inst/shinyapp/shiny-doc/terms.md

In UCSCXenaShiny: Interactive Analysis of UCSC Xena Data

Abbreviations

TCGA cancer types

| Study Abbreviation | Study Name | | :----------------- | :----------------------------------------------------------- | | LAML | Acute Myeloid Leukemia | | ACC | Adrenocortical carcinoma | | BLCA | Bladder Urothelial Carcinoma | | LGG | Brain Lower Grade Glioma | | BRCA | Breast invasive carcinoma | | CESC | Cervical squamous cell carcinoma and endocervical adenocarcinoma | | CHOL | Cholangiocarcinoma | | LCML | Chronic Myelogenous Leukemia | | COAD | Colon adenocarcinoma | | CNTL | Controls | | ESCA | Esophageal carcinoma | | FPPP | FFPE Pilot Phase II | | GBM | Glioblastoma multiforme | | HNSC | Head and Neck squamous cell carcinoma | | KICH | Kidney Chromophobe | | KIRC | Kidney renal clear cell carcinoma | | KIRP | Kidney renal papillary cell carcinoma | | LIHC | Liver hepatocellular carcinoma | | LUAD | Lung adenocarcinoma | | LUSC | Lung squamous cell carcinoma | | DLBC | Lymphoid Neoplasm Diffuse Large B-cell Lymphoma | | MESO | Mesothelioma | | MISC | Miscellaneous | | OV | Ovarian serous cystadenocarcinoma | | PAAD | Pancreatic adenocarcinoma | | PCPG | Pheochromocytoma and Paraganglioma | | PRAD | Prostate adenocarcinoma | | READ | Rectum adenocarcinoma | | SARC | Sarcoma | | SKCM | Skin Cutaneous Melanoma | | STAD | Stomach adenocarcinoma | | TGCT | Testicular Germ Cell Tumors | | THYM | Thymoma | | THCA | Thyroid carcinoma | | UCS | Uterine Carcinosarcoma | | UCEC | Uterine Corpus Endometrial Carcinoma | | UVM | Uveal Melanoma |

TCGA sample type codes

| Code | Definition | Short Letter Code | | :--- | :------------------------------------------------ | :---------------- | | 01 | Primary Solid Tumor | TP | | 02 | Recurrent Solid Tumor | TR | | 03 | Primary Blood Derived Cancer - Peripheral Blood | TB | | 04 | Recurrent Blood Derived Cancer - Bone Marrow | TRBM | | 05 | Additional - New Primary | TAP | | 06 | Metastatic | TM | | 07 | Additional Metastatic | TAM | | 08 | Human Tumor Original Cells | THOC | | 09 | Primary Blood Derived Cancer - Bone Marrow | TBM | | 10 | Blood Derived Normal | NB | | 11 | Solid Tissue Normal | NT | | 12 | Buccal Cell Normal | NBC | | 13 | EBV Immortalized Normal | NEBV | | 14 | Bone Marrow Normal | NBM | | 15 | sample type 15 | 15SH | | 16 | sample type 16 | 16SH | | 20 | Control Analyte | CELLC | | 40 | Recurrent Blood Derived Cancer - Peripheral Blood | TRB | | 50 | Cell Lines | CELL | | 60 | Primary Xenograft Tissue | XP | | 61 | Cell Line Derived Xenograft Tissue | XCL | | 99 | sample type 99 | 99SH |

