TCGA analysis
Workflow reference paper
Chinese CRC vs TCGA Chinese CRC vs TCGA online
TCGA-LUAD
Data Category: Simple Nucleotide Variation
Data Type: Masked Somatic Mutation (WES 데이터를 포함)
194729 obs
141 variables
분석 using maftools
MAF 파일 로드
MAF (Mutation Annotation Format)
## -Validating
## -Silent variants: 47915
## -Summarizing
## --Possible FLAGS among top ten genes:
## TTN
## MUC16
## USH2A
## FLG
## -Processing clinical data
## --Missing clinical data
## -Finished in 7.740s elapsed (7.384s cpu)
MAF 요약 정보
## An object of class MAF
## Index: <ID>
## ID summary Mean Median
## <char> <char> <num> <num>
## 1: NCBI_Build GRCh38 NA NA
## 2: Center BI NA NA
## 3: Samples 616 NA NA
## 4: nGenes 16642 NA NA
## 5: Frame_Shift_Del 4256 6.909 4.0
## 6: Frame_Shift_Ins 1290 2.094 1.0
## 7: In_Frame_Del 406 0.659 0.0
## 8: In_Frame_Ins 49 0.080 0.0
## 9: Missense_Mutation 126254 204.958 137.5
## 10: Nonsense_Mutation 10454 16.971 10.0
## 11: Nonstop_Mutation 175 0.284 0.0
## 12: Splice_Site 3719 6.037 3.0
## 13: Translation_Start_Site 211 0.343 0.0
## 14: total 146814 238.334 158.5## Tumor_Sample_Barcode Variants
## <fctr> <int>
## 1: TCGA-17-Z031-01A-01W-0746-08 1877
## 2: TCGA-55-8506-01A-11D-2393-08 1458
## 3: TCGA-05-4382-01A-01D-1931-08 1404
## 4: TCGA-78-7155-01A-11D-2036-08 1285
## 5: TCGA-55-7994-01A-11D-2184-08 1279
## ---
## 612: TCGA-L4-A4E6-01A-11D-A24D-08 4
## 613: TCGA-17-Z054-01A-01W-0747-08 4
## 614: TCGA-17-Z019-01A-01W-0746-08 2
## 615: TCGA-55-8513-01A-11D-2393-08 1
## 616: TCGA-49-AARR-01A-11D-A410-08 1## Tumor_Sample_Barcode DEL INS ONP SNP TNP total
## <fctr> <int> <int> <int> <int> <int> <num>
## 1: TCGA-17-Z031-01A-01W-0746-08 43 10 0 1824 0 1877
## 2: TCGA-55-8506-01A-11D-2393-08 122 37 0 1299 0 1458
## 3: TCGA-05-4382-01A-01D-1931-08 23 9 0 1372 0 1404
## 4: TCGA-78-7155-01A-11D-2036-08 58 4 0 1222 1 1285
## 5: TCGA-55-7994-01A-11D-2184-08 52 14 0 1213 0 1279
## ---
## 612: TCGA-17-Z054-01A-01W-0747-08 0 0 0 4 0 4
## 613: TCGA-L4-A4E6-01A-11D-A24D-08 0 0 0 4 0 4
## 614: TCGA-17-Z019-01A-01W-0746-08 0 1 0 1 0 2
## 615: TCGA-49-AARR-01A-11D-A410-08 0 0 0 1 0 1
## 616: TCGA-55-8513-01A-11D-2393-08 0 0 0 1 0 1## Tumor_Sample_Barcode Frame_Shift_Del Frame_Shift_Ins In_Frame_Del
## <fctr> <int> <int> <int>
## 1: TCGA-17-Z031-01A-01W-0746-08 38 10 1
## 2: TCGA-55-8506-01A-11D-2393-08 109 37 12
## 3: TCGA-05-4382-01A-01D-1931-08 22 9 1
## 4: TCGA-78-7155-01A-11D-2036-08 49 3 7
## 5: TCGA-55-7994-01A-11D-2184-08 49 13 2
## ---
## 612: TCGA-17-Z054-01A-01W-0747-08 0 0 0
## 613: TCGA-L4-A4E6-01A-11D-A24D-08 0 0 0
## 614: TCGA-17-Z019-01A-01W-0746-08 0 1 0
## 615: TCGA-49-AARR-01A-11D-A410-08 0 0 0
## 616: TCGA-55-8513-01A-11D-2393-08 0 0 0
## In_Frame_Ins Missense_Mutation Nonsense_Mutation Nonstop_Mutation
## <int> <int> <int> <int>
## 1: 0 1655 123 2
## 2: 0 1171 87 1
## 3: 0 1225 100 2
## 4: 1 1098 79 2
## 5: 1 1093 91 1
## ---
## 612: 0 4 0 0
## 613: 0 4 0 0
## 614: 0 1 0 0
## 615: 0 1 0 0
## 616: 0 1 0 0
## Splice_Site Translation_Start_Site total
## <int> <int> <num>
## 1: 44 4 1877
## 2: 36 5 1458
## 3: 43 2 1404
## 4: 43 3 1285
## 5: 27 2 1279
## ---
## 612: 0 0 4
## 613: 0 0 4
## 614: 0 0 2
## 615: 0 0 1
## 616: 0 0 1## Hugo_Symbol Frame_Shift_Del Frame_Shift_Ins In_Frame_Del In_Frame_Ins
## <char> <int> <int> <int> <int>
## 1: TP53 36 4 6 0
## 2: TTN 15 3 0 0
## 3: MUC16 8 6 0 0
## 4: CSMD3 12 3 0 0
## 5: RYR2 10 3 0 0
## ---
## 16638: ZNHIT2 0 0 0 0
## 16639: ZNRD2 0 0 0 0
## 16640: ZPBP2 0 0 0 0
## 16641: ZSCAN26 0 0 0 0
## 16642: ZSCAN32 0 0 0 0
## Missense_Mutation Nonsense_Mutation Nonstop_Mutation Splice_Site
## <int> <int> <int> <int>
## 1: 193 61 0 21
## 2: 580 25 0 1
## 3: 368 37 0 0
## 4: 340 44 0 12
## 5: 323 22 0 0
## ---
## 16638: 1 0 0 0
## 16639: 1 0 0 0
## 16640: 1 0 0 0
## 16641: 0 1 0 0
## 16642: 1 0 0 0
## Translation_Start_Site total MutatedSamples AlteredSamples
## <int> <num> <int> <int>
## 1: 0 321 307 307
## 2: 0 624 262 262
## 3: 0 419 253 253
## 4: 0 411 242 242
## 5: 0 358 209 209
## ---
## 16638: 0 1 1 1
## 16639: 0 1 1 1
## 16640: 0 1 1 1
## 16641: 0 1 1 1
## 16642: 0 1 1 1## Indices: <Variant_Type>, <Hugo_Symbol>
## X1 Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome
