Analysis
PANDA Dataset
Description of datasets used for PANDA analyses
Clinical data are the data provided by TCGA
| Tumor | Tumor Samples | NAT Samples |
|---|---|---|
| ACC | 79 | 0 |
| BLCA | 402 | 19 |
| BRCA | 1067 | 99 |
| CESC | 296 | 3 |
| CHOL | 36 | 9 |
| COAD | 442 | 41 |
| DLBC | 47 | 0 |
| ESCA | 152 | 11 |
| GBM | 142 | 0 |
| HNSC | 495 | 44 |
| KICH | 65 | 24 |
| KIRC | 522 | 72 |
| KIRP | 287 | 32 |
| LGG | 499 | 0 |
| LIHC | 369 | 50 |
| LUAD | 501 | 58 |
| LUSC | 495 | 49 |
| MESO | 81 | 0 |
| OV | 354 | 0 |
| PAAD | 177 | 4 |
| PCPG | 175 | 3 |
| PRAD | 481 | 51 |
| READ | 163 | 10 |
| SARC | 258 | 2 |
| SKCM | 103 | 1 |
| STAD | 373 | 32 |
| TGCT | 133 | 0 |
| THCA | 497 | 56 |
| THYM | 119 | 2 |
| UCEC | 533 | 23 |
| UCS | 56 | 0 |
| UVM | 77 | 0 |
list of gene types for PANDA analyses
| Gene_type | Num |
|---|---|
| protein_coding | 18070 |
| lncRNA | 13644 |
| processed_pseudogene | 10030 |
| unprocessed_pseudogene | 2412 |
| misc_RNA | 2203 |
| snRNA | 1845 |
| miRNA | 1401 |
| TEC | 1011 |
| snoRNA | 903 |
| transcribed_unprocessed_pseudogene | 851 |
| transcribed_processed_pseudogene | 496 |
| rRNA_pseudogene | 489 |
| IG_V_pseudogene | 180 |
| IG_V_gene | 141 |
| transcribed_unitary_pseudogene | 139 |
| TR_V_gene | 103 |
| TR_J_gene | 73 |
| unitary_pseudogene | 71 |
| scaRNA | 47 |
| rRNA | 35 |
| TR_V_pseudogene | 33 |
| IG_D_gene | 33 |
| Mt_tRNA | 22 |
| artifact | 19 |
| IG_J_gene | 18 |
| IG_C_gene | 14 |
| IG_C_pseudogene | 9 |
| ribozyme | 8 |
| TR_C_gene | 5 |
| vault_RNA | 4 |
| TR_J_pseudogene | 4 |
| TR_D_gene | 3 |
| IG_J_pseudogene | 3 |
| Mt_rRNA | 2 |
| sRNA | 2 |
| scRNA | 1 |
| translated_processed_pseudogene | 1 |
List of clinical Feature avaible for tumor
| Tumor | age_at_initial_pathologic_diagnosis | alcohol_history_documented | diabetes | gender | menopause_status | pathologic_stage | patient_status | radiation_therapy | tobacco_smoking_history |
|---|---|---|---|---|---|---|---|---|---|
| ACC | ✔ | - | - | ✔ | - | ✔ | - | ✔ | - |
| BLCA | ✔ | - | - | ✔ | - | ✔ | ✔ | ✔ | ✔ |
| BRCA | ✔ | - | - | - | ✔ | ✔ | ✔ | ✔ | - |
| CESC | ✔ | - | - | - | ✔ | - | - | ✔ | ✔ |
| CHOL | ✔ | - | - | ✔ | - | ✔ | - | - | - |
| COAD | ✔ | - | - | ✔ | - | ✔ | ✔ | ✔ | - |
| DLBC | ✔ | - | - | ✔ | - | - | - | ✔ | - |
| ESCA | ✔ | ✔ | - | ✔ | - | ✔ | - | ✔ | ✔ |
| GBM | ✔ | - | - | ✔ | - | - | - | ✔ | - |
| HNSC | ✔ | ✔ | - | ✔ | - | ✔ | ✔ | ✔ | ✔ |
| KICH | ✔ | - | - | ✔ | - | ✔ | ✔ | - | ✔ |
| KIRC | ✔ | - | - | ✔ | - | ✔ | ✔ | ✔ | ✔ |
| KIRP | ✔ | - | - | ✔ | - | ✔ | ✔ | ✔ | ✔ |
| LGG | ✔ | - | - | ✔ | - | - | - | ✔ | - |
| LIHC | ✔ | - | - | ✔ | - | ✔ | ✔ | ✔ | - |
| LUAD | ✔ | - | - | ✔ | - | ✔ | ✔ | ✔ | ✔ |
| LUSC | ✔ | - | - | ✔ | - | ✔ | ✔ | ✔ | ✔ |
| MESO | ✔ | - | - | ✔ | - | ✔ | - | ✔ | - |
| OV | ✔ | - | - | - | - | - | - | ✔ | - |
| PAAD | ✔ | ✔ | - | ✔ | - | ✔ | - | ✔ | ✔ |
| PCPG | ✔ | - | - | ✔ | - | - | - | ✔ | - |
| PRAD | ✔ | - | - | - | - | - | ✔ | ✔ | - |
| READ | ✔ | - | - | ✔ | - | ✔ | - | ✔ | - |
| SARC | ✔ | - | - | ✔ | - | - | - | ✔ | - |
| SKCM | ✔ | - | - | ✔ | - | ✔ | - | ✔ | - |
| STAD | ✔ | - | - | ✔ | - | ✔ | ✔ | ✔ | - |
| TGCT | ✔ | - | - | - | - | ✔ | - | ✔ | - |
| THCA | ✔ | - | - | ✔ | - | ✔ | ✔ | ✔ | - |
| THYM | ✔ | - | - | ✔ | - | - | - | ✔ | - |
| UCEC | ✔ | - | ✔ | - | ✔ | - | ✔ | ✔ | - |
| UCS | ✔ | - | ✔ | - | - | - | - | ✔ | - |
| UVM | ✔ | - | - | ✔ | - | ✔ | - | ✔ | - |
Parameters compared for each feature
| Feature | group1 | group2 |
|---|---|---|
| patient_status | Tumor | Ctrl |
| gender | Female | Male |
| pathologic_stage | Stage III-IV | Stage I-II |
| radiation_therapy | YES | NO |
| diabetes | YES | NO |
| tobacco_smoking_history | Smoker | Non_Smoker |
| menopause_status | Post-menopause | Pre-menopause |
| alcohol_history_documented | YES | NO |
| age_at_initial_pathologic_diagnosis | Above the median | Below the median |
TCGA Study Abbreviations
| 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 |
