / Growth / 1,95E-05 / ABTB1, AGT, AREG, BCL2L1, BIRC5, CCND1, CDH1, CDX1, CDX2, COL18A1, CTSD, EDN1, ENC1, IGF2, KLF4, LGALS1, NOS2A, NRG1, RB1, TACSTD1, TMSB4X
Gastrointestinal Disease / Colorectal cancer / 6,48E-14 / ACOT7, ACOX2, ACSL5, ACTA2 (includes EG:59), AKR1C1, AKR1C2, AKR1C3, ANK3, ANXA4, APOC1, ARHGDIA, BUB1 (includes EG:699), C1ORF121, C9ORF167, CCL2, CCND2, CEBPD, CLDN3, COL2A1, COL4A1, COL4A2, COL6A3, CRABP2, DCC1, DHFR, DKK1, DLG7, DUSP6, EMP1, EMX2, F12, F2R, FGFR3, FOXF2, GATA6, GDF15, GJA1, GLRX2, GPR177, HMGB2, HOXC6, HTRA1, ID2, IGFBP7, INSIG1, IRS1, JAG1, KCNJ2, MCM4, MCM10, MME, MSX1, NCAPG (includes EG:64151), NEK6, NQO1, NRN1, NUAK1, PBK, PDLIM3, PLAT, POLD1, PRNP, PTGS2, PTMA, QPCT (includes EG:25797), RAB31, RGS4, S100A4, SDC1, SLC16A3, SLC26A2, SLC5A3, SPP1, SRPX, STMN2, TEAD4, TGFBR3, TNFRSF11B, TRIP13, TUBA4A, TUBB3, ZFP36L2
Gastrointestinal Disease / Development / 1,34E-05 / ABTB1, AGT, AREG, BCL2L1, BIRC5, CCND1, CDH1, CDX1, CDX2, COL18A1, CTSD, EDN1, ENC1, GREM1, IGF2, KLF4, LGALS1, NOS2A, NRG1, RB1, TACSTD1, TMSB4X
Gastrointestinal Disease / Growth / 1,95E-05 / ABTB1, AGT, AREG, BCL2L1, BIRC5, CCND1, CDH1, CDX1, CDX2, COL18A1, CTSD, EDN1, ENC1, IGF2, KLF4, LGALS1, NOS2A, NRG1, RB1, TACSTD1, TMSB4X
Gastrointestinal Disease / Cell movement / 3,06E-05 / ARHGEF4, CDH1, CDX1, CDX2, F2, IGF2, IGFBP4, ITGB4, KLF4, MST1, PLEKHC1, PXN, ST6GAL1, TFF2, TMSB4X
Gastrointestinal Disease / Invasion / 3,14E-04 / AGT, IGF2, KLF4, PTGS2, TFF1, TFF2, TFF3, TMSB4X
Gastrointestinal Disease / Invasion / 5,02E-04 / AGT, HAS2, IGF2, KLF4, NRG1, NUAK1, PTGS2, TFF1, TFF2, TFF3, TMSB4X
Gastrointestinal Disease / Colon cancer / 7,63E-04 / ACOT7, ANXA4, APOC1, ARHGDIA, C1ORF121, CLDN3, COL2A1, DCC1, DHFR, F12, GDF15, GJA1, GLRX2, INSIG1, MCM4, MCM10, NQO1, POLD1, PTGS2, PTMA, SLC26A2, SPP1, TEAD4, TRIP13, TUBA4A, TUBB3
Gastrointestinal Disease / Colon carcinoma / 1,22E-03 / ACOT7, ANXA4, ARHGDIA, C1ORF121, DCC1, DHFR, F12, GJA1, GLRX2, INSIG1, MCM4, MCM10, NQO1, POLD1, PTMA, TEAD4, TRIP13, TUBA4A, TUBB3
Gastrointestinal Disease / Migration / 1,59E-03 / ARHGEF4, CDX1, CDX2, IGF2, IGFBP4, ITGB4, KLF4, MST1, PXN, ST6GAL1

Figure 1. Selected pathways created using Ingenuity software for Caco-K and Caco-H differential expression from microarray analysis.

