Gregory Way, 2018
This module stores scripts to download and process gene expression data. The processed files are tracked in this repository, so there is no need to rerun the downloading scripts. All processed files will be used for either training or evaluation.
This data was generated as a multicenter effort to profile over 10,000 tumors from 33 different cancer-types.
The list of data used as part of this effort is listed in the Genomic Data Commons of The National Cancer Institute.
We download, process, and train compression models using the RNA (Final) data listed there.
Therapeutically Applicable Research to Generate Effective Treatments (TARGET) has profiled over 700 cases of pediatric cancer from 7 different cancer-types. We access the TARGET data using UCSC Xena. We use the RSEM FPKM RNAseq processed data.
The Genotype-Tissue Expression (GTEx) project measured gene expression on over 11,000 healthy samples. These samples represent several different tissue types. We use version 7 of GTEx RNAseq data (TPM normalized).
| tissue | n = | dataset |
|---|---|---|
| ACC | 79 | TCGA |
| ALL | 194 | TARGET |
| AML | 196 | TARGET |
| AML-IF | 32 | TARGET |
| Adipose - Subcutaneous | 442 | GTEX |
| Adipose - Visceral (Omentum) | 355 | GTEX |
| Adrenal Gland | 190 | GTEX |
| Artery - Aorta | 299 | GTEX |
| Artery - Coronary | 173 | GTEX |
| Artery - Tibial | 441 | GTEX |
| BLCA | 427 | TCGA |
| BRCA | 1218 | TCGA |
| Bladder | 11 | GTEX |
| Brain - Amygdala | 100 | GTEX |
| Brain - Anterior cingulate cortex (BA24) | 121 | GTEX |
| Brain - Caudate (basal ganglia) | 160 | GTEX |
| Brain - Cerebellar Hemisphere | 136 | GTEX |
| Brain - Cerebellum | 173 | GTEX |
| Brain - Cortex | 158 | GTEX |
| Brain - Frontal Cortex (BA9) | 129 | GTEX |
| Brain - Hippocampus | 123 | GTEX |
| Brain - Hypothalamus | 121 | GTEX |
| Brain - Nucleus accumbens (basal ganglia) | 147 | GTEX |
| Brain - Putamen (basal ganglia) | 124 | GTEX |
| Brain - Spinal cord (cervical c-1) | 91 | GTEX |
| Brain - Substantia nigra | 88 | GTEX |
| Breast - Mammary Tissue | 290 | GTEX |
| CCSK | 13 | TARGET |
| CESC | 310 | TCGA |
| CHOL | 45 | TCGA |
| COAD | 495 | TCGA |
| Cells - EBV-transformed lymphocytes | 130 | GTEX |
| Cells - Transformed fibroblasts | 343 | GTEX |
| Cervix - Ectocervix | 6 | GTEX |
| Cervix - Endocervix | 5 | GTEX |
| Colon - Sigmoid | 233 | GTEX |
| Colon - Transverse | 274 | GTEX |
| DLBC | 48 | TCGA |
| ESCA | 196 | TCGA |
| Esophagus - Gastroesophageal Junction | 244 | GTEX |
| Esophagus - Mucosa | 407 | GTEX |
| Esophagus - Muscularis | 370 | GTEX |
| Fallopian Tube | 7 | GTEX |
| GBM | 172 | TCGA |
| HNSC | 566 | TCGA |
| Heart - Atrial Appendage | 297 | GTEX |
| Heart - Left Ventricle | 303 | GTEX |
| KICH | 91 | TCGA |
| KIRC | 606 | TCGA |
| KIRP | 323 | TCGA |
| Kidney - Cortex | 45 | GTEX |
| LAML | 173 | TCGA |
| LGG | 530 | TCGA |
| LIHC | 423 | TCGA |
| LUAD | 576 | TCGA |
| LUSC | 553 | TCGA |
| Liver | 175 | GTEX |
| Lung | 427 | GTEX |
| MESO | 87 | TCGA |
| Minor Salivary Gland | 97 | GTEX |
| Muscle - Skeletal | 564 | GTEX |
| NBL | 162 | TARGET |
| Nerve - Tibial | 414 | GTEX |
| OV | 308 | TCGA |
| Ovary | 133 | GTEX |
| PAAD | 183 | TCGA |
| PCPG | 187 | TCGA |
| PRAD | 550 | TCGA |
| Pancreas | 248 | GTEX |
| Pituitary | 183 | GTEX |
| Prostate | 152 | GTEX |
| READ | 171 | TCGA |
| RT | 5 | TARGET |
| SARC | 265 | TCGA |
| SKCM | 474 | TCGA |
| STAD | 450 | TCGA |
| Skin - Not Sun Exposed (Suprapubic) | 387 | GTEX |
| Skin - Sun Exposed (Lower leg) | 473 | GTEX |
| Small Intestine - Terminal Ileum | 137 | GTEX |
| Spleen | 162 | GTEX |
| Stomach | 262 | GTEX |
| TGCT | 156 | TCGA |
| THCA | 572 | TCGA |
| THYM | 122 | TCGA |
| Testis | 259 | GTEX |
| Thyroid | 446 | GTEX |
| UCEC | 567 | TCGA |
| UCS | 57 | TCGA |
| UVM | 80 | TCGA |
| Uterus | 111 | GTEX |
| Vagina | 115 | GTEX |
| WT | 132 | TARGET |
| Whole Blood | 407 | GTEX |