Upload 17 files

.gitattributes

@@ -60,3 +60,8 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 hnscc_data/41698_2024_602_MOESM3_ESM.xlsx filter=lfs diff=lfs merge=lfs -text
 hnscc_data/common_genes.23037.sCNV.TCGA.hpvN.scaled.csv filter=lfs diff=lfs merge=lfs -text
 processed_data/combat_corrected_expression_transpose.csv filter=lfs diff=lfs merge=lfs -text
+processed_data/cptac.DGE.msp1_vs_msp2.csv filter=lfs diff=lfs merge=lfs -text
+processed_data/cptac.GE.18094G.csv filter=lfs diff=lfs merge=lfs -text
+processed_data/tcga.95P.1508G.csv filter=lfs diff=lfs merge=lfs -text
+processed_data/tcga.DGE.msp1_vs_msp2.csv filter=lfs diff=lfs merge=lfs -text
+processed_data/tcga.GE.18094G.csv filter=lfs diff=lfs merge=lfs -text

processed_data/cptac.DGE.msp1_vs_msp2.csv

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processed_data/cptac.GE.18094G.csv

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processed_data/hpvN_cptac_PatientID.txt

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processed_data/hpvN_tcga_PatientID.txt

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processed_data/significant_genes_adj_pval_lt_0.05.txt

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+IGKV4-1
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+ADCY10P1
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+CHMP1A
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+RPE
+TAB2
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+DUSP23
+RAB5A
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+PPCS
+OSR1
+BLMH
+ZNF589
+TLCD2
+CRACR2B
+VRK1
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+PAQR3
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+ALDH6A1
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+RADX
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+USP34-DT
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+C1GALT1C1
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+C1orf74
+GPRIN2
+SNCA
+ARFGEF1
+AHSA2P
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+POLA1
+RCN1
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+SPTAN1
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+GEMIN7
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+PRKCQ
+CCDC149
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+CDR2
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+SP140
+GTF2IP4
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+NECTIN1-DT
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+NUBPL
+SNRPC
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+SNHG21
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+WRN
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+ARHGEF26
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+NXT1
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+F2RL3
+PLPP7
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+SLC19A2
+TC2N
+SNHG14
+DUSP10
+BECN1
+PYGO1
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+EVA1B
+SH3BGRL
+PI4KAP1
+LGALS3
+DIS3L2
+NEURL4
+ATP9A
+UCP2
+EHD2
+HLA-L
+DYNC1LI2
+HLA-A
+CORO1C
+C6orf62
+CEP19
+TMEM108
+SRSF7
+RIF1
+BET1
+COG7
+ADNP
+CUTA
+SFRP4
+FANCL
+INSYN1
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+PDK4
+KANSL3
+CYP2R1
+RPL10P16
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+LRRC23
+ARAP1
+PPP1R13B
+ENOX2
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+ZNF710
+AAAS
+ERVK3-1
+ATP8B3
+LINC01569
+RABGAP1L
+PTCH1
+WDTC1
+EBNA1BP2
+HSPA7
+C16orf46
+ZNF792
+EXOC7
+PLEKHM2
+USP13
+GEMIN4
+RANBP9
+RAB7A
+CDK5RAP2
+KLC2
+ZNF644
+A1BG-AS1
+C1orf122
+ALMS1
+FAN1
+C1orf50
+LCLAT1
+AGPAT2
+NUMB
+C12orf54
+ABCD4
+STON1
+GADD45B
+TMED1
+FBXL19
+FAM174B
+CEP250
+MAP3K14-AS1
+RASSF1
+UVRAG
+ZNF678
+SREBF2-AS1
+LINC00665
+CA5B
+PTDSS1
+SIPA1L2
+ADGRG6
+PLPP6
+TBRG1
+ZNRD1ASP
+EIF5AL1
+IGLL5
+UBL7-DT
+ARPC5L
+LLPH
+EOMES
+HDAC5
+ZNF775
+HDAC3
+MRPL45P2
+MAPK8IP3
+CSTF2
+RNMT
+GLUL
+HTRA2
+DHX58
+CCDC107
+ASL
+P2RX5
+PLEKHA4
+CEACAM19
+LNPK
+ITPKC
+ZNF283
+EEF1DP1
+SPRR2G
+ZNF69
+PORCN
+FAM78B
+ATP2C2-AS1
+RASSF5
+KLHL15
+KIF22
+HYKK
+RBM48
+MED7
+OAS2
+PKN3
+ARHGAP32

