Gene Sets for qPCR

Suggested gene lists for some commonly studied pathways for human mouse and rat species are provided. Gene lists for additional human signaling pathways (Notch, TLR , WNT, etc.), biochemical pathways, and genes that have been associated with certain cancers, can be found as a Microsoft Excel file under Extended Gene Set List.

Copy and paste desired genes or gene sets into the search box of the PrimeTime Plates ordering tool to generate the required assays.

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Human

ACTB, B2M, GAPDH, GUSB, HMBS, HPRT1, IPO8, PGK1, POLR2A, PPIA, RN18S1, RPLP0, TBP, TFRC, UBC, YWHAZ

Mouse

ACTB, B2M, GAPDH, GUSB, HMBS, HPRT, IPO8, PGK1, POLR2A, PPIA, RPLP2, TBP, TFRC, UBC, YWHAZ

Rat

ACTB,B2M,GAPDH,GUSB,HMBS,HPRT,IPO8,PGK1,POLR2A,PPIA,RPLP2,TBP,TFRC,UBC,YWHAZ

Housekeeping

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Human

AKT1, APAF1, BAD, BAG3, BAK1, BAX, BCL10, BCL2, BCL2A1, BCL2L1, BCL2L10, BCL2L11, BCL2L2, BFAR, BID, BIK, BIRC3, BIRC6, BNIP3, BNIP3L, BRAF, CASP1, CASP10, CASP14, CASP2, CASP3, CASP4, CASP6, CASP8, CASP9, CD27, CD40LG, CD70, CFLAR, CYCS, DAPK1, DFFA, FADD, FAS, FASLG, HRK, IGF1, IGF1R, IL1B, LTA, MCL1, NAIP, NFKB1, NGF, NGFR, NOD1, NOL3, PYCARD, TNF, TNFRSF10A, TNFRSF10B, TNFRSF9, TNFSF10, TNFSF8, TP53, TP53BP2, TRADD, TRAF2, XIAP

Mouse

BAK1, BAX, BCL10, BCL2L11, BID, BOK, CASP1, CASP12, CASP14, CASP2, CASP3, CASP6, CASP8, CASP8AP2, CIDEB, DAPK1, DFFA, DFFB, DIABLO, FADD, FAS, MAPK1, PYCARD, TNF, TNFRSF10B

Rat

BAK1, BAX, BCL10, BCL2L11, BID, BOK, CASP1, CASP12, CASP14, CASP2, CASP3, CASP6, CASP8, CASP8AP2, CIDEB, DAPK1, DFFA, DFFB, DIABLO, FADD, FAS, MAPK1, PYCARD, TNF, TNFRSF10B

Apoptosis

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Human

ANGPT1, ANGPT2, ANGPTL4, CDH5, COL18A1, COL4A3, CTGF, F3, FGF1, FLT1, FN1, HGF, IL8, ITGAV, ITGB3, KDR, LEP, MDK, MMP2, NRP1, NRP2, PECAM1, PF4, PLG, PROK2, S1PR1, SERPINE1, SERPINF1, TGFA, TGFB1, THBS2, TIE1, TIMP3, TNF, TYMP, VEGFA

Mouse

ANG, ANGPT1, ANGPT2, ANPEP, BAI1, COL18A1, COL4A3, CTGF, ENG, F3, FGF1, FGF2, FGF6, FGFR3, FIGF, FLT1, ITGAV, ITGB3, JAG1, KDR, MAPK14, MMP19, NOS3, NRP1, NRP2, PGF, SERPINE1, SERPINF1, SPHK1, TEK, THBS1, VEGFA, VEGFB, VEGFC

Rat

ANG, ANGPT1, ANGPT2, ANPEP, BAI1, COL18A1, COL4A3, CTGF, ENG, F3, FGF1, FGF2, FGF6, FGFR3, FIGF, FLT1, ITGAV, ITGB3, JAG1, KDR, MAPK14, MMP19, NOS3, NRP1, NRP2, PGF, SERPINE1, SERPINF1, SPHK1, TEK, THBS1, VEGFA, VEGFB, VEGFC

Angiogenesis

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Human

CCL1, CCL13, CCL17, CCL19, CCL20, CCL21, CCL22, CCL24, CCL3, CCL5, CCL7, CCL8, CX3CL1, CXCL1, CXCL10, CXCL11, CXCL12, CXCL16, CXCL5, CXCL9, PF4, PPBP, XCL1

