GAIL (Gene-Gene Association Inference based on biomedical Literature) is a web interface and database that allows the investigation of human gene-gene association networks based on shared gene-GO co-occurrences in PubMed abstracts. To see how the output of GAIL can be analyzed using relevant software (BayesGO), please visit the software page.
GAIL uses a Neo4j graph database to store its data in a graph data structure. The genes and GO terms are stored as graph nodes. Gene-GO associations and gene-gene associations are stored as graph edges. GAIL currently supports search using HUGO Gene Nomenclature Committee (HGNC) IDs and GO IDs. For genes, if you have other identifiers than HGNC IDs, GAIL provides an ID mapper function to translate supported identifiers into HGNC IDs.
| Function | Description |
|---|---|
| Network Query |
The network query currently provides service for user to query a gene-gene association network for a given list of gene, using HUGO Gene Nomenclature Committee (HGNC) official IDs. |
| Gene Query |
The gene query allows user to search a list of interested genes using HGNC official IDs, and get all associated GO terms from our biomedical literature database. Hypergeometric test p-values with or without Bonferroni correction are also given. External links to GeneCard on the page allow user to get more detailed info about the gene. |
| GO Query |
Similarly, the GO query allows user to search a list of interested GO terms using GO IDs, and get all associated genes from our database. Hypergeometric test p-values with or without Bonferroni correction are also given. External links to AmiGO on the page allow user to get more detailed info about the gene. |
| Gene-GO Query |
The gene-GO query allows user to retrieve a gene-GO association p-value matrix. Hypergeometric test p-values with or without Bonferroni correction are also given. |
| ID Mapper |
The gene query and network query require to use official HGNC ID. We provide a simple ID mapper function to map a list of gene names/synonyms to possible official HGNC IDs. A matched list of HGNC IDs will be returned. |