TCGA platform codes

| Platform Code | Platform Alias | Platform Name | | :------------------------------------ | :--------------------------------- | :----------------------------------------------------------- | | HT_HG-U133A | HT_HG-U133A | Affymetrix HT Human Genome U133 Array Plate Set | | HuEx-1_0-st-v2 | HuEx-1_0-st-v2 | Affymetrix Human Exon 1.0 ST Array | | Genome_Wide_SNP_6 | Genome_Wide_SNP_6 | Affymetrix Genome-Wide Human SNP Array 6.0 | | HG-CGH-415K_G4124A | HG-CGH-415K_G4124A | Agilent Human Genome CGH Custom Microarray 2x415K | | WHG-CGH_4x44B | WHG-CGH_4x44B | Agilent Human Genome CGH Microarray 44K | | HG-CGH-244A | HG-CGH-244A | Agilent Human Genome CGH Microarray 244A | | WHG-1x44K_G4112A | 1 x 44K | Agilent Whole Human Genome | | WHG-4x44K_G4112F | 4 x 44K | Agilent Whole Human Genome Microarray Kit | | AgilentG4502A_07_1 | AgilentG4502A_07 | Agilent 244K Custom Gene Expression G4502A-07-1 | | H-miRNA_G4470A | H-miRNA_G4470A | Agilent Human miRNA Microarray | | AgilentG4502A_07_2 | AgilentG4502A_07 | Agilent 244K Custom Gene Expression G4502A-07-2 | | H-miRNA_8x15Kv2 | H-miRNA_8x15K | Agilent Human miRNA Microarray Rel12.0 | | AgilentG4502A_07_3 | AgilentG4502A_07 | Agilent 244K Custom Gene Expression G4502A-07-3 | | H-miRNA_8x15K | H-miRNA_8x15K | Agilent 8 x 15K Human miRNA-specific microarray | | CGH-1x1M_G4447A | CGH-1x1M_G4447A | Agilent SurePrint G3 Human CGH Microarray Kit 1x1M | | H-miRNA_EarlyAccess | H-miRNA_EarlyAccess | Agilent Human miRNA Early Access Array | | IlluminaGG | IlluminaGG | Illumina GoldenGate | | HumanMethylation27 | HumanMethylation27 | Illumina Infinium Human DNA Methylation 27 | | IlluminaDNAMethylation_OMA003_CPI | IlluminaDNAMethylation | Illumina DNA Methylation OMA003 Cancer Panel I | | Human1MDuo | Human1MDuo | Illumina Human1M-Duo BeadChip | | IlluminaDNAMethylation_OMA002_CPI | IlluminaDNAMethylation | Illumina DNA Methylation OMA002 Cancer Panel I | | HumanHap550 | HumanHap550 | Illumina 550K Infinium HumanHap550 SNP Chip | | AgilentG4502A_07 | AgilentG4502A_07 | Agilent 244K Custom Gene Expression G4502A-07 | | bio | bio | Biospecimen Metadata - Complete Set | | biotab | biotab | Biospecimen Metadata - Complete Set - All Samples - Tab-delimited | | minbio | minbio | Biospecimen Metadata - Minimal Set | | minbiotab | minbiotab | Biospecimen Metadata - Minimal Set - All Samples - Tab-delimited | | ABI | ABI | Applied Biosystems Sequence data | | IlluminaHiSeq_DNASeq | Mutation Calling | Illumina HiSeq 2000 DNA Sequencing | | SOLiD_DNASeq | Mutation Calling | ABI SOLiD DNA Sequencing | | IlluminaGA_DNASeq | Mutation Calling | Illumina Genome Analyzer DNA Sequencing | | IlluminaGA_mRNA_DGE | IlluminaGA_mRNA_DGE | Illumina Genome Analyzer mRNA Digital Gene Expression | | 454 | 454 | 454 Life Sciences Genome Sequence data | | HG-U133A_2 | HG-U133A_2 | Affymetrix Human Genome U133A 2.0 Array | | HG-U133_Plus_2 | HG-U133_Plus_2 | Affymetrix Human Genome U133 Plus 2.0 Array | | Mapping250K_Nsp | Mapping250K_Nsp | Affymetrix Human Mapping 250K Nsp Array | | Mapping250K_Sty | Mapping250K_Sty | Affymetrix Human Mapping 250K Sty Array | | GenomeWideSNP_5 | GenomeWideSNP_5 | Affymetrix Genome-Wide Human SNP Array 5.0 | | tissue_images | tissue_images | Tissue Images | | IlluminaGA_RNASeq | IlluminaGA_RNASeq | Illumina Genome Analyzer RNA Sequencing | | IlluminaGA_miRNASeq | IlluminaGA_miRNASeq | Illumina Genome Analyzer miRNA Sequencing | | diagnostic_images | diagnostic_images | Diagnostic Images | | pathology_reports | pathology_reports | Pathology Reports | | MDA_RPPA_Core | MDA_RPPA_Core | M.D. Anderson Reverse Phase