## <fctr> <char> <int> <char> <char> <char>
## 1: 1 ELAPOR1 57535 BI GRCh38 chr1
## 2: 1 YY1AP1 55249 BI GRCh38 chr1
## 3: 1 FCRL3 115352 BI GRCh38 chr1
## 4: 1 HDAC4 9759 BI GRCh38 chr2
## 5: 1 SNTN 132203 BI GRCh38 chr3
## ---
## 47911: 618 PMM1 5372 BI GRCh38 chr22
## 47912: 618 MAGEB10 139422 BI GRCh38 chrX
## 47913: 618 EFHC2 80258 BI GRCh38 chrX
## 47914: 618 PCDH11X 27328 BI GRCh38 chrX
## 47915: 618 TENM1 10178 BI GRCh38 chrX
## Start_Position End_Position Strand Variant_Classification Variant_Type
## <num> <num> <char> <char> <char>
## 1: 109197542 109197542 + Silent SNP
## 2: 155668660 155668660 + Silent SNP
## 3: 157697402 157697402 + Silent SNP
## 4: 239115281 239115281 + Silent SNP
## 5: 63659768 63659768 + Silent SNP
## ---
## 47911: 41578846 41578846 + Silent SNP
## 47912: 27821543 27821543 + Silent SNP
## 47913: 44250320 44250320 + Silent SNP
## 47914: 91877641 91877641 + Silent SNP
## 47915: 124652086 124652086 + Silent SNP
## Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS
## <char> <char> <char> <char>
## 1: C C T <NA>
## 2: G G A <NA>
## 3: C C A <NA>
## 4: C C T <NA>
## 5: T T A <NA>
## ---
## 47911: C C T novel
## 47912: C C T rs1363847270
## 47913: T T C novel
## 47914: C C A novel
## 47915: G G T novel
## dbSNP_Val_Status Tumor_Sample_Barcode
## <char> <fctr>
## 1: <NA> TCGA-38-7271-01A-11D-2036-08
## 2: <NA> TCGA-38-7271-01A-11D-2036-08
## 3: <NA> TCGA-38-7271-01A-11D-2036-08
## 4: <NA> TCGA-38-7271-01A-11D-2036-08
## 5: <NA> TCGA-38-7271-01A-11D-2036-08
## ---
## 47911: <NA> TCGA-17-Z049-01A-01W-0746-08
## 47912: <NA> TCGA-17-Z049-01A-01W-0746-08
## 47913: <NA> TCGA-17-Z049-01A-01W-0746-08
## 47914: <NA> TCGA-17-Z049-01A-01W-0746-08
## 47915: <NA> TCGA-17-Z049-01A-01W-0746-08
## Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1
## <char> <char>
## 1: TCGA-38-7271-11A-01D-2036-08 <NA>
## 2: TCGA-38-7271-11A-01D-2036-08 <NA>
## 3: TCGA-38-7271-11A-01D-2036-08 <NA>
## 4: TCGA-38-7271-11A-01D-2036-08 <NA>
## 5: TCGA-38-7271-11A-01D-2036-08 <NA>
## ---
## 47911: TCGA-17-Z049-11A-01W-0747-08 <NA>
## 47912: TCGA-17-Z049-11A-01W-0747-08 <NA>
## 47913: TCGA-17-Z049-11A-01W-0747-08 <NA>
## 47914: TCGA-17-Z049-11A-01W-0747-08 <NA>
## 47915: TCGA-17-Z049-11A-01W-0747-08 <NA>
## Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2
## <char> <char> <char>
## 1: <NA> <NA> <NA>
## 2: <NA> <NA> <NA>
## 3: <NA> <NA> <NA>
## 4: <NA> <NA> <NA>
## 5: <NA> <NA> <NA>
## ---
## 47911: <NA> <NA> <NA>
## 47912: <NA> <NA> <NA>
## 47913: <NA> <NA> <NA>
## 47914: <NA> <NA> <NA>
## 47915: <NA> <NA> <NA>
## Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2
## <char> <char>
## 1: <NA> <NA>
## 2: <NA> <NA>
## 3: <NA> <NA>
## 4: <NA> <NA>
## 5: <NA> <NA>
## ---
## 47911: <NA> <NA>
## 47912: <NA> <NA>
## 47913: <NA> <NA>
## 47914: <NA> <NA>
## 47915: <NA> <NA>
## Verification_Status Validation_Status Mutation_Status Sequencing_Phase
## <char> <char> <char> <char>
## 1: <NA> <NA> Somatic <NA>
## 2: <NA> <NA> Somatic <NA>
## 3: <NA> <NA> Somatic <NA>
## 4: <NA> <NA> Somatic <NA>
## 5: <NA> <NA> Somatic <NA>
## ---
## 47911: <NA> <NA> Somatic <NA>
## 47912: <NA> <NA> Somatic <NA>
## 47913: <NA> <NA> Somatic <NA>
## 47914: <NA> <NA> Somatic <NA>
## 47915: <NA> <NA> Somatic <NA>
## Sequence_Source Validation_Method Score BAM_File Sequencer
## <char> <char> <char> <char> <char>
## 1: <NA> <NA> <NA> <NA> <NA>
## 2: <NA> <NA> <NA> <NA> <NA>
## 3: <NA> <NA> <NA> <NA> <NA>
## 4: <NA> <NA> <NA> <NA> <NA>
## 5: <NA> <NA> <NA> <NA> <NA>
## ---
## 47911: <NA> <NA> <NA> <NA> <NA>
## 47912: <NA> <NA> <NA> <NA> <NA>
## 47913: <NA> <NA> <NA> <NA> <NA>
## 47914: <NA> <NA> <NA> <NA> <NA>
## 47915: <NA> <NA> <NA> <NA> <NA>
## Tumor_Sample_UUID
## <char>
## 1: 6732ec04-f55f-4b1d-8413-2c00af79f54e
## 2: 6732ec04-f55f-4b1d-8413-2c00af79f54e
## 3: 6732ec04-f55f-4b1d-8413-2c00af79f54e
## 4: 6732ec04-f55f-4b1d-8413-2c00af79f54e
## 5: 6732ec04-f55f-4b1d-8413-2c00af79f54e
## ---
## 47911: ac31bcc6-6ccc-43b7-96f2-3ab47050be76
## 47912: ac31bcc6-6ccc-43b7-96f2-3ab47050be76
## 47913: ac31bcc6-6ccc-43b7-96f2-3ab47050be76
## 47914: ac31bcc6-6ccc-43b7-96f2-3ab47050be76
## 47915: ac31bcc6-6ccc-43b7-96f2-3ab47050be76
## Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short
