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Add MT and WT percentiles to the aggregate report
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@susannasiebert
susannasiebert committed Apr 13, 2020
1 parent 19e8226 commit f26db43
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Showing 9 changed files with 13,489 additions and 13,485 deletions.
6 changes: 5 additions & 1 deletion lib/aggregate_all_epitopes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -114,6 +114,8 @@ def get_best_mut_line(self, df, hla_types, vaf_clonal, max_ic50=1000):
'Num_Peptides': [peptide_count],
'ic50_MT': [best["Median Score"]],
'ic50_WT': ["NA"],
'percentile_MT': [best["Median Percentile"]],
'percentile_WT': ["NA"],
'RNA_expr': ["NA"],
'RNA_VAF': ["NA"],
'RNA_Depth': ["NA"],
Expand All @@ -130,6 +132,8 @@ def get_best_mut_line(self, df, hla_types, vaf_clonal, max_ic50=1000):
'Num_Peptides': [peptide_count],
'ic50_MT': [best["Median MT Score"]],
'ic50_WT': [best["Median WT Score"]],
'percentile_MT': [best["Median MT Percentile"]],
'percentile_WT': [best["Median WT Percentile"]],
'RNA_expr': [best["Gene Expression"]],
'RNA_VAF': [best["Tumor RNA VAF"]],
'RNA_Depth': [best["Tumor RNA Depth"]],
Expand Down Expand Up @@ -190,7 +194,7 @@ def execute(self):
keys = df["key"].unique()

columns = hla_types.tolist()
columns.extend(['Gene', 'AA_change', 'Num_Transcript', 'Peptide', 'Pos', 'Num_Peptides', 'ic50_MT', 'ic50_WT', 'RNA_expr', 'RNA_VAF', 'RNA_Depth', 'DNA_VAF', 'tier'])
columns.extend(['Gene', 'AA_change', 'Num_Transcript', 'Peptide', 'Pos', 'Num_Peptides', 'ic50_MT', 'ic50_WT', 'percentile_MT', 'percentile_WT', 'RNA_expr', 'RNA_VAF', 'RNA_Depth', 'DNA_VAF', 'tier'])
peptide_table = pd.DataFrame(columns=columns)
for key in keys:
df_subset = df[df["key"] == key]
Expand Down
25,718 changes: 12,859 additions & 12,859 deletions tests/test_data/aggregate_all_epitopes/Test.all_epitopes.pvacbind.tsv
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188 changes: 94 additions & 94 deletions tests/test_data/aggregate_all_epitopes/Test.all_epitopes.pvacfuse.tsv
