Skip to main content

Table 1 Genomic and transcriptomic datasets

From: Pan-cancer analysis identifies BIRC5 as a prognostic biomarker

Cancer type and pan-organ system Cohort Number of samples
Genetic alterationsa RNA-seqa Co-expressiona KM plotter
Cancer tissue Normal tissue
Central nervous system
 Glioblastoma multiforme GBM 592 166 5 145  
 Brain lower grade carcinoma LGG 514 530 0 511  
Endocrine
 Adrenocortical carcinoma ACC 91 79 0 78  
 Thyroid carcinoma THCA 500 496 58 480  
Gastrointestinal
 Cholangiocarcinoma CHOL 36 36 9 36  
 Colon adenocarcinoma COADb 594 191 0 524  
 Rectum adenocarcinoma READ 72 0  
 Esophageal Adenocarcinoma ESCAc 182 185 11 181  
 Esophageal squamous carcinoma
 Liver hepatocellular carcinoma LIHC 372 147 50 348  
 Pancreatic adenocarcinoma PAAD 184 56 0 168  
 Stomach adenocarcinoma STADf 440 415 35 407 875
Gynecologic
 Breast invasive carcinoma BRCA 1084 1026 108 994 1879
 Cervical squamous cell carcinoma CESCd 297 159 0 275  
 Ovarian serous cystadenocarcinoma OV 584 265 0 201 1656
 Uterine corpus endometrial carcinoma UCEC 529 369 0 507  
Head and neck
 Head and neck squamous cell carcinoma HNSC 523 425 42 488  
Hematologic and lymphatic malignancies
 Diffuse Large B-cell Lymphoma DLBC 41 48 0 37  
 Acute myeloid leukemia LAML 200 173 0 165  
 Thymoma THYM 123 120 0 119  
Melanocytic
 Skin cutaneous melanoma SKCM 444 472 0 363  
 Uveal melanoma UVM 80 80 0 80  
Neural crest-derived
 Pheochromocytoma and paraganglioma PCPG 178 184 3 161  
Soft tissue
 Sarcoma SARC 255 105 0 251  
 Uterine carcinosarcoma UCS 57 57 0 56  
Thoracic
 Lung adenocarcinoma LUADe 566 490 58 503 1925
 Lung squamous cell carcinoma LUSCe 487 482 50 466
 Mesothelioma MESO 87 87 0 82  
Urologic
 Bladder urothelial carcinoma BLCA 411 223 19 402  
 Kidney chromophobe KICH 65 66 25 65  
 Kidney renal clear cell carcinoma KIRC 511 507 72 352  
 Kidney renal papillary cell carcinoma KIRP 283 161 30 274  
 Prostate adenocarcinoma PRAD 494 498 52 488  
 Testicular germ cell tumors TGCT 145 156 0 144  
Total   8812 8526 627 9351 6335
  1. aTCGA data, see Method
  2. bIn bioPortal COAD+READ was combined for our analysis
  3. cIn RNA-seq data esophageal adenocarcinoma and squamous carcinoma were combined. In analysis of RNA-seq data for gene co-expression there was only data for esophageal adenocarcinoma
  4. dWhen analyzing gene co-expression using the RNA-seq data, cervical squamous cell carcinoma and endocervical adenocarcinoma were both included
  5. eIn KM-plotter both LUAD and LUSC were included in analysis
  6. fStomach cancer was in KM plotter denominated as gastric cancer