Mouse

CCL1, CCL11, CCL17, CCL2, CCL20, CCL22, CCL24, CCL3, CCL4, CCL5, CCL7, CX3CL1, CXCL1, CXCL10, CXCL11, CXCL12, CXCL13, CXCL16, CXCL5, CXCL9, XCL1

Rat

CCL1, CCL11, CCL17, CCL2, CCL20, CCL22, CCL24, CCL3, CCL4, CCL5, CCL7, CX3CL1, CXCL1, CXCL10, CXCL11, CXCL12, CXCL13, CXCL16, CXCL5, CXCL9, XCL1

Chemokines

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Human

ATM, ATR, CCNA1, CCNA2, CCNB1, CCNB2, CCND1, CCND2, CCND3, CCNE1, CCNE2, CCNH, CDC25A, CDK1, CDK2, CDK4, CDK6, CDKN1A, CDKN2A, CDKN2B, CDKN2C, CDKN2D, E2F4, RB1, TGFB1, TP53

Cyclins

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Human

CD40LG, CD70, FASLG, IFNA1, IFNA2, IFNA6, IFNA7, IFNA8, IFNB1, IFNG, IL10, IL12A, IL12B, IL13, IL15, IL16, IL17A, IL18, IL1A, IL1B, IL2, IL3, IL4, IL5, IL6, IL8, IL9, LTA, LTB, TNF, TNFRSF11B, TNFSF10, TNFSF11, TNFSF12, TNFSF13, TNFSF13B, TNFSF14, TNFSF4, TNFSF8

Mouse

CD40LG, CD70, FASL, IL10, IL11, IL12B, IL13, IL15, IL16, IL17A, IL17B, IL17C, IL17F, IL18, IL19, IL1A, IL1B, IL1RN, IL2, IL20, IL21, IL23A, IL25, IL27, IL3, IL4, IL5, IL6, IL7, IL9, LTA, LTB, TNF, TNFRSF11B, TNFSF11, TNFSF12, TNFSF13, TNFSF13B, TNFSF14, TNFSF15, TNFSF18, TNFSF4, TNFSF8, TNFSF9, TXLNA

Rat

CD40LG, CD70, FASL, IL10, IL11, IL12B, IL13, IL15, IL16, IL17A, IL17B, IL17C, IL17F, IL18, IL19, IL1A, IL1B, IL1RN, IL2, IL20, IL21, IL23A, IL25, IL27, IL3, IL4, IL5, IL6, IL7, IL9, LTA, LTB, TNF, TNFRSF11B, TNFSF11, TNFSF12, TNFSF13, TNFSF13B, TNFSF14, TNFSF15, TNFSF18, TNFSF4, TNFSF8, TNFSF9, TXLNA

Cytokines

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Human

BMP1, BMP2, BMP3, BMP4, BMP5, BMP6, BMP7, CNTF, CSF1, CSF2, CSF3, FIGF, GDF2, GDF5, GDF9, INHA, LEFTY2, LIF, MSTN, NODAL, OSM, PDGFA, TGFA, TGFB1, TGFB2, TGFB3, THPO, VEGFA

Mouse

BMP1, BMP3, BMP5, BMP6, BMP7, CD40LG, CD70, CNTF, CSF1, CSF2, CSF3, FASL, FGF10, GDF2, GDF5, GDF9, GREM1, INHA, INHBA, LEFTY1, LIF, LTA, LTB, MSTN, OSM, TGFB1, TGFB2, THPO, TNF, TNFRSF11B, TNFSF11, TNFSF12, TNFSF13, TNFSF13B, TNFSF14, TNFSF15, TNFSF18, TNFSF4, TNFSF8, TNFSF9, VEGFA

Rat

BMP1, BMP3, BMP5, BMP6, BMP7, CD40LG, CD70, CNTF, CSF1, CSF2, CSF3, FASL, FGF10, GDF2, GDF5, GDF9, GREM1, INHA, INHBA, LEFTY1, LIF, LTA, LTB, MSTN, OSM, TGFB1, TGFB2, THPO, TNF, TNFRSF11B, TNFSF11, TNFSF12, TNFSF13, TNFSF13B, TNFSF14, TNFSF15, TNFSF18, TNFSF4, TNFSF8, TNFSF9, VEGFA

Growth Factors

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Human

ARAF, BRAF, CREB1, GRB2, HRAS, KRAS, MAP2K1, MAP2K2, MAP2K4, MAP2K7, MAP4K1, MAPK13, MAPKAPK2, MAPKAPK3, MEF2C, MKNK1, MST1, MYC, NRAS, PAK1, RAC1, RAF1, TP53