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98 changes: 49 additions & 49 deletions tests/test_data/aggregate_all_epitopes/output.pvacbind.tsv
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Original file line number Diff line number Diff line change
@@ -1,49 +1,49 @@
HLA-E*01:01 HLA-G*01:09 HLA-DRB1*11:01 Gene AA_change Num_Transcript Peptide Pos Num_Peptides ic50_MT ic50_WT RNA_expr RNA_VAF RNA_Depth DNA_VAF tier
X NA 41 NA GWEFLASTRLTSELN NA 6 4.8 NA NA NA NA NA NA
X NA 42 NA GWEFLAFTRLTSELN NA 7 5.6 NA NA NA NA NA NA
X X X NA 30 NA RRNWIEALRKTVRPT NA 282 6.9 NA NA NA NA NA NA
X X NA 44_duplicate NA VSLFGALVRSRTYDM NA 8 16.7 NA NA NA NA NA NA
X X NA 44 NA VSLFGALVRSRTYDM NA 8 16.7 NA NA NA NA NA NA
X NA 40 NA KTTVVVTTQKRNSRR NA 7 24.0 NA NA NA NA NA NA
X NA 39 NA TTVVVTAQKRNSRRQ NA 7 26.2 NA NA NA NA NA NA
X X NA 43 NA VSLFGALVHSRTYDM NA 7 27.0 NA NA NA NA NA NA
X NA 37 NA YYSYGLLHTYGSGGY NA 5 28.1 NA NA NA NA NA NA
X NA 38 NA LYYSYGLLHIYGSGG NA 6 41.4 NA NA NA NA NA NA
X NA 25 NA HLSYLSVRGGFNMSS NA 6 60.1 NA NA NA NA NA NA
X NA 26 NA HLSYLSVRGGFNMSS NA 6 60.1 NA NA NA NA NA NA
X NA 33 NA ASVLCQRAKVAMSHF NA 2 80.9 NA NA NA NA NA NA
X NA 10 NA PLELVYCLQKCNVPL NA 3 87.0 NA NA NA NA NA NA
X NA 9 NA PLELAYCLQKCNVPL NA 3 96.8 NA NA NA NA NA NA
X NA 5 NA ATLSRTLLAAAGGSS NA 5 138.3 NA NA NA NA NA NA
X NA 34 NA ASVLCQRAKVEMSHF NA 2 142.6 NA NA NA NA NA NA
X NA 6 NA TLSRTLLLAAAGGSS NA 6 221.4 NA NA NA NA NA NA
X NA 15 NA KTVTISCTRSSGSIA NA 4 242.9 NA NA NA NA NA NA
X NA 32 NA DDMDYLSDRCKILQV NA 1 822.0 NA NA NA NA NA NA
X NA 11 NA KSVNEALNHLLTEEE NA 1 918.7 NA NA NA NA NA NA
X NA 29 NA GGRSAGQHWARLRGE NA 1 960.8 NA NA NA NA NA NA
X NA 17 NA VQWYQQRPGSSPTTV NA 1 981.7 NA NA NA NA NA NA
NA 18 0 VQWYQQRPGSAPTTV NA 0 1177.4 NA NA NA NA NA NA
NA 20 0 VLHHEDLIGKHGGVS NA 0 1181.5 NA NA NA NA NA NA
NA 2 0 LLPLLPLLLLLGASG NA 0 1186.2 NA NA NA NA NA NA
NA 36 0 KFNPQTDYL NA 0 1262.76 NA NA NA NA NA NA
NA 35 0 KFNPETDYL NA 0 1318.61 NA NA NA NA NA NA
NA 31 0 GMYQPCDDM NA 0 1453.47 NA NA NA NA NA NA
NA 7 0 GGSHVWTRSRDPEGS NA 0 2315.7 NA NA NA NA NA NA
NA 16 0 KTVTISCTGSSGSIA NA 0 2827.5 NA NA NA NA NA NA
NA 19 0 LHHEDLIGKPGGVSL NA 0 2938.8 NA NA NA NA NA NA
