| 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 |
| ``` |
