TISSUES is a database of gene–tissue relationships that combines many lines of evidence. Learn more about TISSUES from its website or publication.
This repository creates a single tsv-formatted table (merged.tsv.gz) from the TISSUES datasets. Tissues are converted from BTO to Uberon identifiers. Genes are converted from STRING/Ensembl identifiers to Entrez Gene. We compute two integrated experimental scores not available from the Jensen lab downloads: score_experiment and score_experiment_unbiased, which excludes HPA-IHC data.
merged.tsv.gz is formatted like:
| uberon_id | uberon_name | entrez_gene_id | gene_symbol | score_text | score_knowledge | score_experiment | score_experiment_unbiased | score_integrated |
|---|---|---|---|---|---|---|---|---|
| UBERON:0000002 | uterine cervix | 2 | A2M | 0.8 | 0 | 1 | ||
| UBERON:0000002 | uterine cervix | 9 | NAT1 | 0 | 0.2 | |||
| UBERON:0000002 | uterine cervix | 14 | AAMP | 0 | 0 | 0.5 | ||
| UBERON:0000002 | uterine cervix | 16 | AARS | 1 | 1 | 1.7 | ||
| UBERON:0000002 | uterine cervix | 19 | ABCA1 | 0.6 | 0 | 0.7 | ||
| UBERON:0000002 | uterine cervix | 20 | ABCA2 | 0 | 0.5 | |||
| UBERON:0000002 | uterine cervix | 21 | ABCA3 | 0 | 0.5 | |||
| UBERON:0000002 | uterine cervix | 22 | ABCB7 | 0 | 0.2 | |||
| UBERON:0000002 | uterine cervix | 25 | ABL1 | 0.5 | 0 | 0.8 |
Scores range from 0 to 5 with 5 being the highest level of evidence. Blank values indicate a tissue–gene pair that was not assayed in the corresponding channel.
For more information, see the corresponding Thinklab discussion.
All computation is performed by the tissues.ipynb notebook. Code was written for Python 3.4.
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