Table 3. Molecular functionalities associated with TKI-resistant expression profiles.
| Typea | Functional annotationb | Gene size | P-valuec | Genesd |
|---|---|---|---|---|
| Upregulated | GO/ATPase activity, coupled to transmembrane movement of substances | 22 | 1.7E-06 | ABCA8, ABCB1, TAP1, ABCC1, ABCB9, ABCD4 |
| GO/amino-acid transport | 28 | 1.2E-05 | SLC12A7, SLC38A6, XK, SLC38A1, SLC43A1, MGC15523, SLC7A8 | |
| GO/immune response | 163 | 0.0001 | IFITM3, TAP1, IFIH1, TNFRSF9, AIM2, PSMB9, IL18RAP, IFITM2, PSME1, IFI16, IFIT3, CD97, DAF, CNIH, CCL5, ISGF3G, IL18R1, PSME2, MR1, EBI2, TNFSF10, LIF, IKBKE, FCGR2B, ACSL1 | |
| GO/amino-acid-polyamine transporter activity | 23 | 0.0002 | SLC12A7, SLC38A6, SLC38A1, MGC15523, SLC7A8 | |
| GenMAPP/Integrin-mediated cell adhesion | 55 | 0.0005 | FYN, SEPP1, ITGB5, RAP1B, CAPN2, RAC2, CAV1, TLN1, AKT1, ITGA4, CAV2, VCL, PAK1 | |
| GO/cell adhesion | 189 | 0.0006 | CD44, TPBG, MCAM, LAMA4, LAMB1, CD36, ITGB5, CPXM, CD9, TNXB, PTPRF, CD97, SELPLG, CD47, PCDH10, CCL5, IGSF1, PCDH17, FAT, URP2, ITGA4, NELL2, FEZ1, C16orf9, VCL, PKP2, CASK | |
| GenMAPP/Smooth_muscle_contraction | 81 | 0.0007 | RGS20, PRKCH, IGFBP4, TNXB, ADM, ITPR2, PRKCZ, GSTO1, CREB3, ACTA2, GJA1, NOS3, ATF5, ATP2A3, NFKB1 | |
| GO/non-membrane spanning protein tyrosine kinase activity | 11 | 0.0009 | SYK, FYN | |
| Downregulated | GO/sterol biosynthesis | 19 | 0.0002 | FDFT1, SC4MOL, NSDHL, MVK, HMGCR, IDI1, CYP51A1, DHCR24, SC5DL |
| GenMAPP/Cholesterol_Biosynthesis | 14 | 0.0003 | FDFT1, SC4MOL, NSDHL, MVK, HMGCR, IDI1, LSS, CYP51A1, SC5DL | |
| GO/steroid biosynthesis | 30 | 0.0003 | HSD17B7, HSD17B8, FDFT1, SC4MOL, HSD17B1, NSDHL, MVK, HMGCR, IDI1, LSS, CYP51A1, DHCR24, SC5DL | |
| GO/cholesterol biosynthesis | 16 | 0.0006 | FDFT1, NSDHL, MVK, HMGCR, IDI1, CYP51A1, DHCR24 |
Abbreviation: TKI, tyrosine kinase inhibitors.
a
The signatures were distinguished for upregulated and downregulated gene sets in TKI-resistant sublines.
b
Three databases (GO, KEGG and GenMAPP) used to collect the gene sets are denoted in the respective gene sets.
c
The significance for enrichment is calculated using parametric gene set enrichment analysis algorithm based on z-statistics, and unadjusted P<0.10 was considered significance.
d
Among the genes belonging to the gene set, the ‘leading edge subset' are listed for genes whose corresponding signal-to-noise ratio is above mean+s.d. (upregulated) or below mean−s.d. (downregulated).