Mouse

ARAF, ATF2, CDC42, CHUK, CREB1, CREBBP, DLK1, EGFR, ETS1, ETS2, GRB2, JUN, KCNN1, KRAS, MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K5, MAP2K6, MAP2K7, MAP3K1, MAP3K3, MAP3K4, MAP4K1, MAPK1, MAPK10, MAPK13, MAPK14, MAPK3, MAPK6, MAPK7, MAPK8, MAPK9, MAPKAPK2, MAX, MEF2C, MKNK1, MYC, NFATC4, NRAS, PAK1, RAC1, RAF1, SMAD4

Rat

ARAF, ATF2, CDC42, CHUK, CREB1, CREBBP, DLK1, EGFR, ETS1, ETS2, GRB2, JUN, KCNN1, KRAS, MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K5, MAP2K6, MAP2K7, MAP3K1, MAP3K3, MAP3K4, MAP4K1, MAPK1, MAPK10, MAPK13, MAPK14, MAPK3, MAPK6, MAPK7, MAPK8, MAPK9, MAPKAPK2, MAX, MEF2C, MKNK1, MYC, NFATC4, NRAS, PAK1, RAC1, RAF1, SMAD4

MAP Kinase

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Human

DDR2, EPHA2, EPHA3, EPHA4, EPHA5, EPHA7, EPHA8, EPHB2, EPHB4, EPHB6, ERBB3, ERBB4, FGFR2, FGFR3, FGFR4, FLT3, INSR, INSRR, LTK, MERTK, MST1R, NTRK2, NTRK3, PDGFRB, PTK7, RET, ROS1, RYK, TYRO3

Mouse

ALK, AXL, DDR1, DDR2, EGFR, EPHA1, EPHA2, EPHA3, EPHA4, EPHA5, EPHA7, EPHA8, EPHB1, EPHB2, EPHB3, EPHB6, ERBB3, ERBB4, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, IGF1R, IGF2R, INSR, INSRR, LTK, MERTK, PDGFRA, PDGFRB, ROR1, ROR2, TIE1, TYRO3

Rat

ALK, AXL, DDR1, DDR2, EGFR, EPHA1, EPHA2, EPHA3, EPHA4, EPHA5, EPHA7, EPHA8, EPHB1, EPHB2, EPHB3, EPHB6, ERBB3, ERBB4, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, IGF1R, IGF2R, INSR, INSRR, LTK, MERTK, PDGFRA, PDGFRB, ROR1, ROR2, TIE1, TYRO3

Protein Tyrosine Kinases

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Human

APC, CXCR4, EWSR1, HTATIP2, IGF1, IL18, IL1B, ITGA7, KRAS, MYC, NF2, NME1, NME2, NR4A3, RB1, RORB, SSTR2, SYK, TGFB1, TIMP3, TNFSF10, TP53, TSHR, VEGFA

Mouse

APC, BRMS1, CCL7, CDKN2A, CHD4, CSF1, CTBP1, CXCR4, HRAS1, HTATIP2, IGF1, IL18, IL1B, ITGA7, KISS1, KISS1R, KRAS, MCAM, MDM2, MET, MYC, MYCL1, NF2, NME1, NME2, NME4, NR4A3, PLAUR, PNN, PTEN, RB1, RORB, SET, SMAD2, SMAD4, SRC, SSTR2, SYK, TCF20, TGFB1, TIMP3, TRP53, TSHR, VEGFA

Rat

APC, BRMS1, CCL7, CDKN2A, CHD4, CSF1, CTBP1, CXCR4, HRAS1, HTATIP2, IGF1, IL18, IL1B, ITGA7, KISS1, KISS1R, KRAS, MCAM, MDM2, MET, MYC, MYCL1, NF2, NME1, NME2, NME4, NR4A3, PLAUR, PNN, PTEN, RB1, RORB, SET, SMAD2, SMAD4, SRC, SSTR2, SYK, TCF20, TGFB1, TIMP3, TRP53, TSHR, VEGFA

Tumor Metastasis

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Gene lists for additional signaling pathways (Notch, TLR , WNT, etc.), biochemical pathways, and genes that have been associated with certain cancers are available in Extended Human Target Gene List, a subset of data downloaded from the Broad Institute Molecular Signatures Database (MSigDB) [1], Version 3.1, September 2012.


References

  1. Subramanian A, Tamayo P, et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA, 102(43):15545–15550.

Extended Gene Set List