NA 24 0 MVCELAGNL NA 0 3454.02 NA NA NA NA NA NA
NA 8 0 GGSHVWTHSRDPEGS NA 0 3960.3 NA NA NA NA NA NA
NA 28 0 SLLHTVSPEPARPPQ NA 0 4264.2 NA NA NA NA NA NA
NA 27 0 LLHTVSPEP NA 0 4478.16 NA NA NA NA NA NA
NA 1_duplicate 0 PLLPLLLLLLGASGG NA 0 4650.0 NA NA NA NA NA NA
NA 1 0 PLLPLLLLLLGASGG NA 0 4650.0 NA NA NA NA NA NA
NA 12 0 SVNEALNNL NA 0 4989.87 NA NA NA NA NA NA
NA 14 0 VQGIANQDAAQGIAK NA 0 5209.8 NA NA NA NA NA NA
NA 45 0 RTEASGSES NA 0 5267.25 NA NA NA NA NA NA
NA 46 0 GYESRVEPP NA 0 5620.54 NA NA NA NA NA NA
NA 13 0 AVQGIANED NA 0 5743.49 NA NA NA NA NA NA
NA 22 0 KTQEVKVKE NA 0 7366.35 NA NA NA NA NA NA
NA 23 0 SLMVCELAGNPFNCE NA 0 7387.3 NA NA NA NA NA NA
NA 21 0 KSPVKEEEK NA 0 10081.44 NA NA NA NA NA NA
NA 3 0 VIPTVSTPP NA 0 10992.95 NA NA NA NA NA NA
NA 4 0 VIPTVSTPP NA 0 10992.95 NA NA NA NA NA NA
HLA-E*01:01 HLA-G*01:09 HLA-DRB1*11:01 Gene AA_change Num_Transcript Peptide Pos Num_Peptides ic50_MT ic50_WT percentile_MT percentile_WT RNA_expr RNA_VAF RNA_Depth DNA_VAF tier
X NA 41 NA GWEFLASTRLTSELN NA 6 4.8 NA 0.21 NA NA NA NA NA NA
X NA 42 NA GWEFLAFTRLTSELN NA 7 5.6 NA 0.34 NA NA NA NA NA NA
X X X NA 30 NA RRNWIEALRKTVRPT NA 282 6.9 NA 0.61 NA NA NA NA NA NA
X X NA 44_duplicate NA VSLFGALVRSRTYDM NA 8 16.7 NA 2.85 NA NA NA NA NA NA
X X NA 44 NA VSLFGALVRSRTYDM NA 8 16.7 NA 2.85 NA NA NA NA NA NA
X NA 40 NA KTTVVVTTQKRNSRR NA 7 24.0 NA 4.39 NA NA NA NA NA NA
X NA 39 NA TTVVVTAQKRNSRRQ NA 7 26.2 NA 4.83 NA NA NA NA NA NA
X X NA 43 NA VSLFGALVHSRTYDM NA 7 27.0 NA 4.97 NA NA NA NA NA NA
X NA 37 NA YYSYGLLHTYGSGGY NA 5 28.1 NA 5.17 NA NA NA NA NA NA
X NA 38 NA LYYSYGLLHIYGSGG NA 6 41.4 NA 7.33 NA NA NA NA NA NA
X NA 25 NA HLSYLSVRGGFNMSS NA 6 60.1 NA 9.78 NA NA NA NA NA NA
X NA 26 NA HLSYLSVRGGFNMSS NA 6 60.1 NA 9.78 NA NA NA NA NA NA
X NA 33 NA ASVLCQRAKVAMSHF NA 2 80.9 NA 12.01 NA NA NA NA NA NA
X NA 10 NA PLELVYCLQKCNVPL NA 3 87.0 NA 12.6 NA NA NA NA NA NA
X NA 9 NA PLELAYCLQKCNVPL NA 3 96.8 NA 13.46 NA NA NA NA NA NA
X NA 5 NA ATLSRTLLAAAGGSS NA 5 138.3 NA 16.63 NA NA NA NA NA NA
X NA 34 NA ASVLCQRAKVEMSHF NA 2 142.6 NA 16.92 NA NA NA NA NA NA
X NA 6 NA TLSRTLLLAAAGGSS NA 6 221.4 NA 21.36 NA NA NA NA NA NA