## <char> <char> <char> <char>
## 1: dbc07446-ca03-467e-ac72-576d1eefda30 c.2190C>T p.Phe730= p.F730=
## 2: dbc07446-ca03-467e-ac72-576d1eefda30 c.984C>T p.Leu328= p.L328=
## 3: dbc07446-ca03-467e-ac72-576d1eefda30 c.582G>T p.Leu194= p.L194=
## 4: dbc07446-ca03-467e-ac72-576d1eefda30 c.1548G>A p.Arg516= p.R516=
## 5: dbc07446-ca03-467e-ac72-576d1eefda30 c.189T>A p.Thr63= p.T63=
## ---
## 47911: 19f580ae-ea08-4615-b7ed-f6fdcbb35e4e c.510G>A p.Leu170= p.L170=
## 47912: 19f580ae-ea08-4615-b7ed-f6fdcbb35e4e c.237C>T p.His79= p.H79=
## 47913: 19f580ae-ea08-4615-b7ed-f6fdcbb35e4e c.732A>G p.Gly244= p.G244=
## 47914: 19f580ae-ea08-4615-b7ed-f6fdcbb35e4e c.1401C>A p.Thr467= p.T467=
## 47915: 19f580ae-ea08-4615-b7ed-f6fdcbb35e4e c.1407C>A p.Val469= p.V469=
## Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth
## <char> <char> <int> <int> <int> <int>
## 1: ENST00000369939 16/22 74 68 6 74
## 2: ENST00000295566 9/11 148 140 8 94
## 3: ENST00000368184 6/15 57 52 5 92
## 4: ENST00000345617 13/27 125 113 12 82
## 5: ENST00000343837 3/4 107 95 11 96
## ---
## 47911: ENST00000216259 6/8 11 2 9 22
## 47912: ENST00000356790 3/3 16 0 16 18
## 47913: ENST00000420999 5/15 27 2 25 29
## 47914: ENST00000373094 2/7 105 23 82 165
## 47915: ENST00000371130 8/31 107 9 98 104
## n_ref_count n_alt_count
## <char> <char>
## 1: <NA> <NA>
## 2: <NA> <NA>
## 3: <NA> <NA>
## 4: <NA> <NA>
## 5: <NA> <NA>
## ---
## 47911: <NA> <NA>
## 47912: <NA> <NA>
## 47913: <NA> <NA>
## 47914: <NA> <NA>
## 47915: <NA> <NA>
## all_effects
## <char>
## 1: ELAPOR1,synonymous_variant,p.F730=,ENST00000369939,NM_020775.5&NM_001284352.2,c.2190C>T,LOW,YES,,,1;ELAPOR1,synonymous_variant,p.F643=,ENST00000529753,NM_001267048.2&NM_001284353.1,c.1929C>T,LOW,,,,1;ELAPOR1,synonymous_variant,p.F680=,ENST00000457623,,c.2040C>T,LOW,,,,1;ELAPOR1,non_coding_transcript_exon_variant,,ENST00000369938,,n.2271C>T,MODIFIER,,,,1;ELAPOR1,3_prime_UTR_variant,,ENST00000527996,,c.*1880C>T,MODIFIER,,,,1;ELAPOR1,non_coding_transcript_exon_variant,,ENST00000369936,,n.1347C>T,MODIFIER,,,,1;ELAPOR1,downstream_gene_variant,,ENST00000464345,,,MODIFIER,,,,1;ELAPOR1,upstream_gene_variant,,ENST00000527501,,,MODIFIER,,,,1
## 2: YY1AP1,synonymous_variant,p.L420=,ENST00000368339,NM_001198903.1,c.1260C>T,LOW,YES,,,-1;YY1AP1,synonymous_variant,p.L400=,ENST00000368340,NM_001198904.1,c.1200C>T,LOW,,,,-1;YY1AP1,synonymous_variant,p.L271=,ENST00000361831,NM_139121.2&NM_018253.3,c.813C>T,LOW,,,,-1;YY1AP1,synonymous_variant,p.L251=,ENST00000407221,,c.753C>T,LOW,,,,-1;YY1AP1,synonymous_variant,p.L271=,ENST00000359205,NM_001198900.1&NM_001198899.1,c.813C>T,LOW,,,,-1;YY1AP1,synonymous_variant,p.L251=,ENST00000311573,,c.753C>T,LOW,,,,-1;YY1AP1,synonymous_variant,p.L282=,ENST00000355499,NM_139119.2,c.846C>T,LOW,,,,-1;YY1AP1,synonymous_variant,p.L262=,ENST00000404643,NM_001198905.1,c.786C>T,LOW,,,,-1;YY1AP1,synonymous_variant,p.L328=,ENST00000295566,NM_139118.2&NM_001198906.2,c.984C>T,LOW,,,,-1;YY1AP1,synonymous_variant,p.L282=,ENST00000368330,NM_001198901.1,c.846C>T,LOW,,,,-1;YY1AP1,synonymous_variant,p.L282=,ENST00000347088,NM_001198902.1,c.846C>T,LOW,,,,-1;YY1AP1,synonymous_variant,p.L420=,ENST00000405763,,c.1260C>T,LOW,,,,-1;YY1AP1,downstream_gene_variant,,ENST00000443231,,,MODIFIER,,,,-1;YY1AP1,downstream_gene_variant,,ENST00000454523,,,MODIFIER,,,,-1;YY1AP1,non_coding_transcript_exon_variant,,ENST00000488784,,n.539C>T,MODIFIER,,,,-1;YY1AP1,non_coding_transcript_exon_variant,,ENST00000477470,,n.456C>T,MODIFIER,,,,-1;YY1AP1,intron_variant,,ENST00000493625,,n.758+1660C>T,MODIFIER,,,,-1;YY1AP1,downstream_gene_variant,,ENST00000466366,,,MODIFIER,,,,-1;YY1AP1,downstream_gene_variant,,ENST00000476027,,,MODIFIER,,,,-1;YY1AP1,downstream_gene_variant,,ENST00000476093,,,MODIFIER,,,,-1;YY1AP1,3_prime_UTR_variant,,ENST00000361140,,c.*344C>T,MODIFIER,,,,-1;YY1AP1,3_prime_UTR_variant,,ENST00000436865,,c.*855C>T,MODIFIER,,,,-1;YY1AP1,3_prime_UTR_variant,,ENST00000354691,,c.