| HPV16+ versus HPV−
|
lncRNA ‘targets’ |
Oncogenes (N=17) |
BCL2, BCL6, CDH11, CHCHD7, GNAS, JUN, KDSR, MYC, NCKIPSD, PCM1, PDE4DIP, POU5F1, RABEP1, RUNX1T1, SEPT9, TCF12
, TCF3
|
|
|
|
Tumour suppressors (N=5) |
BLM, CDKN2A, PIK3R1, TSC2, XPA
|
|
|
|
Protein kinases (N=22) |
ACVR2A, BMP2K, BMPR1B, CDC42BPB, CDK1, DYRK1A, DYRK1B, EPHB1, HSPB8, MAP2K6, MAP3K9, MAPKAPK5, PDK2, PIK3R4, PXK, RYK, SGK1, STK3, TNK2, ULK1, CDS1, PIK3C3
|
|
|
|
Cell differentiation markers (N=13) |
BMPR1B, CD177, CD83, CDH5, EPCAM, ICOSLG, ITGA3, ITGA4, ITGA6, ITGB1, KLRD1, SIRPG, THBD
|
|
|
|
TFs (N=59) |
ACVR2A, AHR, ARID3B, BCL6, BRD7, CIR1, CITED2, DLX1, DMRTA2, DPF1, EN1, FAM20C, FOXC1, FOXE1, FOXF2, FOXM1, GRHL1, GTPBP1, IKZF2, IKZF3, IRF2, IRX2, JUN, KEAP1, KLF10, KLF11, KLF13, KLF7, MEF2A, MEOX1, MYC, NFIA, NKX2-3, POU5F1, PPARGC1A, PRDM11, PRDM2, PRDM8, RCOR1, RNF13, RNF144A, RUNX1T1, SOX21, SOX4, SOX5, SREBF2, ST18, TCF12, TCF3, TEAD4, TSC22D2, ZBTB25, ZEB2, ZFY, ZNF180, ZNF235, ZNF423, ZNF461, ZNF706
|
|
|
|
RNA-binding proteins (N=35) |
TNPO1, NOL10, RDM1, CAPRIN2, PARN, XRN2, SMNDC1, PUS1, RNASE10, RPP14, FAM46A, CRYZ, CNOT7, LSM14A, LSM14B, EXOSC5, AGO1, AGO3, PPARGC1A, CWC27, LUC7L, TYW5, RAE1, HNRNPD, SMN2, DHX8, RPS4Y1, KRR1, EIF4B, EFTUD1, FRG1B, FRG1, ANGEL1, GTPBP1, MAGOHB
|
|
|
|
Cytokines and growth factors (N=11) |
BMP7, CCL5, CTGF, CXCL14, CXCL17, DKK1, IL16, NRG1, RABEP1, SECTM1, STC2
|
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|
|
|
|
|
|
asRNA ‘targets’ |
Oncogenes (N=8) |
CDK6, CREB1, GATA2, HOXC13, KDSR, KTN1, MLLT6, RPL22
|
|
|
|
Tumour suppressors (N=2) |
FANCA, SOCS1
|
|
|
|
Protein kinases (N=8) |
CAMK4, CDK6, GSG2, MAP4K1, MAPK6, MAST4, PDK1, ZAK
|
|
|
|
Cell differentiation markers (N=9) |
BSG, CD44, ITGA6, ITGAE, ITGB2, NRP1, PROCR, SIRPA, THY1
|
|
|
|
TFs (N=32) |
BRPF3, CORO1A, CREB1, CSRP1, CTCF, FOXA1, FOXD3, GATA2, GTF3C2, GTPBP1, HDAC2, HOXA5, HOXA7, HOXC13, IRX4, KLF11, LSR, MLLT6, NAB1, NRIP1, PAX9, PER3, POU6F2, PRDM6, SATB2, SIM2, SOX15, SPEN, TBX2, ZFY, ZNF131, ZNF337
|
|
|
|
RNA-binding proteins (N=24) |
DHX29, PSPC1, TEFM, SLTM, DDX49, EIF1, INTS8, RBM19, ZCCHC24, MOV10, FXR2, CTU2, EIF2B4, DDX28, MRPL14, CPEB2, SPEN, NOB1, TRNT1, RPL22, GTPBP1, IFIT1, IFIT2, IFIT3, YARS2