X NA 15 NA KTVTISCTRSSGSIA NA 4 242.9 NA 22.37 NA NA NA NA NA NA
X NA 32 NA DDMDYLSDRCKILQV NA 1 822.0 NA 37.87 NA NA NA NA NA NA
X NA 11 NA KSVNEALNHLLTEEE NA 1 918.7 NA 39.5 NA NA NA NA NA NA
X NA 29 NA GGRSAGQHWARLRGE NA 1 960.8 NA 40.17 NA NA NA NA NA NA
X NA 17 NA VQWYQQRPGSSPTTV NA 1 981.7 NA 40.49 NA NA NA NA NA NA
NA 18 0 VQWYQQRPGSAPTTV NA 0 1177.4 NA 43.24 NA NA NA NA NA NA
NA 20 0 VLHHEDLIGKHGGVS NA 0 1181.5 NA 43.29 NA NA NA NA NA NA
NA 2 0 LLPLLPLLLLLGASG NA 0 1186.2 NA 43.35 NA NA NA NA NA NA
NA 36 0 KFNPQTDYL NA 0 1262.76 NA 0.5 NA NA NA NA NA NA
NA 35 0 KFNPETDYL NA 0 1318.61 NA 0.6 NA NA NA NA NA NA
NA 31 0 GMYQPCDDM NA 0 1453.47 NA 0.7 NA NA NA NA NA NA
NA 7 0 GGSHVWTRSRDPEGS NA 0 2315.7 NA 54.4 NA NA NA NA NA NA
NA 16 0 KTVTISCTGSSGSIA NA 0 2827.5 NA 57.9 NA NA NA NA NA NA
NA 19 0 LHHEDLIGKPGGVSL NA 0 2938.8 NA 58.59 NA NA NA NA NA NA
NA 24 0 MVCELAGNL NA 0 3454.02 NA 4.1 NA NA NA NA NA NA
NA 8 0 GGSHVWTHSRDPEGS NA 0 3960.3 NA 64.06 NA NA NA NA NA NA
NA 28 0 SLLHTVSPEPARPPQ NA 0 4264.2 NA 65.43 NA NA NA NA NA NA
NA 27 0 LLHTVSPEP NA 0 4478.16 NA 6.1 NA NA NA NA NA NA
NA 1 0 PLLPLLLLLLGASGG NA 0 4650.0 NA 67.09 NA NA NA NA NA NA
NA 1_duplicate 0 PLLPLLLLLLGASGG NA 0 4650.0 NA 67.09 NA NA NA NA NA NA
NA 12 0 SVNEALNNL NA 0 4989.87 NA 7.3 NA NA NA NA NA NA
NA 14 0 VQGIANQDAAQGIAK NA 0 5209.8 NA 69.23 NA NA NA NA NA NA
NA 45 0 RTEASGSES NA 0 5267.25 NA 7.9 NA NA NA NA NA NA
NA 46 0 GYESRVEPP NA 0 5620.54 NA 8.7 NA NA NA NA NA NA
NA 13 0 AVQGIANED NA 0 5743.49 NA 9.0 NA NA NA NA NA NA
NA 22 0 KTQEVKVKE NA 0 7366.35 NA 14.0 NA NA NA NA NA NA
NA 23 0 SLMVCELAGNPFNCE NA 0 7387.3 NA 75.99 NA NA NA NA NA NA
NA 21 0 KSPVKEEEK NA 0 10081.44 NA 21.0 NA NA NA NA NA NA
NA 4 0 VIPTVSTPP NA 0 10992.95 NA 23.0 NA NA NA NA NA NA
NA 3 0 VIPTVSTPP NA 0 10992.95 NA 23.0 NA NA NA NA NA NA
6 changes: 3 additions & 3 deletions tests/test_data/aggregate_all_epitopes/output.pvacfuse.tsv
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
HLA-A*29:02 H2-IAb Gene AA_change Num_Transcript Peptide Pos Num_Peptides ic50_MT ic50_WT RNA_expr RNA_VAF RNA_Depth DNA_VAF tier
