Uterine Corpus Endometrial Carcinoma
UCEC-v2.1.0.RdA document describing the TCGA cancer code
Details
> experiments( UCEC )
ExperimentList class object of length 17:
[1] UCEC_CNASeq-20160128: RaggedExperiment with 36400 rows and 213 columns
[2] UCEC_CNASNP-20160128: RaggedExperiment with 619412 rows and 1083 columns
[3] UCEC_CNVSNP-20160128: RaggedExperiment with 127094 rows and 1078 columns
[4] UCEC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 539 columns
[5] UCEC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 98 rows and 539 columns
[6] UCEC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 539 columns
[7] UCEC_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 54 columns
[8] UCEC_Mutation-20160128: RaggedExperiment with 184861 rows and 248 columns
[9] UCEC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 190 columns
[10] UCEC_RNASeq2GeneNorm_illuminaga-20160128: SummarizedExperiment with 20501 rows and 380 columns
[11] UCEC_RNASeq2GeneNorm_illuminahiseq-20160128: SummarizedExperiment with 20501 rows and 190 columns
[12] UCEC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 269 columns
[13] UCEC_RPPAArray-20160128: SummarizedExperiment with 208 rows and 440 columns
[14] UCEC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 433 columns
[15] UCEC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18515 rows and 569 columns
[16] UCEC_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 118 columns
[17] UCEC_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 466 columns
> rownames( UCEC )
CharacterList of length 17
[["UCEC_CNASeq-20160128"]] character(0)
[["UCEC_CNASNP-20160128"]] character(0)
[["UCEC_CNVSNP-20160128"]] character(0)
[["UCEC_GISTIC_AllByGene-20160128"]] character(0)
[["UCEC_GISTIC_Peaks-20160128"]] 51 52 1 2 3 4 5 53 ... 98 45 46 47 99 48 100
[["UCEC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["UCEC_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["UCEC_Mutation-20160128"]] character(0)
[["UCEC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["UCEC_RNASeq2GeneNorm_illuminaga-20160128"]] A1BG A1CF ... psiTPTE22 tAKR
...
<7 more elements>
> colnames( UCEC )
CharacterList of length 17
[["UCEC_CNASeq-20160128"]] TCGA-A5-A0G5-01A-11D-A043-02 ...
[["UCEC_CNASNP-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_CNVSNP-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_GISTIC_AllByGene-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_GISTIC_Peaks-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_GISTIC_ThresholdedByGene-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_mRNAArray-20160128"]] TCGA-A5-A0G2-01A-11R-A040-07 ...
[["UCEC_Mutation-20160128"]] TCGA-A5-A0G3-01A-11W-A062-09 ...
[["UCEC_RNASeq2Gene-20160128"]] TCGA-2E-A9G8-01A-11R-A40A-07 ...
[["UCEC_RNASeq2GeneNorm_illuminaga-20160128"]] TCGA-A5-A0G1-01A-11R-A118-07...
...
<7 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 UCEC_CNASeq-20160128 1 Mb
2 UCEC_CNASNP-20160128 16.9 Mb
3 UCEC_CNVSNP-20160128 3.7 Mb
4 UCEC_GISTIC_AllByGene-20160128 105.5 Mb
5 UCEC_GISTIC_Peaks-20160128 0.6 Mb
6 UCEC_GISTIC_ThresholdedByGene-20160128 105.3 Mb
7 UCEC_mRNAArray-20160128 9.6 Mb
8 UCEC_Mutation-20160128 73.1 Mb
9 UCEC_RNASeq2Gene-20160128 32.3 Mb
10 UCEC_RNASeq2GeneNorm_illuminaga-20160128 62 Mb
11 UCEC_RNASeq2GeneNorm_illuminahiseq-20160128 32.3 Mb
12 UCEC_RNASeqGene-20160128 44.7 Mb
13 UCEC_RPPAArray-20160128 0.8 Mb
14 UCEC_miRNASeqGene-20160128 3.7 Mb
15 UCEC_RNASeq2GeneNorm-20160128 82.8 Mb
16 UCEC_Methylation_methyl27-20160128 4.9 Mb
17 UCEC_Methylation_methyl450-20160128 75.1 Mb
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Available sample meta-data:
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days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
50.0 367.0 709.0 881.8 1063.0 3423.0 457
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-6.0 543.0 948.5 1195.1 1753.2 6859.0 92
tumor_tissue_site:
endometrial other specify
547 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1995 2007 2009 2009 2010 2013 9
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
145 404 729 1405 2096 4144 535
radiation_therapy:
no yes NA's
295 228 25
histological_type:
endometrioid endometrial adenocarcinoma
411
mixed serous and endometrioid
22
serous endometrial adenocarcinoma
115
residual_tumor:
r0 r1 r2 rx NA's
376 22 16 41 93
Including an additional 1779 columns