dwb2023/hgnc_sl_tsg_genes_202410

Dataset Card for Synthetic Lethal Tumor Suppressor Genes (SL TSG)

This dataset was created with the goal of providing cancer researchers and bioinformaticians with a comprehensive resource for studying synthetic lethality in tumor suppressor genes (TSGs). By identifying genetic interactions that lead to cancer cell death when both a tumor suppressor gene and its synthetic lethal partner are mutated or deactivated, this dataset aims to support the development of novel cancer therapeutics.

It is currently a highly filtered list of ~90 genes and intended to be used in combination with the dwb2023/pmc_35559673_table_s6 dataset.

In creating this dataset, we are grateful for the rich, publicly available data curated by the HUGO Gene Nomenclature Committee (HGNC). Their dedication to maintaining high-quality gene data has been instrumental to this work.

Dataset Details

Dataset Description

This dataset consists of curated information on synthetic lethal interactions involving tumor suppressor genes. The fields in this dataset include gene symbols, gene IDs, and additional metadata sourced from public bioinformatics databases, including HGNC, ENSEMBL, NCBI Entrez, and others. Researchers can leverage this dataset to study gene-gene interactions in cancer biology, particularly those that lead to synthetic lethality, an emerging therapeutic strategy in cancer treatment.

We would like to acknowledge HGNC as the primary source of the gene nomenclature and ID data used in this dataset. HGNC provides freely accessible gene data under the Creative Commons Public Domain (CC0) license. While attribution is not required, we believe in giving credit to the dedicated curators who make such valuable resources available.

Dataset Sources

• Source File: HGNC Complete Set JSON
• Paper: Genenames.org: the HGNC resources in 2023 by Ruth L. Seal, et al.

Uses

Direct Use

This dataset is primarily intended for use in cancer research. Specifically, it supports the study of synthetic lethal interactions involving tumor suppressor genes, helping researchers:

• Identify potential therapeutic targets in cancer cells harboring TSG mutations.
• Explore gene-gene dependencies that may reveal vulnerabilities in cancer cells.
• Integrate synthetic lethal interactions with other cancer data to guide precision medicine.

Out-of-Scope Use

• This dataset is not designed for clinical decision-making or to predict individual genetic predispositions to diseases.
• Using the dataset for commercial purposes without proper validation and clinical trials is discouraged.

Dataset Structure

The dataset contains the following fields, each of which is essential for understanding the synthetic lethal interactions and genetic relationships in cancer:

Field Name	Description
hgnc_id	HGNC ID. A unique ID created by the HGNC for every approved symbol.
symbol	The HGNC approved gene symbol. Equates to the "Approved symbol" field within the gene symbol report.
name	HGNC approved name for the gene. Equates to the "Approved name" field within the gene symbol report.
locus_group	A group name for a set of related locus types as defined by the HGNC (e.g. non-coding RNA).
locus_type	The locus type as set by the HGNC.
status	Status of the symbol report, which can be either "Approved" or "Entry Withdrawn".
location	Cytogenetic location of the gene (e.g. 2q34).
alias_symbol	Other symbols used to refer to this gene as seen in the "Alias symbols" field in the gene symbol report.
alias_name	Other names used to refer to this gene as seen in the "Alias names" field in the gene symbol report.
prev_symbol	Gene symbols previously approved by the HGNC for this gene. Equates to the "Previous symbols" field within the gene symbol report.
prev_name	Gene names previously approved by the HGNC for this gene. Equates to the "Previous names" field within the gene symbol report.
gene_group	The gene group name as set by the HGNC and seen at the top of the gene group reports.
gene_group_id	ID used to designate a gene group the gene has been assigned to.
date_approved_reserved	The date the entry was first approved.
date_symbol_changed	The date the approved symbol was last changed.
date_name_changed	The date the approved name was last changed.
date_modified	Date the entry was last modified.
entrez_id	NCBI gene ID. Found within the "Gene resources" section of the gene symbol report.
ensembl_gene_id	Ensembl gene ID. Found within the "Gene resources" section of the gene symbol report.
vega_id	Vega gene ID. Found within the "Gene resources" section of the gene symbol report.
ucsc_id	UCSC gene ID. Found within the "Gene resources" section of the gene symbol report.
ena	International Nucleotide Sequence Database Collaboration (GenBank, ENA and DDBJ) accession number(s). Found within the "Nucleotide resources" section of the gene symbol report.
refseq_accession	RefSeq nucleotide accession(s). Found within the "Nucleotide resources" section of the gene symbol report.
ccds_id	Consensus CDS ID. Found within the "Nucleotide resources" section of the gene symbol report.
uniprot_ids	UniProt protein accession. Found within the "Protein resource" section of the gene symbol report.
pubmed_id	Pubmed and Europe Pubmed Central PMID(s).
mgd_id	Mouse genome informatics database ID. Found within the "Homologs" section of the gene symbol report.
rgd_id	Rat genome database gene ID. Found within the "Homologs" section of the gene symbol report.
lsdb	The name of the Locus Specific Mutation Database and URL for the gene separated by a
cosmic	Symbol used within the Catalogue of somatic mutations in cancer for the gene. (No longer updated!).
omim_id	Online Mendelian Inheritance in Man (OMIM) ID
bioparadigms_slc	Symbol used to link to the SLC tables database at bioparadigms.org for the gene
orphanet	Orphanet ID
merops	ID used to link to the MEROPS peptidase database
iuphar	The objectId used to link to the IUPHAR/BPS Guide to PHARMACOLOGY database.
cd	Symbol used within the Human Cell Differentiation Molecule database for the gene
enzyme_id	ENZYME EC accession number
agr	The HGNC ID that the Alliance of Genome Resources (AGR) have linked to their record of the gene.
mane_select	NCBI and Ensembl transcript IDs/acessions including the version number for one high-quality representative transcript per protein-coding gene.
gencc	The HGNC ID used within the GenCC database as the unique identifier of their gene reports within the GenCC database.
uuid	Unique identifier (not in original description, but present in the JSON list)
rna_central_id	RNA Central ID (not in original description, but present in the JSON list)
curator_notes	Curator notes (not in original description, but present in the JSON list)