|
|
|
|
Cytokines and growth factors (N=8) |
CCL3L3, CCL4L1, CXCL14, FGF1, NAMPT, PTHLH, SEMA6A, UTS2
|
|
|
|
|
|
|
|
pseudogene ‘targets’ |
Oncogenes (N=3) |
NPM1, PDE4DIP, USP6
|
|
|
|
Protein kinases (N=2) |
CAMKK1
|
|
|
|
TFs (N=4) |
GTF2A2, HMGN2, TAF5L, TBC1D10B
|
|
|
|
RNA-binding proteins (N=16) |
RPL37, PSPC1, SNRPD2, RPLP1, GAPDH, RPS24, NUDT16, UBA52, MPHOSPH10, NPM1, POLR2K, MRPL39, FCF1, EIF4H, RPL23, MAGOH
|
|
|
|
Cell differentiation markers (N=1) |
CD8B
|
|
|
|
|
|
| Tumours versus controls |
lncRNA ‘targets’ |
Oncogenes (N=5) |
BCL7A, CD79B, ETV1, ETV6, HMGA1
|
|
|
|
Tumour suppressors (N=1) |
FBXW7
|
|
|
|
Protein kinases (N=5) |
ERN1, GSK3B, MYLK3, RPS6KA5, STK35
|
|
|
|
Cell differentiation markers (N=5) |
CCR7, CD247, CD79B, ICAM2, MME
|
|
|
|
TFs (N=24) |
BANP, BRF1, CREG1, ETV1, ETV6, FOXA1, FOXD1, HES1, HMGA1, HNF4G, HOXD8, MIS18BP1, MLXIP, MSX2, NFE2L3, NR4A1, PKNOX1, SMARCAL1, SP3, TCF4, ZFPM1, ZHX2, ZNF157, ZNF304
|
|
|
|
RNA-binding proteins (N=8) |
RPL14, OASL, ADARB2, PET112, CNOT2, AAR2, ERN1, OBFC1, WDR61
|
|
|
|
Cytokines and growth factors (N=5) |
CCL16, CCL18, CSF3, NTF3, SEMA5A
|
|
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|
|
|
|
|
asRNA ‘targets’ |
Oncogenes (N=4) |
EWSR1, IL6ST, MYH11, RARA
|
|
|
|
Tumour suppressors |
CDKN2A
|
|
|
|
Protein kinases (N=8) |
EPHA2, GUCY2C, IGF1R, LRRK1, MAPK6, PDK1, PDPK1, SNRK
|
|
|
|
Cell differentiation markers (N=9) |
ATP1B3, CD151, IGF1R, IL6ST, ITGA2, ITGA6, MFI2, PVRL2, TNFRSF10B
|
|
|
|
TFs (N=12) |
CASZ1, EGR3, GTPBP1, HOXB7, LBX2, MYBBP1A, RARA, SP2, TBC1D10B, TSHZ2, ZBTB47, ZNF35
|
|
|
|
RNA-binding proteins (N=15) |
FARS2, POLR2B, RBMS3, CWF19L1, NOA1, TARBP2, U2AF2, POLR2L, WARS, LENG9, PTRHD1, HNRNPA1, EWSR1, THOC6, GTPBP1
|
|
|
|
Cytokines and growth factors (N=4) |
BMP8A, FAM3D, IL6ST, S100A6
|
|
|
|
|
|
|
|
pseudogene ‘targets’ |
Oncogenes (N=1) |
PDE4DIP
|
|
|
|
Protein kinases (N=2) |
PAK4, SMG1
|
|
|
|
RNA-binding proteins (N=10) |
RPL37, RPS27A, RPS27, SMAD2, BMS1, SMG1, HNRNPA1, FAM98B, RPL29, RPL35A
|
|
|
|
TFs (N=3) |
BPTF, SMAD2, ZNF461
|