processed_data/survival_associated_genes.txt

@@ -0,0 +1,570 @@
+ABCE1
+ACAP3
+ADI1
+AHCTF1
+AHCYL2
+AKAP1
+ALDH1A1
+AP1AR
+ARHGAP12
+ARMCX3
+AS3MT
+ASXL2
+ATAD1
+ATP5S
+ATP6V0D1
+BCLAF1
+BEND3
+BMP2K
+BPGM
+BRD2
+C15orf40
+C2orf49
+C5orf22
+C8orf82
+CAP1
+CAPG
+CAPN5
+CAPNS2
+CARHSP1
+CBX8
+CCAR1
+CCAR2
+CCDC90B
+CCNDBP1
+CDC40
+CDC5L
+CDK19
+CDK2AP1
+CHAMP1
+CHCHD1
+CHD4
+CHD9
+CHTOP
+CLEC16A
+CLP1
+CLPP
+COIL
+COMMD1
+COMMD10
+CPD
+CPOX
+CPSF1
+CSNK2B
+CSTB
+CWC15
+CXorf57
+DCTN5
+DDX54
+DHX35
+DNAJC21
+DNASE2
+DSG2
+EBNA1BP2
+ELL2
+EMSY
+ENDOU
+ERH
+FAM114A2
+FAM32A
+FAM89B
+FBN2
+FOXK2
+FRK
+FUBP3
+GAB1
+GABPB2
+GGCT
+GNA11
+GPALPP1
+GPATCH1
+GSPT1
+GTF2F1
+GTF2F2
+HCFC1
+HDAC3
+HDGFL2
+HELZ
+HMOX2
+HNRNPA0
+HNRNPL
+HNRNPLL
+HNRNPM
+HOPX
+HSD17B4
+HSPB1
+IL1RN
+IL36G
+ILF3
+INIP
+INSR
+INTS1
+INTS12
+INTS2
+INTS4
+INTS6
+INTS7
+INTS8
+ITGA1
+JUND
+KHSRP
+KIFC1
+KLC3
+KPNA6
+KRT18
+KRT6B
+KRT6C
+LCE3D
+LDLRAP1
+LMBRD2
+LMNB2
+LUC7L2
+LUC7L3
+LYPD3
+MAD1L1
+MAPK14
+MAU2
+MCUR1
+MDC1
+MED12
+MED16
+MED28
+METRNL
+MFAP1
+MGST1
+MIPEP
+MRPL17
+MRPL41
+MRPL58
+MRPS12
+MRPS30
+MTUS1
+NACC1
+NADK2
+NAGK
+NARS2
+NDUFAF4
+NDUFAF7
+NDUFAF8
+NEPRO
+NIPBL
+NOL7
+NOP58
+NPEPPS
+NR2F2
+NRBP2
+NUBP1
+NUDT19
+NUP107
+NUP153
+NUP98
+NXN
+OXCT1
+OXSR1
+PAIP1
+PAK1IP1
+PCF11
+PCNP
+PDPK1
+PDS5B
+PHF2
+PHF3
+PLCB3
+PLCD4
+PLCG1
+PLEK
+PLEKHG5
+POLR1D
+POLR2E
+PQBP1
+PRCP
+PRKDC
+PRPF3
+PRPF38A
+PRPF4B
+PRPF8
+PSMB4
+PTPRK
+PUM2
+PUS1
+R3HDM1
+RAB3IL1
+RAI1
+RANBP2
+RANBP3
+RAVER1
+RBM14
+RBM26
+RECQL
+RELT
+RNASEH2A
+RNASEH2B
+RNASEH2C
+RNASET2
+RRS1
+RSF1
+RSRC2
+S100A8
+S100A9
+SAFB
+SFN
+SIRT5
+SMC1A
+SMC3
+SNRNP40
+SNX15
+SNX29
+SP140
+SRA1
+SRSF2
+SRSF3
+SRSF7
+SRSF9