*110C>T,MODIFIER,,,,-1;YY1AP1,non_coding_transcript_exon_variant,,ENST00000442834,,n.890C>T,MODIFIER,,,,-1;YY1AP1,downstream_gene_variant,,ENST00000496324,,,MODIFIER,,,,-1
## 3: FCRL3,synonymous_variant,p.L194=,ENST00000368184,NM_052939.4,c.582G>T,LOW,,,,-1;FCRL3,synonymous_variant,p.L194=,ENST00000368186,NM_001320333.2,c.582G>T,LOW,YES,,,-1;FCRL3,synonymous_variant,p.L194=,ENST00000496769,,c.582G>T,LOW,,,,-1;FCRL3,non_coding_transcript_exon_variant,,ENST00000473231,,n.612G>T,MODIFIER,,,,-1;FCRL3,non_coding_transcript_exon_variant,,ENST00000480682,,n.981G>T,MODIFIER,,,,-1;FCRL3,intron_variant,,ENST00000478179,,n.262-108G>T,MODIFIER,,,,-1;FCRL3,intron_variant,,ENST00000494724,,n.725-73G>T,MODIFIER,,,,-1;FCRL3,synonymous_variant,p.L194=,ENST00000492769,,c.582G>T,LOW,,,,-1;FCRL3,synonymous_variant,p.L194=,ENST00000485028,,c.582G>T,LOW,,,,-1;FCRL3,intron_variant,,ENST00000477837,,c.559+257G>T,MODIFIER,,,,-1;AL356276.1,downstream_gene_variant,,ENST00000453692,,,MODIFIER,YES,,,1
## 4: HDAC4,synonymous_variant,p.R516=,ENST00000345617,NM_001378417.1&NM_001378416.1&NM_006037.4,c.1548G>A,LOW,,,,-1;HDAC4,synonymous_variant,p.R521=,ENST00000543185,NM_001378415.1&NM_001378414.1,c.1563G>A,LOW,YES,,,-1;HDAC4,non_coding_transcript_exon_variant,,ENST00000493582,,n.2035G>A,MODIFIER,,,,-1;HDAC4,non_coding_transcript_exon_variant,,ENST00000463007,,n.2000G>A,MODIFIER,,,,-1;HDAC4,non_coding_transcript_exon_variant,,ENST00000535493,,n.1906G>A,MODIFIER,,,,-1;AC017028.1,non_coding_transcript_exon_variant,,ENST00000656551,,n.424C>T,MODIFIER,YES,,,1
## 5: SNTN,synonymous_variant,p.T59=,ENST00000496807,,c.177T>A,LOW,,,,1;SNTN,synonymous_variant,p.T63=,ENST00000343837,NM_001080537.2,c.189T>A,LOW,,,,1;SNTN,synonymous_variant,p.T63=,ENST00000469440,NM_001348756.2,c.189T>A,LOW,YES,,,1
## ---
## 47911: PMM1,synonymous_variant,p.L170=,ENST00000216259,NM_002676.3,c.510G>A,LOW,YES,,,-1;CSDC2,downstream_gene_variant,,ENST00000306149,NM_014460.4,,MODIFIER,YES,,,1;CSDC2,downstream_gene_variant,,ENST00000460790,,,MODIFIER,,,,1;PMM1,non_coding_transcript_exon_variant,,ENST00000463617,,n.1844G>A,MODIFIER,,,,-1;PMM1,non_coding_transcript_exon_variant,,ENST00000482178,,n.1326G>A,MODIFIER,,,,-1;PMM1,non_coding_transcript_exon_variant,,ENST00000472620,,n.910G>A,MODIFIER,,,,-1;PMM1,non_coding_transcript_exon_variant,,ENST00000485648,,n.745G>A,MODIFIER,,,,-1
## 47912: MAGEB10,synonymous_variant,p.H79=,ENST00000356790,NM_182506.3,c.237C>T,LOW,YES,,,1;MAGEB10,synonymous_variant,p.H79=,ENST00000614159,,c.237C>T,LOW,,,,1
## 47913: EFHC2,synonymous_variant,p.G244=,ENST00000420999,NM_025184.4,c.732A>G,LOW,YES,,,-1
## 47914: PCDH11X,synonymous_variant,p.T467=,ENST00000373094,NM_032968.4,c.1401C>A,LOW,YES,,,1;PCDH11X,synonymous_variant,p.T467=,ENST00000373097,NM_032969.4,c.1401C>A,LOW,,,,1;PCDH11X,synonymous_variant,p.T467=,ENST00000406881,NM_001168360.1,c.1401C>A,LOW,,,,1;PCDH11X,synonymous_variant,p.T467=,ENST00000361655,NM_001168363.1,c.1401C>A,LOW,,,,1;PCDH11X,synonymous_variant,p.T467=,ENST00000373088,NM_001168362.1,c.1401C>A,LOW,,,,1;PCDH11X,synonymous_variant,p.T467=,ENST00000504220,NM_001168361.1,c.1401C>A,LOW,,,,1;PCDH11X,non_coding_transcript_exon_variant,,ENST00000298274,,n.2034C>A,MODIFIER,,,,1;PCDH11X,non_coding_transcript_exon_variant,,ENST00000361724,,n.2246C>A,MODIFIER,,,,1
## 47915: TENM1,synonymous_variant,p.V469=,ENST00000422452,NM_001163279.1&NM_001163278.1,c.1407C>A,LOW,YES,,,-1;TENM1,synonymous_variant,p.V469=,ENST00000371130,NM_014253.3,c.1407C>A,LOW,,,,-1
## Allele Gene Feature Feature_type One_Consequence
## <char> <char> <char> <char> <char>
## 1: T ENSG00000116299 ENST00000369939 Transcript synonymous_variant
## 2: A ENSG00000163374 ENST00000295566 Transcript synonymous_variant
## 3: A ENSG00000160856 ENST00000368184 Transcript synonymous_variant
## 4: T ENSG00000068024 ENST00000345617 Transcript synonymous_variant
## 5: A ENSG00000188817 ENST00000343837 Transcript synonymous_variant
## ---
## 47911: T ENSG00000100417 ENST00000216259 Transcript synonymous_variant
## 47912: T ENSG00000177689 ENST00000356790 Transcript synonymous_variant
## 47913: C ENSG00000183690 ENST00000420999 Transcript synonymous_variant
## 47914: A ENSG00000102290 ENST00000373094 Transcript synonymous_variant
## 47915: T ENSG00000009694 ENST00000371130 Transcript synonymous_variant
## Consequence cDNA_position CDS_position Protein_position