X MPDU1>>GLP2R 17 / 17 | -1 / 9760739 | 7490589 / -1 2 PAVWGLPGPNLHFHS NA 5 108.7 NA 0.0 0.0 0.0 0.0 NoExpr
EIF3K>>CYP39A1 19 / 6 | -1 / -1 | 39123136 / 46607405 0 DSVRKSSIPKNVFLA NA 0 1633.4 NA 0.0 0.0 0.0 0.0 NoExpr
HLA-A*29:02 H2-IAb Gene AA_change Num_Transcript Peptide Pos Num_Peptides ic50_MT ic50_WT percentile_MT percentile_WT RNA_expr RNA_VAF RNA_Depth DNA_VAF tier
X MPDU1>>GLP2R 17 / 17 | -1 / 9760739 | 7490589 / -1 2 PAVWGLPGPNLHFHS NA 5 108.7 NA 1.71 NA 0.0 0.0 0.0 0.0 NoExpr
EIF3K>>CYP39A1 19 / 6 | -1 / -1 | 39123136 / 46607405 0 DSVRKSSIPKNVFLA NA 0 1633.4 NA 16.74 NA 0.0 0.0 0.0 0.0 NoExpr
48 changes: 24 additions & 24 deletions tests/test_data/aggregate_all_epitopes/output.tsv
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@@ -1,24 +1,24 @@
HLA-E*01:01 HLA-G*01:09 Gene AA_change Num_Transcript Peptide Pos Num_Peptides ic50_MT ic50_WT RNA_expr RNA_VAF RNA_Depth DNA_VAF tier
X X TRIOBP Frameshift 1 KYQDVYVEL 0 4 323.04 NA 0.0 0.0 0.0 0.768 NoExpr
ACO2 E510Q 0 KFNPQTDYL 5 0 1262.76 1318.61 0.0 0.0 0.0 0.25 NoExpr
PKDREJ T1875I 0 LYYSYGLLHI 10 0 1469.28 2365.16 0.0 0.0 0.0 0.233 NoExpr
IGLV6-57 S63A 0 WYQQRPGSA 9 0 2781.92 3567.97 0.0 0.0 0.0 0.571 NoExpr
CACNA1I C107Y 0 MYQPCDDMDY 10 0 2904.96 2873.7 0.0 0.0 0.0 0.043 NoExpr
USP18 A124V 0 LVYCLQKCN 2 0 3099.81 6399.79 0.0 0.0 0.0 0.053 NoExpr
ELFN2 P186L 0 MVCELAGNL 9 0 3454.02 10191.11 0.0 0.0 0.0 0.135 NoExpr
PANX2 S147F 0 AFTRLTSEL 2 0 3807.28 8387.64 0.0 0.0 0.0 0.959 NoExpr
PRICKLE4 -287-288L 0 ATLSRTLLL 9 0 3816.925 14131.865 0.0 0.0 0.0 0.158 NoExpr
TUBGCP6 H220R 0 RSRTYDMDV 1 0 4576.12 7609.38 0.0 0.0 0.0 0.686 NoExpr
IGFBP2 L20LLP 0 LLPLLPLLL 6 0 4721.43 6167.26 0.0 0.0 0.0 0.891 NoExpr
CLTCL1 H1469N 0 SVNEALNNL 8 0 4989.87 7775.84 0.0 0.0 0.0 0.1 NoExpr
CECR2 R535H 0 WTHSRDPEG 3 0 5500.22 19932.31 0.0 0.0 0.0 0.071 NoExpr
PPP6R2 S414Y 0 GYESRVEPP 2 0 5620.54 22209.93 0.0 0.0 0.0 0.043 NoExpr
FAM230A E322Q 0 ANQDAAQGI 3 0 5681.68 9654.43 0.0 0.0 0.0 0.5 NoExpr
GGA1 P484A 0 ARPPQQPVP 1 0 6693.895 10556.225 0.0 0.0 0.0 0.486 NoExpr
NEFH P830T 0 KTQEVKVKE 2 0 7366.35 25842.4 0.0 0.0 0.0 0.038 NoExpr
IGLV6-57 R43G 0 KTVTISCTG 9 0 9447.76 15208.39 0.0 0.0 0.0 1.0 NoExpr