Protein Array Core | | microsat_i | microsat_i | Microsatellite Instability Analysis | | HumanMethylation450 | HumanMethylation450 | Illumina Infinium Human DNA Methylation 450 | | IlluminaHiSeq_mRNA_DGE | IlluminaHiSeq_mRNA_DGE | Illumina HiSeq 2000 mRNA Digital Gene Expression | | IlluminaHiSeq_miRNASeq | IlluminaHiSeq_miRNASeq | Illumina HiSeq 2000 miRNA Sequencing | | IlluminaHiSeq_RNASeq | IlluminaHiSeq_RNASeq | Illumina HiSeq 2000 RNA Sequencing | | IlluminaHiSeq_DNASeqC | IlluminaHiSeq_DNASeqC | Illumina HiSeq for Copy Number Variation | | fh_analyses | fh_analyses | Firehose Analyses | | fh_stddata | fh_stddata | Firehose Standardized Data | | fh_reports | fh_reports | Firehose Reports | | IlluminaGA_RNASeqV2 | IlluminaGA_RNASeqV2 | Illumina Genome Analyzer RNA Sequencing Version 2 analysis | | IlluminaHiSeq_RNASeqV2 | IlluminaHiSeq_RNASeqV2 | Illumina HiSeq 2000 RNA Sequencing Version 2 analysis | | IlluminaHiSeq_DNASeq_Cont | Mutation Calling | Illumina HiSeq 2000 DNA Sequencing - Controlled | | IlluminaGA_DNASeq_Cont | Mutation Calling | Illumina Genome Analyzer DNA Sequencing - Controlled | | IlluminaHiSeq_TotalRNASeqV2 | IlluminaHiSeq_TotalRNASeqV2 | Illumina HiSeq 2000 Total RNA Sequencing Version 2 analysis | | SOLiD_DNASeq_Cont | Mutation Calling | ABI SOLiD DNA Sequencing - Controlled | | Mixed_DNASeq | Mutation Calling | Mixed DNA Sequencing | | Mixed_DNASeq_Cont | Mutation Calling | Mixed DNA Sequencing - Controlled | | IlluminaHiSeq_WGBS | IlluminaHiSeq_WGBS | Illumina HiSeq 2000 Bisulfite-converted DNA Sequencing | | IlluminaHiSeq_DNASeq_automated | Automated Mutation Calling | IlluminaHiSeq automated DNA sequencing | | IlluminaHiSeq_DNASeq_curated | Curated Mutation Calling | IlluminaHiSeq curated DNA sequencing | | IlluminaGA_DNASeq_automated | Automated Mutation Calling | IlluminaGA automated DNA sequencing | | IlluminaGA_DNASeq_curated | Curated Mutation Calling | IlluminaGA curated DNA sequencing | | SOLiD_DNASeq_automated | Automated Mutation Calling | SOLiD automated DNA sequencing | | SOLiD_DNASeq_curated | Curated Mutation Calling | SOLiD curated DNA sequencing | | Mixed_DNASeq_automated | Automated Mutation Calling | Mixed automated DNA sequencing | | Mixed_DNASeq_curated | Curated Mutation Calling | Mixed curated DNA sequencing | | IlluminaHiSeq_DNASeq_Cont_automated | Automated Mutation Calling | IlluminaHiSeq automated DNA sequencing - controlled | | IlluminaHiSeq_DNASeq_Cont_curated | Curated Mutation Calling | IlluminaHiSeq curated DNA sequencing - controlled | | IlluminaGA_DNASeq_Cont_automated | Automated Mutation Calling | IlluminaGA automated DNA sequencing - controlled | | IlluminaGA_DNASeq_Cont_curated | Curated Mutation Calling | IlluminaGA curated DNA sequencing - controlled | | SOLiD_DNASeq_Cont_automated | Automated Mutation Calling | SOLiD automated DNA sequencing - controlled | | SOLiD_DNASeq_Cont_curated | Curated Mutation Calling | SOLiD curated DNA sequencing - controlled | | Mixed_DNASeq_Cont_automated | Automated Mutation Calling | Mixed automated DNA sequencing - controlled | | Mixed_DNASeq_Cont_curated | Curated Mutation Calling | Mixed curated DNA sequencing - controlled | | supplemental_clinical | supplemental_clinical | supplemental_clinical | | Multicenter_mutation_calling_MC3 | Multicenter Mutation Calling (MC3) | Multi-Center Mutations | | Multicenter_mutation_calling_MC3_Cont | Multicenter Mutation Calling (MC3) | Multi-Center Mutations - Controlled |

All TCGA code tables are available at https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/

UCSCXenaShiny documentation built on March 7, 2023, 7 p.m.