About WikiORA

WikiORA integrates Wikidata, Gene Ontology, PanglaoDB, and Wikipedia for a seamless, encyclopedic enrichment analysis.

WikiORA is a tool designed to simplify the process of gene set over-representation analysis by integrating data from Wikidata and Wikipedia. Our goal is to provide researchers with an intuitive platform to identify significantly enriched gene sets in their data using curated information from various sources.

How It Works

WikiORA follows these steps to perform over-representation analysis:

1. Users submit a list of genes.
2. For each gene set on the library, we calculate the overlap between the user-provided gene list and the genes in the gene set.
3. The p-value is computed using the hypergeometric test to determine the likelihood of observing the overlap by chance.
4. We apply the Benjamini-Hochberg correction to adjust p-values for multiple testing.
5. Results are sorted by p-value to identify the most significantly over-represented terms.

Statistical Metrics Explained

Here are the definitions of the various metrics generated by WikiORA. While only some metrics are shown in the dashboard, they are all available upon downloading the tsv.

• Term: The identifier of the gene set.
• Description: A brief description of the gene set.
• Wikipedia URL: A link to the Wikipedia page associated with the gene set.
• Overlap: The genes from the user list that overlap with the genes in the gene set. Each gene includes a link to its Wikipedia page and its status.
• Count: The number of overlapping genes.
• p-value: The probability of observing the overlap by chance, calculated using the hypergeometric test.
• q-value: The p-value adjusted for multiple testing using the Benjamini-Hochberg correction.
• Odds Ratio: Measures the association strength, calculated as:

  odds_ratio = (overlap_count * (total_genes - gene_set_size - input_gene_list_size + overlap_count)) / max((gene_set_size - overlap_count) * (input_gene_list_size - overlap_count), 1)

• Combined Score: An overall significance measure, calculated as:

  combined_score = -log10(p_value) * odds_ratio

• Gene Ratio: The ratio of overlapping genes to the total genes in the gene set, calculated as:

  gene_ratio = overlap_count / gene_set_size

• Gene Set Size: The number of genes listed in this particular gene set.

Citing

Manuscript in preparation.

Lubiana, T., & Nakaya, H. (2024).WikiORA (version 0.2.4). Retrieved from https://wikiora.sysbio.tools

WikiORA uses Wikidata as a data source for the gene sets. It combines community curation with imports from diverse sources.We recommend also citing the major sources of information used to feed Wikidata. When using the cell type markers, we suggest also citing PanglaoDB. For gene ontology gene sets, we suugest citing also the Gene Ontology Annotation (GOA) Database and the Gene Ontology Resource .

Team

WikiORA is developed in Brazil by a team of bioinformaticians passionate about open knowledge. The project is led by Tiago Lubiana at the Computational Systems Biology Laboratory, headed by Prof. Helder Nakaya.

Contact Us

If you have any questions, feedback, or suggestions, please contact us via GitHub.

GitHub

If you like our project, give us a ⭐ on GitHub!