ACO2 A33E 0 KVEMSHFEP 3 0 9972.95 31060.99 0.0 0.0 0.0 0.044 NoExpr
MOV10L1 A482T 0 KTTVVVTTQ 8 0 10874.65 16763.86 0.0 0.0 0.0 0.042 NoExpr
LGALS2 E132Q 0 NMSSFKLKQ 9 0 17113.26 17432.18 0.0 0.0 0.0 0.496 NoExpr
TPST2 P274H 0 IGKHGGVSL 4 0 18405.335 11610.23 0.0 0.0 0.0 0.179 NoExpr
RBM47 AAAAAAAA495-502A 0 SAAAAAAAV 9 0 28125.2 29506.67 0.0 0.0 0.0 0.977 NoExpr
HLA-E*01:01 HLA-G*01:09 Gene AA_change Num_Transcript Peptide Pos Num_Peptides ic50_MT ic50_WT percentile_MT percentile_WT RNA_expr RNA_VAF RNA_Depth DNA_VAF tier
X X TRIOBP Frameshift 1 KYQDVYVEL 0 4 323.04 NA 0.2 NA 0.0 0.0 0.0 0.768 NoExpr
ACO2 E510Q 0 KFNPQTDYL 5 0 1262.76 1318.61 0.5 0.6 0.0 0.0 0.0 0.25 NoExpr
PKDREJ T1875I 0 LYYSYGLLHI 10 0 1469.28 2365.16 0.3 0.4 0.0 0.0 0.0 0.233 NoExpr
IGLV6-57 S63A 0 WYQQRPGSA 9 0 2781.92 3567.97 2.7 4.3 0.0 0.0 0.0 0.571 NoExpr
CACNA1I C107Y 0 MYQPCDDMDY 10 0 2904.96 2873.7 0.5 0.5 0.0 0.0 0.0 0.043 NoExpr
USP18 A124V 0 LVYCLQKCN 2 0 3099.81 6399.79 3.3 12.0 0.0 0.0 0.0 0.053 NoExpr
ELFN2 P186L 0 MVCELAGNL 9 0 3454.02 10191.11 4.1 21.0 0.0 0.0 0.0 0.135 NoExpr
PANX2 S147F 0 AFTRLTSEL 2 0 3807.28 8387.64 4.8 16.0 0.0 0.0 0.0 0.959 NoExpr
PRICKLE4 -287-288L 0 ATLSRTLLL 9 0 3816.925 14131.865 0.5 4.0 0.0 0.0 0.0 0.158 NoExpr
TUBGCP6 H220R 0 RSRTYDMDV 1 0 4576.12 7609.38 6.3 15.0 0.0 0.0 0.0 0.686 NoExpr
IGFBP2 L20LLP 0 LLPLLPLLL 6 0 4721.43 6167.26 0.75 1.15 0.0 0.0 0.0 0.891 NoExpr
CLTCL1 H1469N 0 SVNEALNNL 8 0 4989.87 7775.84 7.3 15.0 0.0 0.0 0.0 0.1 NoExpr
CECR2 R535H 0 WTHSRDPEG 3 0 5500.22 19932.31 8.4 40.0 0.0 0.0 0.0 0.071 NoExpr
PPP6R2 S414Y 0 GYESRVEPP 2 0 5620.54 22209.93 8.7 44.0 0.0 0.0 0.0 0.043 NoExpr
FAM230A E322Q 0 ANQDAAQGI 3 0 5681.68 9654.43 8.8 20.0 0.0 0.0 0.0 0.5 NoExpr
GGA1 P484A 0 ARPPQQPVP 1 0 6693.895 10556.225 0.4 3.3 0.0 0.0 0.0 0.486 NoExpr
NEFH P830T 0 KTQEVKVKE 2 0 7366.35 25842.4 14.0 50.0 0.0 0.0 0.0 0.038 NoExpr
IGLV6-57 R43G 0 KTVTISCTG 9 0 9447.76 15208.39 19.0 31.0 0.0 0.0 0.0 1.0 NoExpr
ACO2 A33E 0 KVEMSHFEP 3 0 9972.95 31060.99 21.0 56.0 0.0 0.0 0.0 0.044 NoExpr
MOV10L1 A482T 0 KTTVVVTTQ 8 0 10874.65 16763.86 23.0 34.0 0.0 0.0 0.0 0.042 NoExpr
