Commit
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515c2cf
1
Parent(s):
955ccd8
fix
Browse files
README.md
CHANGED
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@@ -1,16 +1,15 @@
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This
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from [GTEX](https://gtexportal.org/home/downloads/adult-gtex/bulk_tissue_expression) (
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file: GTEx_Analysis_2017-06-05_v8_RSEMv1.3.0_transcript_tpm.gct.gz )
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It measures the transcription level of each human transcripts ( 4-5 per genes ) in every
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31 tissues (for the V1, 50 more specific tissues for the V2).
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expression
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Each sample of the dataset correspond to:
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* A unique (gene_id, transcript_id) pair
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* the quantified level of expressions across several tissues
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* the DNA sequence
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* the RNA sequence (ATCG format)
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* the protein sequence
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@@ -36,3 +35,94 @@ Each sample of the dataset correspond to:
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### NOTE
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Only coding genes are included at the moment, there there the RNA is actually mRNA
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+
This dataset describes transcript expression levels based on the data
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from [GTEX](https://gtexportal.org/home/downloads/adult-gtex/bulk_tissue_expression) (
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file: GTEx_Analysis_2017-06-05_v8_RSEMv1.3.0_transcript_tpm.gct.gz )
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It measures the transcription level of each human transcripts ( 4-5 per genes ) in every
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31 tissues (for the V1, 50 more specific tissues for the V2).
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The expression per tissues is the result from averaging across several patients and measurements.
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Each sample of the dataset correspond to:
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* A unique (gene_id, transcript_id) pair
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* the quantified level of expressions across several tissues, which are log-transformed ( x -> log(x+1) )
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* the DNA sequence
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* the RNA sequence (ATCG format)
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* the protein sequence
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### NOTE
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Only coding genes are included at the moment, there there the RNA is actually mRNA
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### List of tissues V1
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```
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Adipose Tissue
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Adrenal Gland
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Bladder
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Blood
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Blood Vessel
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Brain
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Breast
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Cervix Uteri
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Colon
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Esophagus
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Fallopian Tube
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Heart
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Kidney
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Liver
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Lung
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Muscle
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Nerve
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Ovary
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Pancreas
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Pituitary
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Prostate
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Salivary Gland
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Skin
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Small Intestine
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Spleen
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Stomach
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Testis
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Thyroid
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Uterus
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Vagina
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```
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### List of tissues V2
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```
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Adipose_Subcutaneous
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Adipose_Visceral (Omentum)
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Adrenal Gland
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Artery_Aorta
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Artery_Coronary
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Artery_Tibial
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Bladder
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Brain_Amygdala
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Brain_Anterior cingulate cortex (BA24)
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Brain_Caudate (basal ganglia)
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Brain_Cerebellar Hemisphere
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Brain_Cerebellum
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Brain_Cortex
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Brain_Frontal Cortex (BA9)
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Brain_Hippocampus
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Brain_Hypothalamus
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Brain_Nucleus accumbens (basal ganglia)
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Brain_Putamen (basal ganglia)
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Brain_Spinal cord (cervical c-1)
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Brain_Substantia nigra
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Breast_Mammary Tissue
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Cells_Cultured fibroblasts
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Cells_EBV-transformed lymphocytes
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Cervix_Ectocervix
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Cervix_Endocervix
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Colon_Sigmoid
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Colon_Transverse
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Esophagus_Gastroesophageal Junction
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Esophagus_Mucosa
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Esophagus_Muscularis
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Fallopian Tube
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Heart_Atrial Appendage
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Heart_Left Ventricle
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Kidney_Cortex
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Kidney_Medulla
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Liver
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Lung
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Minor Salivary Gland
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Muscle_Skeletal
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Nerve_Tibial
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Ovary
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Pancreas
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Pituitary
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Prostate
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Skin_Not Sun Exposed (Suprapubic)
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Skin_Sun Exposed (Lower leg)
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Small Intestine_Terminal Ileum
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Spleen
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Stomach
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Testis
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Thyroid
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Uterus
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Vagina
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Whole Blood
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```
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