Table 1. nCounter custom codeset.
| nCounter custom codeset | |
|---|---|
| FUNCTIONAL ANNOTATION | GENES |
| ACETYLATION | ACSL1, ASS1, DNMT1, EEF2, EIF4G1, GNAQ, SMARCA4, TNPO2, TOP2A, XPOT |
| CELL ADHESION | BMP1, CD44, CDH1, CDH11, CLDN15, COL16A1, CTNNA1, CXADR, EGFR, FN1, ITGA3, ITGA4, ITGA5, ITGA7, ITGAM, ITGB4, LAMA3, LAMC1, LGALS3BP, MSLN, NME2, PECAM1, SELE, THBS2, VWF |
| CELL CYCLE | AURKA, BIRC5, BUB1, CCNB1, CCNB2, CCNO, CDK1, CDK4, CDK7, CDKN2A, CDKN2B, CENPF, CHEK1, EGFR, FANCI, MAD2L1, MCM2, MCM4, MK167, NDC80, PCNA, PLK1, PLK2, RAD21, TACC1, TUBB2B |
| DNA MODIFICATOR | DNMT1, DNMT3 |
| ECM RECEPTOR INTERACTION | CD44, COL1A1, COL4A2, FN1, ITGA3, ITGA4, ITGA5, ITGA7, ITGB4, LAMA3, LAMC1, SOD1, THBS2, VWF |
| EXTRACELLULAR MATRIX | ADAMTS8, CD44, COL16A1, COL1A1, COL4A2, FN1, HEG1, LAMA3, LAMC1, LGALS3, LGALS3BP, MMP1, MMP10, MMP12, MMP14, MMP3, MMP7, MMP9, SFRP1, SOD1, TIMP3, VEGFA, VWF |
| FOCAL ADHESION | CAV1, COL1A1, COL4A2, EGFR, FN1, ITGA3, ITGA4, ITGA5, ITGA7, ITGB4, LAMA3, LAMC1, PAK4, PDGFRB, PIK3CA, THBS2, VEGFA, VWF |
| INTRACELLULAR NON MEMBRANE BOUNDED ORGANELLE | DNMT3A, DSP, JUNB, MICAL2, MYH11, SMARCA4, TERT, TOP2A, TPPP |
| METAL ION BINDING | GALNT7, PKM2, PTGIS, SDHB |
| NUCLEOTIDE BINDING | ACSL1, ADCY4, ASS1, EEF2, EGR3, EMX2, GNAQ, JUNB, MYH11, PPARA, SMARCA4, TERT, TOP2A, UBE2T |
| NUCLEUS | DNMT3A, DNTM1, EGR3, EMX2, JUNB, PPARA, SMARCA4, TERT, TNPO2, TOP2A, TPPP, XPOT |
| PATHWAYS IN CANCER | BIRC5, CDH1, CDKN2A, CDKN2B, COL4A2, CTNNA1, EGFR, FGF2, FN1, GLI1, GLI2, ITGA3, LAMA3, LAMP1, MMP1, MMP9, PDGFRB, PIK3CA, PTGS2, TGFBR2, VEGFA |
| REGULATION OF CELL PROLIFERATION | ADAMTS8, BAP1, CAV1, CD274, CDK4, CDKN2A, CDKN2B, CHEK1, CXADR, EGFR, ESR2, FGF2, GLI1, GLI2, IFITM1, JAG1, KRT5, LAMC1, MAGED1, MMP12, MMP7, NF2, NME2, NOTCH1, PDGFRB, PTGS2, SERPINE1, TGFR2, VEGFA |
| SIGNALING | ADAMTS8, BMP1, CD274, CD44, CDH1, CDH11, CFB, COL16A1, COL1A1, COL4A2, CXADR, EGFR, FN1, HEG1, ITGA3, ITGA4, ITGA5, ITGA7, ITGAM, ITGB4, JAG1, LAMA3, LAMC1, LGALS3BP, MMP1, MMP10, MMP14, MMP3, MMP7, MMP9, MSLN, NMU, NOTCH1, PAPPA, PDCD1, PDGFRB, PECAM1, SDC1, SELE, SERPINE1, SULF1, THBS2, TIMP3, VEGFA, VWF |
| REFERENCE GENES | CLTC, GAPDH, GUSB, HPRT1, PGK1, TUBB |
Genes included in the nanoString custom panel. Functional annotation of the selected genes was obtained from the Database for Annotation, Visualization and Integrated Discovery (DAVID-david.ncifcrf.gov).