## <char> <char> <char> <char>
## 1: synonymous_variant 2259/6880 2190/3042 730/1013
## 2: synonymous_variant 1008/2626 984/2391 328/796
## 3: synonymous_variant 786/4638 582/2205 194/734
## 4: synonymous_variant 2340/8976 1548/3255 516/1084
## 5: synonymous_variant 202/1574 189/444 63/147
## ---
## 47911: synonymous_variant 545/1242 510/789 170/262
## 47912: synonymous_variant 482/1953 237/1044 79/347
## 47913: synonymous_variant 816/3257 732/2250 244/749
## 47914: synonymous_variant 2246/9179 1401/4044 467/1347
## 47915: synonymous_variant 1471/12875 1407/8178 469/2725
## Amino_acids Codons Existing_variation DISTANCE TRANSCRIPT_STRAND
## <char> <char> <char> <char> <int>
## 1: F ttC/ttT COSV64040717 <NA> 1
## 2: L ctC/ctT COSV55122694 <NA> -1
## 3: L ctG/ctT COSV63843051 <NA> -1
## 4: R cgG/cgA COSV61869217 <NA> -1
## 5: T acT/acA COSV59539137 <NA> 1
## ---
## 47911: L ctG/ctA <NA> <NA> -1
## 47912: H caC/caT rs1363847270 <NA> 1
## 47913: G ggA/ggG <NA> <NA> -1
## 47914: T acC/acA <NA> <NA> 1
## 47915: V gtC/gtA <NA> <NA> -1
## SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS
## <char> <char> <char> <char> <char> <char>
## 1: ELAPOR1 HGNC HGNC:29618 protein_coding YES CCDS794.1
## 2: YY1AP1 HGNC HGNC:30935 protein_coding <NA> CCDS1115.1
## 3: FCRL3 HGNC HGNC:18506 protein_coding <NA> CCDS1167.1
## 4: HDAC4 HGNC HGNC:14063 protein_coding <NA> CCDS2529.1
## 5: SNTN HGNC HGNC:33706 protein_coding <NA> CCDS33779.1
## ---
## 47911: PMM1 HGNC HGNC:9114 protein_coding YES CCDS14020.1
## 47912: MAGEB10 HGNC HGNC:25377 protein_coding YES CCDS35221.1
## 47913: EFHC2 HGNC HGNC:26233 protein_coding YES CCDS55405.1
## 47914: PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1
## 47915: TENM1 HGNC HGNC:8117 protein_coding <NA> CCDS14609.1
## ENSP SWISSPROT TREMBL UNIPARC UNIPROT_ISOFORM
## <char> <char> <char> <char> <char>
## 1: ENSP00000358955 Q6UXG2.134 <NA> UPI00002051E0 Q6UXG2-1
## 2: ENSP00000295566 Q9H869.132 <NA> UPI0000141A85 Q9H869-1
## 3: ENSP00000357167 Q96P31.154 <NA> UPI000006D60E Q96P31-1
## 4: ENSP00000264606 P56524.208 <NA> UPI000013D541 P56524-1
## 5: ENSP00000341442 A6NMZ2.87 <NA> UPI000015D697 <NA>
## ---
## 47911: ENSP00000216259 Q92871.177 A0A024R1U5.36 UPI00000302B6 <NA>
## 47912: ENSP00000368304 Q96LZ2.116 <NA> UPI000013F050 <NA>
## 47913: ENSP00000404232 Q5JST6.139 <NA> UPI00000717F2 Q5JST6-1
## 47914: ENSP00000362186 Q9BZA7.155 <NA> UPI0000070BD8 Q9BZA7-1
## 47915: ENSP00000360171 Q9UKZ4.156 <NA> UPI0000050EDD Q9UKZ4-1
## RefSeq MANE APPRIS FLAGS
## <char> <char> <char> <char>
## 1: NM_020775.5;NM_001284352.2 NM_020775.5 P1 <NA>
## 2: NM_139118.2;NM_001198906.2 <NA> A2 <NA>
## 3: NM_052939.4 NM_052939.4 A2 <NA>
## 4: NM_001378417.1;NM_001378416.1;NM_006037.4 <NA> P2 <NA>
## 5: NM_001080537.2 NM_001080537.2 P1 <NA>
## ---
## 47911: NM_002676.3 NM_002676.3 P1 <NA>
## 47912: NM_182506.3 NM_182506.3 P1 <NA>
## 47913: NM_025184.4 NM_025184.4 P1 <NA>
## 47914: NM_032968.4 <NA> P4 <NA>
## 47915: NM_014253.3 <NA> <NA> <NA>
## SIFT PolyPhen EXON INTRON
## <char> <char> <char> <char>
## 1: <NA> <NA> 16/22 <NA>
## 2: <NA> <NA> 9/11 <NA>
## 3: <NA> <NA> 6/15 <NA>
## 4: <NA> <NA> 13/27 <NA>
## 5: <NA> <NA> 3/4 <NA>
## ---
## 47911: <NA> <NA> 6/8 <NA>
## 47912: <NA> <NA> 3/3 <NA>
## 47913: <NA> <NA> 5/15 <NA>
## 47914: <NA> <NA> 2/7 <NA>
## 47915: <NA> <NA> 8/31 <NA>
## DOMAINS
## <char>
## 1: PANTHER:PTHR22727;PANTHER:PTHR22727:SF13;Superfamily:SSF50911
## 2: PANTHER:PTHR16088;PANTHER:PTHR16088:SF9
## 3: Gene3D:2.60.40.10;Pfam:PF13895;PROSITE_profiles:PS50835;PANTHER:PTHR11481;PANTHER:PTHR11481:SF93;Superfamily:SSF48726
## 4: PIRSF:PIRSF037911;PANTHER:PTHR45364;PANTHER:PTHR45364:SF3;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite
## 5: CDD:cd00213;PANTHER:PTHR11639;PANTHER:PTHR11639:SF24;Gene3D:1.10.238.10;SMART:SM01394;Superfamily:SSF47473
## ---
## 47911: PDB-ENSP_mappings:2fuc.A;PDB-ENSP_mappings:2fue.A;PDB-ENSP_mappings:6cfr.A;PDB-ENSP_mappings:6cfs.A;PDB-ENSP_mappings:6cft.A;PDB-ENSP_mappings:6cfu.A;PDB-ENSP_mappings:6cfv.A;SFLD:SFLDS00003;SFLD:SFLDF00445;CDD:cd02585;PANTHER:PTHR10466;PANTHER:PTHR10466:SF1;Gene3D:3.30.1240.20;TIGRFAM:TIGR01484;Pfam:PF03332;Gene3D:3.40.50.1000;Superfamily:SSF56784
