FAQ

(Frequently Asked Questions)

If you publish research that involved GEneSTATION for preliminary analysis or exploration, please cite:
Kim M, Cooper BA, Venkat R, Phillips JB, Eidem HR, Hirbo J, Nutakki S, Williams S, Muglia LJ, Capra JA, Petren K, Abbot P, Rokas A, McGary KL. GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes. Nucleic Acids Res. In press.
Each page or subsection has an information icon that links to the relevant section of the methods page.
For ease of access, each major category on the gene page, EVOLUTIONARY, ORGANISMAL and MOLECULAR, is presented on a separate tab that is divided into subsections, e.g., Evolution in Mammals, Phenotype, Gene Annotation. See, for example the gene page for human FSHR. These subsections are intended to expand and include additional related types of data in future versions of GEneSTATION.
We use a standard PubMed search and quality review for studies with publicly available data. For more details, see our methods page.
The following organisms are included in the database: African Elephant, Chimpanzee, Cow, Crab-eating Macaque, Domesticated Cat, Domesticated Dog, Goat, Guinea Pig, Horse, Human, Mouse, Northern White-cheeked Gibbon, Norway Rat, Olive Baboon, Platypus, Prairie Vole, Rabbit, Rhesus Monkey, Sheep, Sumatran Orangutan, Western Lowland Gorilla, White tufted ear Marmoset, and Wild Boar.
The download link for data ( Download) is in the bottom left corner of gene pages (e.g., FSHR), SynTHy result pages, and analysis pages. The data is in JSON format.
We welcome contributions to GEneSTATION using the Upload page. In the first tab, you can upload your data and submit a request to add it to GEneSTATION. In the second and third tabs, we provide two ways to suggest the inclusion of published or publically available data.
The p-value for the gene set analysis is calculated using the cumulative hypergeometric probability, which is closely related to Fisher's exact test. The set analysis calculates the probability using the number of background genes evaluated in the analysis set (e.g., only genes with a reported dN/dS value in a study or only the genes present on a microarray), the number genes in a user's submitted set, the number of genes in each gene set stored in GEneSTATION, and the number of genes in the overlap of the submitted set and the test set.

Each type of analysis set has its own definition. Category based annotations are straightforward (e.g., gene ontology and gene age). Gene expression sets are the significantly differentially expressed genes and uses a genome wide p-val correction with a 0.05 cutoff. Selection uses the top 5% and bottom 5% of genes for dN and dS. dN/dS has a raw set and a filtered set. It is possible to have very large dN/dS values due to very small dS values, so the filtered set omits genes in the bottom 5% of dS.