InstaDeepAI/multi_omics_transcript_expression

This dataset describes transcript expression levels based on the data from GTEX ( 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

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