## 47912: SMART:SM01392;Gene3D:1.10.10.1200;Pfam:PF12440;PANTHER:PTHR11736;PANTHER:PTHR11736:SF36;Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite
## 47913: PROSITE_profiles:PS51336;PANTHER:PTHR12086:SF11;PANTHER:PTHR12086;Pfam:PF06565;SMART:SM00676
## 47914: Gene3D:2.60.40.60;Prints:PR00205;PROSITE_profiles:PS50268;PANTHER:PTHR24028;PANTHER:PTHR24028:SF254;Superfamily:SSF49313
## 47915: PANTHER:PTHR11219;PANTHER:PTHR11219:SF7
## 1000G_AF 1000G_AFR_AF 1000G_AMR_AF 1000G_EAS_AF 1000G_EUR_AF
## <char> <char> <char> <char> <char>
## 1: <NA> <NA> <NA> <NA> <NA>
## 2: <NA> <NA> <NA> <NA> <NA>
## 3: <NA> <NA> <NA> <NA> <NA>
## 4: <NA> <NA> <NA> <NA> <NA>
## 5: <NA> <NA> <NA> <NA> <NA>
## ---
## 47911: <NA> <NA> <NA> <NA> <NA>
## 47912: <NA> <NA> <NA> <NA> <NA>
## 47913: <NA> <NA> <NA> <NA> <NA>
## 47914: <NA> <NA> <NA> <NA> <NA>
## 47915: <NA> <NA> <NA> <NA> <NA>
## 1000G_SAS_AF ESP_AA_AF ESP_EA_AF gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF
## <char> <char> <char> <char> <char> <char>
## 1: <NA> <NA> <NA> <NA> <NA> <NA>
## 2: <NA> <NA> <NA> <NA> <NA> <NA>
## 3: <NA> <NA> <NA> <NA> <NA> <NA>
## 4: <NA> <NA> <NA> <NA> <NA> <NA>
## 5: <NA> <NA> <NA> <NA> <NA> <NA>
## ---
## 47911: <NA> <NA> <NA> <NA> <NA> <NA>
## 47912: <NA> <NA> <NA> 5.563e-06 0 0
## 47913: <NA> <NA> <NA> <NA> <NA> <NA>
## 47914: <NA> <NA> <NA> <NA> <NA> <NA>
## 47915: <NA> <NA> <NA> <NA> <NA> <NA>
## gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF
## <char> <char> <char> <char> <char>
## 1: <NA> <NA> <NA> <NA> <NA>
## 2: <NA> <NA> <NA> <NA> <NA>
## 3: <NA> <NA> <NA> <NA> <NA>
## 4: <NA> <NA> <NA> <NA> <NA>
## 5: <NA> <NA> <NA> <NA> <NA>
## ---
## 47911: <NA> <NA> <NA> <NA> <NA>
## 47912: 0 7.294e-05 0 0 0
## 47913: <NA> <NA> <NA> <NA> <NA>
## 47914: <NA> <NA> <NA> <NA> <NA>
## 47915: <NA> <NA> <NA> <NA> <NA>
## gnomAD_SAS_AF MAX_AF MAX_AF_POPS gnomAD_non_cancer_AF
## <char> <char> <char> <char>
## 1: <NA> <NA> <NA> <NA>
## 2: <NA> <NA> <NA> <NA>
## 3: <NA> <NA> <NA> <NA>
## 4: <NA> <NA> <NA> <NA>
## 5: <NA> <NA> <NA> <NA>
## ---
## 47911: <NA> <NA> <NA> <NA>
## 47912: 0 7.294e-05 gnomAD_EAS <NA>
## 47913: <NA> <NA> <NA> <NA>
## 47914: <NA> <NA> <NA> <NA>
## 47915: <NA> <NA> <NA> <NA>
## gnomAD_non_cancer_AFR_AF gnomAD_non_cancer_AMI_AF
## <char> <char>
## 1: <NA> <NA>
## 2: <NA> <NA>
## 3: <NA> <NA>
## 4: <NA> <NA>
## 5: <NA> <NA>
## ---
## 47911: <NA> <NA>
## 47912: <NA> <NA>
## 47913: <NA> <NA>
## 47914: <NA> <NA>
## 47915: <NA> <NA>
## gnomAD_non_cancer_AMR_AF gnomAD_non_cancer_ASJ_AF
## <char> <char>
## 1: <NA> <NA>
## 2: <NA> <NA>
## 3: <NA> <NA>
## 4: <NA> <NA>
## 5: <NA> <NA>
## ---
## 47911: <NA> <NA>
## 47912: <NA> <NA>
## 47913: <NA> <NA>
## 47914: <NA> <NA>
## 47915: <NA> <NA>
## gnomAD_non_cancer_EAS_AF gnomAD_non_cancer_FIN_AF
## <char> <char>
## 1: <NA> <NA>
## 2: <NA> <NA>
## 3: <NA> <NA>
## 4: <NA> <NA>
## 5: <NA> <NA>
## ---
## 47911: <NA> <NA>
## 47912: <NA> <NA>
## 47913: <NA> <NA>
## 47914: <NA> <NA>
## 47915: <NA> <NA>
## gnomAD_non_cancer_MID_AF gnomAD_non_cancer_NFE_AF
## <char> <char>
## 1: <NA> <NA>
## 2: <NA> <NA>
## 3: <NA> <NA>
## 4: <NA> <NA>
## 5: <NA> <NA>
## ---
## 47911: <NA> <NA>
## 47912: <NA> <NA>
## 47913: <NA> <NA>
## 47914: <NA> <NA>
## 47915: <NA> <NA>
## gnomAD_non_cancer_OTH_AF gnomAD_non_cancer_SAS_AF
## <char> <char>
## 1: <NA> <NA>
## 2: <NA> <NA>
## 3: <NA> <NA>
## 4: <NA> <NA>
## 5: <NA> <NA>
## ---
## 47911: <NA> <NA>
## 47912: <NA> <NA>
## 47913: <NA> <NA>
## 47914: <NA> <NA>
## 47915: <NA> <NA>
## gnomAD_non_cancer_MAX_AF_adj gnomAD_non_cancer_MAX_AF_POPS_adj CLIN_SIG
## <char> <char> <char>
## 1: <NA> <NA> <NA>
## 2: <NA> <NA> <NA>
## 3: <NA> <NA> <NA>
## 4: <NA> <NA> <NA>
## 5: <NA> <NA> <NA>
## ---
## 47911: <NA> <NA> <NA>
## 47912: <NA> <NA> <NA>
## 47913: <NA> <NA> <NA>
## 47914: <NA> <NA> <NA>
## 47915: <NA> <NA> <NA>
## SOMATIC PUBMED TRANSCRIPTION_FACTORS MOTIF_NAME MOTIF_POS HIGH_INF_POS
## <char> <char> <char> <char> <char> <char>
## 1: 1 <NA> <NA> <NA> <NA> <NA>
## 2: 1 <NA> <NA> <NA> <NA> <NA>
## 3: 1 <NA> <NA> <NA> <NA> <NA>
## 4: 1 <NA> <NA> <NA> <NA> <NA>
## 5: 1 <NA> <NA> <NA> <NA> <NA>
## ---
## 47911: <NA> <NA> <NA> <NA> <NA> <NA>
## 47912: <NA> <NA> <NA> <NA> <NA> <NA>
## 47913: <NA> <NA> <NA> <NA> <NA> <NA>
## 47914: <NA> <NA> <NA> <NA> <NA> <NA>
## 47915: <NA> <NA> <NA> <NA> <NA> <NA>
## MOTIF_SCORE_CHANGE miRNA IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET
## <char> <char> <char> <int> <char> <int> <int>
## 1: <NA> <NA> LOW 1 SNV 5 NA
## 2: <NA> <NA> LOW NA SNV 2 NA
## 3: <NA> <NA> LOW NA SNV 1 NA
## 4: <NA> <NA> LOW NA SNV 1 NA
## 5: <NA> <NA> LOW NA SNV 2 NA
## ---
## 47911: <NA> <NA> LOW 1 SNV 1 NA
## 47912: <NA> <NA> LOW 1 SNV 1 NA
## 47913: <NA> <NA> LOW 1 SNV 1 NA
## 47914: <NA> <NA> LOW 1 SNV 1 NA
## 47915: <NA> <NA> LOW NA SNV 1 NA
## PHENO GENE_PHENO CONTEXT tumor_bam_uuid
## <char> <char> <char> <char>
## 1: 1 <NA> GGGTTCTCCAA bdfa0e34-32ec-4451-b2ff-4692491456af
## 2: 1 1 ATGTTGAGGTT bdfa0e34-32ec-4451-b2ff-4692491456af
## 3: 1 <NA> GCTCTCAGCAC bdfa0e34-32ec-4451-b2ff-4692491456af
## 4: 1 1 GGCTGCCGGGC bdfa0e34-32ec-4451-b2ff-4692491456af
## 5: 1 <NA> ACCACTGCTCT bdfa0e34-32ec-4451-b2ff-4692491456af
## ---
## 47911: <NA> <NA> GTTTTCAGGGC 78b0fd7a-c1d7-4fda-aecd-c52565aca381
## 47912: <NA> <NA> TCACACACAAG 78b0fd7a-c1d7-4fda-aecd-c52565aca381
## 47913: <NA> <NA> CGGTCTCCAAA 78b0fd7a-c1d7-4fda-aecd-c52565aca381
## 47914: <NA> <NA> TTCACCCAGTC 78b0fd7a-c1d7-4fda-aecd-c52565aca381
## 47915: <NA> 1 TGCTTGACCAG 78b0fd7a-c1d7-4fda-aecd-c52565aca381
## normal_bam_uuid
## <char>
## 1: ab53e5d6-3430-4b61-8560-0ab1cc922288
## 2: ab53e5d6-3430-4b61-8560-0ab1cc922288
## 3: ab53e5d6-3430-4b61-8560-0ab1cc922288
## 4: ab53e5d6-3430-4b61-8560-0ab1cc922288
## 5: ab53e5d6-3430-4b61-8560-0ab1cc922288
## ---
## 47911: bbefa7cb-0db1-4d9f-b78e-41e8f8e19d3d
## 47912: bbefa7cb-0db1-4d9f-b78e-41e8f8e19d3d
## 47913: bbefa7cb-0db1-4d9f-b78e-41e8f8e19d3d
## 47914: bbefa7cb-0db1-4d9f-b78e-41e8f8e19d3d
## 47915: bbefa7cb-0db1-4d9f-b78e-41e8f8e19d3d
## case_id GDC_FILTER COSMIC
## <char> <char> <char>
## 1: 8214a0d1-5e2d-4a7a-acb1-e5580755db83 <NA> COSM6120128
## 2: 8214a0d1-5e2d-4a7a-acb1-e5580755db83 <NA> COSM6121448;COSM6121449
## 3: 8214a0d1-5e2d-4a7a-acb1-e5580755db83 <NA> COSM6121643;COSM6121644
## 4: 8214a0d1-5e2d-4a7a-acb1-e5580755db83 <NA> COSM1531244;COSM4311326
## 5: 8214a0d1-5e2d-4a7a-acb1-e5580755db83 <NA> COSM6165265
## ---
## 47911: d6a08727-affd-4a59-837b-ea71741d7f09 <NA> <NA>
## 47912: d6a08727-affd-4a59-837b-ea71741d7f09 <NA> <NA>
## 47913: d6a08727-affd-4a59-837b-ea71741d7f09 <NA> <NA>
## 47914: d6a08727-affd-4a59-837b-ea71741d7f09 <NA> <NA>
## 47915: d6a08727-affd-4a59-837b-ea71741d7f09 <NA> <NA>
## hotspot RNA_Support RNA_depth RNA_ref_count RNA_alt_count
## <char> <char> <char> <char> <char>
## 1: N Unknown <NA> <NA> <NA>
## 2: N Unknown <NA> <NA> <NA>
## 3: N Unknown <NA> <NA> <NA>
## 4: N Unknown <NA> <NA> <NA>
## 5: N Unknown <NA> <NA> <NA>
## ---
## 47911: N Unknown <NA> <NA> <NA>
## 47912: N Unknown <NA> <NA> <NA>
## 47913: N Unknown <NA> <NA> <NA>
## 47914: N Unknown <NA> <NA> <NA>
## 47915: N Unknown <NA> <NA> <NA>
## callers
## <char>
## 1: muse;mutect2
## 2: muse;mutect2
## 3: muse;mutect2
## 4: muse;mutect2;varscan2
## 5: muse;mutect2;varscan2
## ---
## 47911: muse;mutect2;varscan2
## 47912: muse;mutect2;varscan2
## 47913: muse;mutect2;varscan2
## 47914: muse;mutect2;varscan2
## 47915: muse;mutect2;varscan2## Tumor_Sample_Barcode
## <char>
## 1: TCGA-05-4244-01A-01D-1105-08
## 2: TCGA-05-4249-01A-01D-1105-08
## 3: TCGA-05-4250-01A-01D-1105-08
## 4: TCGA-05-4382-01A-01D-1931-08
## 5: TCGA-05-4384-01A-01D-1753-08
## ---
## 612: TCGA-NJ-A55O-01A-11D-A25L-08
## 613: TCGA-NJ-A55R-01A-11D-A25L-08
## 614: TCGA-NJ-A7XG-01A-12D-A397-08
## 615: TCGA-O1-A52J-01A-11D-A25L-08
## 616: TCGA-S2-AA1A-01A-12D-A397-08## Tumor_Sample_Barcode Frame_Shift_Del Frame_Shift_Ins In_Frame_Del
## <fctr> <int> <int> <int>
## 1: TCGA-17-Z031-01A-01W-0746-08 38 10 1
## 2: TCGA-55-8506-01A-11D-2393-08 109 37 12
## 3: TCGA-05-4382-01A-01D-1931-08 22 9 1
## 4: TCGA-78-7155-01A-11D-2036-08 49 3 7
## 5: TCGA-55-7994-01A-11D-2184-08 49 13 2
## ---
## 612: TCGA-17-Z054-01A-01W-0747-08 0 0 0
## 613: TCGA-L4-A4E6-01A-11D-A24D-08 0 0 0
## 614: TCGA-17-Z019-01A-01W-0746-08 0 1 0
## 615: TCGA-49-AARR-01A-11D-A410-08 0 0 0
## 616: TCGA-55-8513-01A-11D-2393-08 0 0 