(A)Acute phase signalling pathway showing differentially expressed genes for Caco-K from microarray analysis. Differentially expressed genes include TNFRS11B (-5,9 fold), MAPK13 (-6,6 fold), SOCS2 (-2,8 fold), Serpina1 (-20,8 fold), Ferritin (-2,1 fold), FGG (-10,2 fold), FGB (-11,3 fold), FGA (-3,6 fold), AGT (7,0 fold), FN1 (60,1 fold), C3F (-3,5 fold), AHSG (-21,1 fold), TTR (-6,7 fold), APOH (-19,3 fold), APOA1 (-103,1 fold), ALB (-7,4 fold), C3 (-2,9 fold), F2 (-13,1 fold) and socs1 (2,9 fold), (B) Actin Cytoskeleton signalling pathway showing differentially expressed genes for Caco-K. Differentially expressed genes include F2 (-13,1 fold), FN1 (-60,1 fold), Integrin1 (-2,7 fold), ROCK2 (-2,0 fold), DNAPTP6 (-6,6 fold), RAB34 (18,3 fold), RAB31 (7,4 fold), RAB38 (3,7 fold), IRTKS (2,1 fold), VAV3 (2,4 fold), ARHGEF4 (3,1 fold), ARHGEF2 (2,0 fold), ARPC1A (2,1 fold), LIMK (4,5 fold), ERMAP (2,4 fold). (C) TGF-β signalling pathway showing differentially expressed genes for Caco-H. Differentially expressed genes include INHBB (-4,2 fold), ACVR1B (-3,1 fold), ACVR1B (-3,1 fold), BMP7 (-2,8 fold), SMAD3 (2,0 fold), SMURF2 (5,1 fold), RAB20 (3,0 fold), RAB10 (2,6 fold), RAB3C (2,0 fold), BMP4 (5,6 fold). (D)Notch signalling pathway showing differentially expressed genes for Caco-H. Genes include HES1 (-2,2 fold), JAG1 (3,5 fold), CNTN1 (11,8 fold), NOTCH1 (3,5 fold), FURIN (2,2 fold), HEY1 (14,5 fold), HEY2 (5,0 fold).

Figure 2. Linked networks of EMT genes for Caco-H.

Overlapping networks of interconnected proteins for genes that are differentially expressed in the Caco-H cell line and that have been identified as being involved in EMT. Genes for proteins highlighted in red are upregulated and genes for proteins highlighted in green are downregulated. Proteins highlighted in white are not differentially expressed on these microarrays but are believed to be connected to them based on the Ingenuity database. Proteins from genes from microarray analysis include SPARC (106,8 fold), S100A4 (25,8 fold), ANXA2 (2,1 fold), NFATC1 (3,2 fold), VIM (119,1 fold), CDH11 (19,4 fold), PRKCDBP (4,5 fold), LOXL2 (7,2 fold), LPHN2 (2,7 fold), TMSB4X (3,9 fold), SNAI2 (9,7 fold), COL6A3 (7,4 fold), WNT5A (2,8 fold), LEF1 (3,6 fold), MMP2 (3,6 fold), MMP9 (2,3 fold), MMP1 (2,1 fold), ZEB1 (2,2 fold), PIK3CD (3,1 fold), ITGB4 (9,5 fold), NOTCH1 (3,5 fold), HEY1 (14,5 fold), HEY2 (5,0 fold), JAG1 (3,5 fold), CCND1 (5,8 fold), FN1 (-31,1 fold), CEBPA (-9,8 fold), FOXA2 (-4,0 fold), FOXA3 (-2,2 fold), AFP (-7,6 fold), CLDN1 (-8,1 fold), CLDN3 (-2,5 fold), CLDN7 (-7,2 fold), OCLN (-4,2 fold), MUCDH (-2,0 fold), FOXP1 (-3,3 fold) and CDH3 (-3,8 fold).