Dataset Creation

Curation Rationale

The curation of this dataset was driven by a need for a well-organized, comprehensive source of synthetic lethal interactions in tumor suppressor genes. These relationships offer a promising avenue for cancer therapies that specifically target cancer cells, leaving healthy cells unaffected.

Source Data

Data Collection and Processing

The data was collected from multiple publicly available sources, including:

• HGNC: Providing gene nomenclature and IDs.
• ENSEMBL: Offering curated genomic annotations.
• NCBI Entrez: Supplying cross-referenced gene IDs.

Data was processed to ensure consistency across gene symbols and IDs, with normalization steps applied to ensure accuracy and usability in bioinformatics workflows.

Who are the source data producers?

• HGNC (HUGO Gene Nomenclature Committee): Providing standardized gene symbols and IDs (https://www.genenames.org/)
• ENSEMBL: Offering detailed genome annotations (https://www.ensembl.org/)
• NCBI Entrez: Supplying gene-related data (https://www.ncbi.nlm.nih.gov/gene/)

Annotations [optional]

No manual annotations were added to the dataset.

Bias, Risks, and Limitations

Recommendations

This dataset is intended for research purposes only. Users should be aware that synthetic lethal interactions are still under active research, and many interactions need experimental validation. Users are encouraged to critically evaluate the dataset before applying it in any therapeutic development context.

Citation

Please cite the original dataset using the following format:

BibTeX:

@article{10.1093/nar/gkac888,
    author = {Seal, Ruth L and Braschi, Bryony and Gray, Kristian and Jones, Tamsin E M and Tweedie, Susan and Haim-Vilmovsky, Liora and Bruford, Elspeth A},
    title = "{Genenames.org: the HGNC resources in 2023}",
    journal = {Nucleic Acids Research},
    volume = {51},
    number = {D1},
    pages = {D1003-D1009},
    year = {2022},
    month = {10},
    abstract = "{The HUGO Gene Nomenclature Committee (HGNC) assigns unique symbols and names to human genes. The HGNC database (www.genenames.org) currently contains over 43 000 approved gene symbols, over 19 200 of which are assigned to protein-coding genes, 14 000 to pseudogenes and nearly 9000 to non-coding RNA genes. The public website, www.genenames.org, displays all approved nomenclature within Symbol Reports that contain data curated by HGNC nomenclature advisors and links to related genomic, clinical, and proteomic information. Here, we describe updates to our resource, including improvements to our search facility and new download features.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkac888},
    url = {https://doi.org/10.1093/nar/gkac888},
    eprint = {https://academic.oup.com/nar/article-pdf/51/D1/D1003/48441239/gkac888.pdf},
}

Dataset Card Authors

• Author: dwb2023

Dataset Card Contact

• Contact: dwb2023

---

This card now includes proper attribution for HGNC and other contributors, aligning with their recommendations for proper citation and respecting their curation efforts. Let me know if there are any final adjustments!