PCR Array plate design and layout

PCR Array Plate layout:

PCR array 1,2,3 plate layout.png

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
--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