LGALS2 E132Q 0 NMSSFKLKQ 9 0 17113.26 17432.18 8.5 8.95 0.0 0.0 0.0 0.496 NoExpr
TPST2 P274H 0 IGKHGGVSL 4 0 18405.335 11610.23 15.3 9.7 0.0 0.0 0.0 0.179 NoExpr
RBM47 AAAAAAAA495-502A 0 SAAAAAAAV 9 0 28125.2 29506.67 39.0 45.0 0.0 0.0 0.0 0.977 NoExpr
48 changes: 24 additions & 24 deletions tests/test_data/pvacseq/MHC_Class_I/Test.all_epitopes.aggregated.tsv
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Original file line number Diff line number Diff line change
@@ -1,24 +1,24 @@
HLA-E*01:01 HLA-G*01:09 Gene AA_change Num_Transcript Peptide Pos Num_Peptides ic50_MT ic50_WT RNA_expr RNA_VAF RNA_Depth DNA_VAF tier
X X TRIOBP Frameshift 1 KYQDVYVEL 0 4 323.04 NA 0.0 0.0 0.0 0.768 NoExpr
ACO2 E510Q 0 KFNPQTDYL 5 0 1262.76 1318.61 0.0 0.0 0.0 0.25 NoExpr
PKDREJ T1875I 0 LYYSYGLLHI 10 0 1469.28 2365.16 0.0 0.0 0.0 0.233 NoExpr
IGLV6-57 S63A 0 WYQQRPGSA 9 0 2781.92 3567.97 0.0 0.0 0.0 0.571 NoExpr
CACNA1I C107Y 0 MYQPCDDMDY 10 0 2904.96 2873.7 0.0 0.0 0.0 0.043 NoExpr
USP18 A124V 0 LVYCLQKCN 2 0 3099.81 6399.79 0.0 0.0 0.0 0.053 NoExpr
ELFN2 P186L 0 MVCELAGNL 9 0 3454.02 10191.11 0.0 0.0 0.0 0.135 NoExpr
PANX2 S147F 0 AFTRLTSEL 2 0 3807.28 8387.64 0.0 0.0 0.0 0.959 NoExpr
PRICKLE4 -287-288L 0 ATLSRTLLL 9 0 3816.925 14131.865 0.0 0.0 0.0 0.158 NoExpr
TUBGCP6 H220R 0 RSRTYDMDV 1 0 4576.12 7609.38 0.0 0.0 0.0 0.686 NoExpr
IGFBP2 L20LLP 0 LLPLLPLLL 6 0 4721.43 6167.26 0.0 0.0 0.0 0.891 NoExpr
CLTCL1 H1469N 0 SVNEALNNL 8 0 4989.87 7775.84 0.0 0.0 0.0 0.1 NoExpr
CECR2 R535H 0 WTHSRDPEG 3 0 5500.22 19932.31 0.0 0.0 0.0 0.071 NoExpr
PPP6R2 S414Y 0 GYESRVEPP 2 0 5620.54 22209.93 0.0 0.0 0.0 0.043 NoExpr
FAM230A E322Q 0 ANQDAAQGI 3 0 5681.68 9654.43 0.0 0.0 0.0 0.5 NoExpr
GGA1 P484A 0 ARPPQQPVP 1 0 6693.895 10556.225 0.0 0.0 0.0 0.486 NoExpr
NEFH P830T 0 KTQEVKVKE 2 0 7366.35 25842.4 0.0 0.0 0.0 0.038 NoExpr
IGLV6-57 R43G 0 KTVTISCTG 9 0 9447.76 15208.39 0.0 0.0 0.0 1.0 NoExpr
ACO2 A33E 0 KVEMSHFEP 3 0 9972.95 31060.99 0.0 0.0 0.0 0.044 NoExpr
MOV10L1 A482T 0 KTTVVVTTQ 8 0 10874.65 16763.86 0.0 0.0 0.0 0.042 NoExpr
LGALS2 E132Q 0 NMSSFKLKQ 9 0 17113.26 17432.18 0.0 0.0 0.0 0.496 NoExpr
TPST2 P274H 0 IGKHGGVSL 4 0 18405.335 11610.23 0.0 0.0 0.0 0.179 NoExpr