+STAG2
+STEAP3
+STEAP4
+TACO1
+TASP1
+TCEA1
+TDRD3
+TIMM50
+TIMM8A
+TLK2
+TMEM154
+TMEM159
+TMEM181
+TMEM258
+TNIP1
+TOP3A
+TOP3B
+TPR
+TSPAN3
+TTC19
+UTP6
+VGLL4
+WBP11
+WDR33
+WDR5
+WRN
+WRNIP1
+XPO4
+ZC3H4
+ZFR
+ZMYND8
+ZNF185
+ZNF292
+ZNF318
+ZNF326
+ZNF330
+ZNF512
+ZNF512B
+ZNF598
+ZNF672
+ZRANB2
+ALKBH3
+AP1G1
+APPBP2
+ARID1A
+BTF3L4
+C2orf76
+CALHM6
+CDK13
+CLIC3
+CLPB
+COA5
+COA6
+CSAD
+DEFB103A
+DERL3
+DPYSL4
+DYNC1LI2
+EIF4E
+ENG
+ENTPD7
+EXOC3
+EXOC4
+EXOC6B
+FAM160B2
+FGGY
+FKBP5
+FUOM
+FZR1
+GSKIP
+GSTT1
+GTF2IRD1
+HIST3H2BB
+KANK1
+KBTBD2
+KIF13A
+KRT75
+LCE3A
+LRRC17
+LY75-CD302
+LYNX1-SLURP2
+MCM3AP
+MCMBP
+MOB4
+MTMR3
+NACAD
+NDE1
+NDRG4
+NEK3
+NOC3L
+NOP16
+NRBP1
+NRK
+NUP58
+PANK3
+PAXBP1
+PET100
+PLA2R1
+POM121C
+PPP1R11
+PSMC3
+PSMC6
+RABGAP1
+RNF144A
+RPL23
+RPL37
+RPL9
+RPS15A
+RRN3
+RRP1B
+SAR1A
+SAR1B
+SCFD1
+SCYL3
+SH3RF2
+SLPI
+SPART
+SRP72
+STARD5
+STRN
+STXBP1
+TANK
+TDRD5
+TRHDE
+UBXN2A
+ULK1
+VPS13D
+VPS26A
+ADGRL1
+ADNP
+AHNAK2
+ANXA2
+AP3B2
+ARHGAP23
+ARHGEF1
+ATG2A
+BAZ2B
+BBX
+BCL7A
+BCLAF3
+BPTF
+C1orf198
+CAAP1
+CALML3
+CBX6
+CCDC130
+CCDC86
+CD44
+CDH3
+CKAP2
+CPSF2
+CPSF6
+CRMP1
+CRYBG2
+CTPS2
+CUL9
+CYB5B
+DDX42
+DDX51
+DDX60
+DIDO1
+DPH2
+EIF4G1
+ELOA
+EP300
+EVPL
+FAM122B
+FANCD2
+FBLN1
+FCHO2
+GALNT11
+GDAP1
+GPHN
+HDAC2
+HEATR3
+HNRNPDL
+HP1BP3
+INTS5
+IRS2
+IWS1
+KCTD5
+KDM6A
+KMT2A
+KRIT1
+LGALS7B
+LUZP1
+LZTS3
+MAFG
+MAP1S
+MAPK3
+MARK4
+MAVS
+MED15
+MLX
+MORC4
+MTFR1L
+N4BP1
+NCF2
+NIPAL4
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processed_data/survival_cptac.csv

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processed_data/survival_tcga.csv

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