PCR Array plate design and layout

Introduction

PCR Array Plate layout:

PCR Array plates design for Ten cancer hallmarks and target genes:

Array #	Cancer Hallmark Pathways	Census Cancer Genes
Array #1	Sustaining Proliferative Signaling
	--MAP kinase pathway	MAP2K1, MAP2K2
	--PI3K/AKT signaling	AKT1, AKT2, MTCP1, PIK3CA, PIK3R1, PTEN, TCL1A
	--RAS signaling	JUN, FOS
	--PTEN signaling	AKT1, CDKN1B, FOXO3, PTEN
	mTOR pathways	AKT1, PTEN, TSC1, TSC2
	--Evading Growth Suppressors
	p53 Signaling Pathway
	--p53 Activation	TP53, ATM, ATR, BRCA1, CDKN2A, CHEK2, FOXO3, MDM2, MSH2
	--p53 Targets for apotosis	EGFR, ESR1, FAS, TP53
	RB1 Signaling Pathway
	--RB1 Activation	CCNE1, CDK4, CDK4, CCND2, CCND3, CCND1
	--RB1 downstream targets for cell cycle arrest	RB1, MDM2
	TGFB signaling pathway	EP300
	LKB1 signaling pathways	STK11
	NF2 Contact Inhibition	NF2, TAZ, YAP1
	Resisting Cell Death
	--Pro-Apoptotic	ABL1, CYLD, FAS, TP53
	--Anti-Apoptotic	AKT1, BCL2, BIRC3
	--Death Domain Receptors	CRADD, DAPK1, FADD, TRADD
Array #2	--Autophagy	AKT1, BCL2, ESR1, FAS, TP53
	--Necrosis	CYLD
	--Caspases	CASP8
	--Caspase Activation	TP53
	--Caspase Inhibition	CD27, XIAP
	Enabling Replicative Immortality
	--Senescence Pathway	ATM, CCND1, CCNE1, CDK4, CDK6, CDKN2A, CHEK2, MDM2, RB1, TP53
	--p53 / pRb Signaling & the Cell Cycle	ABl1, AKT1, CDKN2C, MYC, PIK3CA
	--Telomere Maintenance	BLM, ERCC4, MYC, NBN, POT1, TERT
	--Telomerase Regulation	ABL1, AKT1, BCL2, KRAS, MEN1, MYC, PAX8, PPARG, PPP2R1A, RB1, TP53
	--Telomere-Associated Complexes	POT1, TERF2, TERT, ERCC4, MSH2, TERF2
	--Other Telomere-Associated Genes	ATM, CHEK2, HNRNPA2B1, HSP90AA1
	Inducing Angiogenesis
	--Growth Factors & Receptors	KDR
	--AKT & PI3 Kinase Signaling	AKT1, AKT2, PIK3CA, PIK3R1
	--Small G-Protein Signaling	HRAS, KRAS, NRAS, RAC1, RAF1
	--Inhibition of Angiogenesis by TSP1	JUN
	--MAP Kinase Signaling	MAP2K1, MAP2K2
	--NFAT Signaling	NFATC2
	--Angiogenesis Transcription Factors	ARNT, NFATC2
	Activating Invasion and Metastasis
	--JAK-STAT signaling	JAK1, JAK3, STAT3, STAT5B, STAT6, PTPN11, PTPRC, GATA2, SOCS1, SMAD4, FAS
	--MAPK pathway	MAP2K1, MAP2K2
	--Wnt signaling pathway	APC, AXIN1, AXIN2, BCL9, CTNNB1, WIF1, AXIN2, CCND1, CCND2, JUN, MYC
Array #3	--Cell Adhesion Molecules	APC, CDH1, CDH11, ITGA7, SYK, ITGA7
	Extracellular Matrix Molecules
	--Regulation of the Cell Cycle	APC, CDKN2A, HRAS, KRAS, NF2, PTEN, RB1, TP53
	--Negative Regulation of Cell Proliferation	CDKN2A, MDM2, NF2
	--Positive Regulation of Cell Proliferation	TSHR
	--Transcription Factors & Regulators	ETV4, EWSR1, MYC, MYCL, NR4A3, RB1, SMAD4, TP53
	Deregulating cellular energetics
	--TCA Cycle	FH, IDH1, IDH2, SDHB, SDHC, SDHD
	--HIF1 & Co-Transcription Factors	ARNT, NCOA1, PER1, TP53
	--MYC & Co-Transcription Factors	MAX, MYCL, MYCN
	Avoiding immune destruction
	--Innate Immunity	HLA-A, MYD88
	--Th2 Markers & Immune Response	GATA3, STAT6
	--Th17 Markers:	STAT3
	--Cytokines	IL2
	--Other Adaptive Immunity Genes:	HLA-A, JAK2
	--Defense Response to Bacteria	MYD88
	--Defense Response to Viruses	HLA-A
	Tumor promoting inflammation
	--Inflammatory Response	STAT3
	--Pro-Inflammatory Genes	IL2
	--Antigen Presentation	HLA-A
	--Interferon-Responsive Genes	MYD88
	--Chemokine Receptors	ACKR3
	--Interleukins	IL2
	--STAT Targets	MYC
	Genome instability & mutation
	--ATM / ATR Signaling	ATM, ATR, BRCA1, CHEK2, FANCD2, TP53
	--Nucleotide Excision Repair	DDB2, ERCC2, TP53, XPA, XPC
	--Base Excision Repair	TP53
	--Mismatch Repair	ABL1, MLH1, MSH2, PMS1, PMS2
	--Double-Strand Break Repair	ATM, BLM, BRCA1, MLH1, NBN
	--Other DNA Repair Genes	ATR, ATRX, BRIP1, CHEK2, FANCA, FANCD2, FANCG, RAD21, RAD51B