RBM47 AAAAAAAA495-502A 0 SAAAAAAAV 9 0 28125.2 29506.67 0.0 0.0 0.0 0.977 NoExpr
HLA-E*01:01 HLA-G*01:09 Gene AA_change Num_Transcript Peptide Pos Num_Peptides ic50_MT ic50_WT percentile_MT percentile_WT RNA_expr RNA_VAF RNA_Depth DNA_VAF tier
X X TRIOBP Frameshift 1 KYQDVYVEL 0 4 323.04 NA 0.2 NA 0.0 0.0 0.0 0.768 NoExpr
ACO2 E510Q 0 KFNPQTDYL 5 0 1262.76 1318.61 0.5 0.6 0.0 0.0 0.0 0.25 NoExpr
PKDREJ T1875I 0 LYYSYGLLHI 10 0 1469.28 2365.16 0.3 0.4 0.0 0.0 0.0 0.233 NoExpr
IGLV6-57 S63A 0 WYQQRPGSA 9 0 2781.92 3567.97 2.7 4.3 0.0 0.0 0.0 0.571 NoExpr
CACNA1I C107Y 0 MYQPCDDMDY 10 0 2904.96 2873.7 0.5 0.5 0.0 0.0 0.0 0.043 NoExpr
USP18 A124V 0 LVYCLQKCN 2 0 3099.81 6399.79 3.3 12.0 0.0 0.0 0.0 0.053 NoExpr
ELFN2 P186L 0 MVCELAGNL 9 0 3454.02 10191.11 4.1 21.0 0.0 0.0 0.0 0.135 NoExpr
PANX2 S147F 0 AFTRLTSEL 2 0 3807.28 8387.64 4.8 16.0 0.0 0.0 0.0 0.959 NoExpr
PRICKLE4 -287-288L 0 ATLSRTLLL 9 0 3816.925 14131.865 0.5 4.0 0.0 0.0 0.0 0.158 NoExpr
TUBGCP6 H220R 0 RSRTYDMDV 1 0 4576.12 7609.38 6.3 15.0 0.0 0.0 0.0 0.686 NoExpr
IGFBP2 L20LLP 0 LLPLLPLLL 6 0 4721.43 6167.26 0.75 1.15 0.0 0.0 0.0 0.891 NoExpr
CLTCL1 H1469N 0 SVNEALNNL 8 0 4989.87 7775.84 7.3 15.0 0.0 0.0 0.0 0.1 NoExpr
CECR2 R535H 0 WTHSRDPEG 3 0 5500.22 19932.31 8.4 40.0 0.0 0.0 0.0 0.071 NoExpr
PPP6R2 S414Y 0 GYESRVEPP 2 0 5620.54 22209.93 8.7 44.0 0.0 0.0 0.0 0.043 NoExpr
FAM230A E322Q 0 ANQDAAQGI 3 0 5681.68 9654.43 8.8 20.0 0.0 0.0 0.0 0.5 NoExpr
GGA1 P484A 0 ARPPQQPVP 1 0 6693.895 10556.225 0.4 3.3 0.0 0.0 0.0 0.486 NoExpr
NEFH P830T 0 KTQEVKVKE 2 0 7366.35 25842.4 14.0 50.0 0.0 0.0 0.0 0.038 NoExpr
IGLV6-57 R43G 0 KTVTISCTG 9 0 9447.76 15208.39 19.0 31.0 0.0 0.0 0.0 1.0 NoExpr
ACO2 A33E 0 KVEMSHFEP 3 0 9972.95 31060.99 21.0 56.0 0.0 0.0 0.0 0.044 NoExpr
MOV10L1 A482T 0 KTTVVVTTQ 8 0 10874.65 16763.86 23.0 34.0 0.0 0.0 0.0 0.042 NoExpr
LGALS2 E132Q 0 NMSSFKLKQ 9 0 17113.26 17432.18 8.5 8.95 0.0 0.0 0.0 0.496 NoExpr
TPST2 P274H 0 IGKHGGVSL 4 0 18405.335 11610.23 15.3 9.7 0.0 0.0 0.0 0.179 NoExpr
RBM47 AAAAAAAA495-502A 0 SAAAAAAAV 9 0 28125.2 29506.67 39.0 45.0 0.0 0.0 0.0 0.977 NoExpr
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