| This dataset describes transcript expression levels based on the data | |
| from [GTEX](https://gtexportal.org/home/downloads/adult-gtex/bulk_tissue_expression) ( | |
| file: GTEx_Analysis_2017-06-05_v8_RSEMv1.3.0_transcript_tpm.gct.gz ) | |
| It measures the transcription level of each human transcripts ( 4-5 per genes ) in every | |
| 31 tissues (for the V1, 50 more specific tissues for the V2). | |
| The expression per tissues is the result from averaging across several patients and measurements. | |
| Each sample of the dataset correspond to: | |
| * A unique (gene_id, transcript_id) pair | |
| * the quantified level of expressions across several tissues, which are log-transformed ( x -> log(x+1) ) | |
| * the DNA sequence | |
| * the RNA sequence (ATCG format) | |
| * the protein sequence | |
| ## Splits Statistics | |
| | | train | test | evaluation | | |
| |--------------|-------|------|------------| | |
| | # Genes | 17648 | 980 | 981 | | |
| | # Transcript | 82205 | 4718 | 4318 | | |
| <img src="./tr_per_gene.png" width="512"/> | |
| <img src="./tr_expr_among_gene.png" width="512"/> | |
| <img src="./rna_length.png" width="512"/> | |
| <img src="./protein_length.png" width="512"/> | |
| ### NOTE | |
| Only coding genes are included at the moment, there there the RNA is actually mRNA | |
| ### List of tissues V1 | |
| ``` | |
| Adipose Tissue | |
| Adrenal Gland | |
| Bladder | |
| Blood | |
| Blood Vessel | |
| Brain | |
| Breast | |
| Cervix Uteri | |
| Colon | |
| Esophagus | |
| Fallopian Tube | |
| Heart | |
| Kidney | |
| Liver | |
| Lung | |
| Muscle | |
| Nerve | |
| Ovary | |
| Pancreas | |
| Pituitary | |
| Prostate | |
| Salivary Gland | |
| Skin | |
| Small Intestine | |
| Spleen | |
| Stomach | |
| Testis | |
| Thyroid | |
| Uterus | |
| Vagina | |
| ``` | |
| ### List of tissues V2 | |
| ``` | |
| Adipose_Subcutaneous | |
| Adipose_Visceral (Omentum) | |
| Adrenal Gland | |
| Artery_Aorta | |
| Artery_Coronary | |
| Artery_Tibial | |
| Bladder | |
| Brain_Amygdala | |
| Brain_Anterior cingulate cortex (BA24) | |
| Brain_Caudate (basal ganglia) | |
| Brain_Cerebellar Hemisphere | |
| Brain_Cerebellum | |
| Brain_Cortex | |
| Brain_Frontal Cortex (BA9) | |
| Brain_Hippocampus | |
| Brain_Hypothalamus | |
| Brain_Nucleus accumbens (basal ganglia) | |
| Brain_Putamen (basal ganglia) | |
| Brain_Spinal cord (cervical c-1) | |
| Brain_Substantia nigra | |
| Breast_Mammary Tissue | |
| Cells_Cultured fibroblasts | |
| Cells_EBV-transformed lymphocytes | |
| Cervix_Ectocervix | |
| Cervix_Endocervix | |
| Colon_Sigmoid | |
| Colon_Transverse | |
| Esophagus_Gastroesophageal Junction | |
| Esophagus_Mucosa | |
| Esophagus_Muscularis | |
| Fallopian Tube | |
| Heart_Atrial Appendage | |
| Heart_Left Ventricle | |
| Kidney_Cortex | |
| Kidney_Medulla | |
| Liver | |
| Lung | |
| Minor Salivary Gland | |
| Muscle_Skeletal | |
| Nerve_Tibial | |
| Ovary | |
| Pancreas | |
| Pituitary | |
| Prostate | |
| Skin_Not Sun Exposed (Suprapubic) | |
| Skin_Sun Exposed (Lower leg) | |
| Small Intestine_Terminal Ileum | |
| Spleen | |
| Stomach | |
| Testis | |
| Thyroid | |
| Uterus | |
| Vagina | |
| Whole Blood | |
| ``` |