0
## In_Frame_Ins Missense_Mutation Nonsense_Mutation Nonstop_Mutation
## <int> <int> <int> <int>
## 1: 0 1655 123 2
## 2: 0 1171 87 1
## 3: 0 1225 100 2
## 4: 1 1098 79 2
## 5: 1 1093 91 1
## ---
## 612: 0 4 0 0
## 613: 0 4 0 0
## 614: 0 1 0 0
## 615: 0 1 0 0
## 616: 0 1 0 0
## Splice_Site Translation_Start_Site total
## <int> <int> <num>
## 1: 44 4 1877
## 2: 36 5 1458
## 3: 43 2 1404
## 4: 43 3 1285
## 5: 27 2 1279
## ---
## 612: 0 0 4
## 613: 0 0 4
## 614: 0 0 2
## 615: 0 0 1
## 616: 0 0 1## Hugo_Symbol Frame_Shift_Del Frame_Shift_Ins In_Frame_Del In_Frame_Ins
## <char> <int> <int> <int> <int>
## 1: TP53 36 4 6 0
## 2: TTN 15 3 0 0
## 3: MUC16 8 6 0 0
## 4: CSMD3 12 3 0 0
## 5: RYR2 10 3 0 0
## ---
## 16638: ZNHIT2 0 0 0 0
## 16639: ZNRD2 0 0 0 0
## 16640: ZPBP2 0 0 0 0
## 16641: ZSCAN26 0 0 0 0
## 16642: ZSCAN32 0 0 0 0
## Missense_Mutation Nonsense_Mutation Nonstop_Mutation Splice_Site
## <int> <int> <int> <int>
## 1: 193 61 0 21
## 2: 580 25 0 1
## 3: 368 37 0 0
## 4: 340 44 0 12
## 5: 323 22 0 0
## ---
## 16638: 1 0 0 0
## 16639: 1 0 0 0
## 16640: 1 0 0 0
## 16641: 0 1 0 0
## 16642: 1 0 0 0
## Translation_Start_Site total MutatedSamples AlteredSamples
## <int> <num> <int> <int>
## 1: 0 321 307 307
## 2: 0 624 262 262
## 3: 0 419 253 253
## 4: 0 411 242 242
## 5: 0 358 209 209
## ---
## 16638: 0 1 1 1
## 16639: 0 1 1 1
## 16640: 0 1 1 1
## 16641: 0 1 1 1
## 16642: 0 1 1 1
특정 유전자의 lollipop plot
## HGNC refseq.ID protein.ID aa.length
## <char> <char> <char> <num>
## 1: TP53 NM_000546 NP_000537 393
## 2: TP53 NM_001126112 NP_001119584 393
## 3: TP53 NM_001126113 NP_001119585 346
## 4: TP53 NM_001126114 NP_001119586 341
## 5: TP53 NM_001126115 NP_001119587 261
## 6: TP53 NM_001126116 NP_001119588 209
## 7: TP53 NM_001126117 NP_001119589 214
## 8: TP53 NM_001126118 NP_001119590 354
공변이 및 상호 배제 패턴 분석
## gene1 gene2 pValue oddsRatio 00 11 01 10
## <char> <char> <num> <num> <int> <int> <num> <num>
## 1: LRP1B MUC16 1.122434e-18 4.8823496 296 133 120 67
## 2: CSMD3 TTN 3.465805e-18 4.4337881 267 155 107 87
## 3: USH2A CSMD3 1.326806e-17 4.8686787 313 118 124 61
## 4: TTN MUC16 6.281772e-17 4.1314320 259 158 95 104
## 5: APOB MUC16 1.693377e-16 6.4215723 337 84 169 26
## ---
## 296: ADAMTS12 KRAS 8.066362e-01 1.0656212 381 28 130 77
## 297: KRAS MUC17 8.105044e-01 0.9177853 374 27 84 131
## 298: XIRP2 KRAS 9.133019e-01 0.9563497 350 36 122 108
## 299: TTN KRAS 1.000000e+00 0.9930231 263 67 91 195
## 300: COL11A1 KRAS 1.000000e+00 1.0103395 366 32 126 92
## pAdj Event pair event_ratio
## <num> <char> <char> <char>
## 1: 2.598226e-17 Co_Occurence LRP1B, MUC16 133/187
## 2: 7.469406e-17 Co_Occurence CSMD3, TTN 155/194
## 3: 2.675013e-16 Co_Occurence CSMD3, USH2A 118/185
## 4: 1.189730e-15 Co_Occurence MUC16, TTN 158/199
## 5: 3.023888e-15 Co_Occurence APOB, MUC16 84/195
## ---
## 296: 8.170950e-01 Co_Occurence ADAMTS12, KRAS 28/207
## 297: 8.183607e-01 Mutually_Exclusive KRAS, MUC17 27/215
## 298: 9.191847e-01 Mutually_Exclusive KRAS, XIRP2 36/230
## 299: 1.000000e+00 Mutually_Exclusive KRAS, TTN 67/286
## 300: 1.000000e+00 Co_Occurence COL11A1, KRAS 32/218주요 기능
- MAF 파일 로드 및 요약:
read.maf(): MAF 파일을 로드합니다.getSampleSummary(): 샘플별 돌연변이 요약 정보를 제공합니다.getGeneSummary(): 유전자별 돌연변이 요약 정보를 제공합니다.
- 시각화 도구:
oncoplot(): Oncoprint를 생성하여 유전자와 샘플 간의 돌연변이 패턴을 시각화합니다.plotmafSummary(): 돌연변이 데이터의 요약 통계를 시각화합니다.lollipopPlot(): 특정 유전자의 돌연변이 위치를 시각화합니다.rainfallPlot(): 돌연변이의 크로모솜 내 분포를 시각화합니다.
- 돌연변이 서브타입 분석:
mafCompare(): 두 집단 간의 돌연변이 패턴을 비교합니다.somaticInteractions(): 공변이 및 상호 배제 패턴을 분석합니다.
- 기능적 영향 분석:
drugInteractions(): 돌연변이와 약물 간의 상호 작용을 분석합니다.oncostrip(): 암 관련 유전자의 변이 정보를 시각화합니다.
Key Differences between TCGA-LUAD and TCGA-LUSC
| Characteristic | TCGA-LUAD (Lung Adenocarcinoma) | TCGA-LUSC (Lung Squamous Cell Carcinoma) |
|---|---|---|
| Location | Peripheral lung, alveoli, and small airways | Central lung, large airways, and bronchi |
| Cell Type | Adenocarcinoma cells, mucus-secreting | Squamous cells, keratinization, and intercellular bridges |
| Cause | Can occur in both smokers and non-smokers; more common in non-smokers | Strongly associated with smoking |
| Common Genetic Mutations | EGFR, ALK, KRAS | TP53, CDKN2A, FGFR1 |