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@benstear
benstear authored Nov 26, 2023
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Expand Up @@ -24,21 +24,18 @@ For clarity, all schema figures in this document follow this node color format:
[GTEx, Expression data (GTEXEXP)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#gtex-expression-data-gtexexp
)
[GTEx, eQTL data (GTEXEQTL)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#gtex-eqtl-data-gtexeqtl)
[GTEx Coexpression data (GTEXCOEXP)]()
[GlyGen (GLYGEN)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#glygen-computational-and-informatics-resources-for-glycoscience-glygen)
[GTEx, Coexpression data (GTEXCOEXP)]()
[GlyGen selected datasets (GLYGEN)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#glygen-computational-and-informatics-resources-for-glycoscience-glygen)
[Homo Sapiens Chromosomal Location Ontology (HSCLO)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#homo-sapiens-chromosomal-location-ontology-hsclo)
[Human gene-phenotype mappings (HGNCHPO)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#human-gene-phenotype-hgnchpo)
[Human-Mouse Orthologs (HGNCHCOP)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#human-mouse-orthologs-hgnchcop)
[Mouse gene-phenotype (HCOPMP)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#mouse-gene-phenotype-hcopmp)
[Human Phenotype Ontology to Mouse Phenotype mappings (HPOMP)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#human-phenotype-ontology-to-mouse-phenotype-mappings-hpomp)
[Human-Rat ENSEMBL orthologs (RATHCOP)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#human-rat-ensembl-orthology-rathcop)

[LINCS L1000 Gene-Perturbagen Associations (LINCS)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#lincs-l1000-gene-perturbagen-associations-lincs)

[Molecular Signatures Database (MSIGDB)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#molecular-signatures-database-msigdb)

[Protein - Protein Interactions (STRING)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#protein---protein-interactions-string)
[Single Cell Fetal Heart expression data (ASP2019)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#single-cell-fetal-heart-expression-data-asp2019)
[Human gene-to-phenotype mappings (HGNCHPO)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#human-gene-phenotype-hgnchpo)
[Human-to-mouse ortholog mappings (HGNCHCOP)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#human-mouse-orthologs-hgnchcop)
[Human-to-mouse phenotype mappings (HPOMP)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#human-phenotype-ontology-to-mouse-phenotype-mappings-hpomp)
[Human-to-rat ENSEMBL mappings (RATHCOP)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#human-rat-ensembl-orthology-rathcop)
[LINCS L1000 (LINCS)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#lincs-l1000-lincs)
[Molecular Signatures Database (MSIGDB)]()
[Mouse gene-to-phenotype (HCOPMP)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#mouse-gene-phenotype-hcopmp)
[Single Cell Fetal Heart data (ASP2019)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#single-cell-fetal-heart-expression-data-asp2019)
[STRING (STRING)](https://github.com/TaylorResearchLab/Petagraph/blob/main/petagraph/data_dict.md#string)



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```

---
## GTEx Coexpression data (GTEXCOEXP)
## GTEx, Coexpression data (GTEXCOEXP)

**Source**: The source of this data is the `GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct` from the GTEx Expression dataset above.

**Preproccessing**: Co-expression of genes was computed using Pearson’s correlation. Gene pairs were included if the Pearson correlation coefficient was greater than 0.99. Computing co-expression pairs for all genes in all tissues resulted in many pairs even after filtering for pairs with a score above 0.99. To reduce the size of the data we included only gene co-expression pairs that are highly co-expressed in at least 5 tissues.
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```

---
## Human gene-phenotype mappings (HGNCHPO)
## Human gene-to-phenotype mappings (HGNCHPO)
**Source**:
We use the Human Phenotype (HPO) Ontology mappings for `genes_to_phenotype.txt` and `phenotype_to_genes.txt`. The HPO annotations can be found here: [https://hpo.jax.org/app/data/annotations](https://hpo.jax.org/app/data/annotations). These data are generated by the HPO group using OMIM disease-gene associations to map HPO phenotypes to genes. These data contain 4,545 genes mapped to at least one phenotype and 10,896 phenotypes mapped to at least one gene

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```

---
## Human-Mouse Ortholog mappings (HGNCHCOP)
## Human-to-mouse ortholog mappings (HGNCHCOP)
**Source**: Mouse genes were downloaded from HGNC Comparisons of Orthology Predictions (HCOP) [https://www.genenames.org/tools/hcop/](https://www.genenames.org/tools/hcop/) (scroll to the bottom, under Bulk Downloads. Select Human - Mouse ortholog data)
The human to mouse orthology mapping data were also obtained in April 2023 from the HGNC HCOP tool.

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```

---
## Human-Rat ENSEMBL orthologs (RATHCOP)
## Human-to-rat ENSEMBL mappings (RATHCOP)
**Source**: The source of the human ENSEMBL to rat ENSEMBL orthologs is the HGNC Comparisons of Orthology Predictions tool. Go to https://www.genenames.org/tools/hcop/, scroll to the Bulk Downloads section at bottom of the page, select `Rat` in the first drop down menu and `15 columns` and download the data.

**Preproccessing**: No preprocessing was needed on these mappings, we simply selected the `human_ensembl_gene` and `rat_ensembl_gene` columns from the dataset.
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