Although human genes are completely supported, other organisms lack support for one or more types of annotations.
|Infer from Network||Yes||Yes||Yes||Yes|
We hope to add support for more organisms and annotations in the future. If your favorite organism or annotation is missing, please let us know!
GATHER accepts Probe Set IDs from the following Human Affymetrix
chips: U133A, U133Av2, U133B, U133+2, U95A, U95Av2, Hu35KA/B/C/D,
Mouse Affymetrix chips: U74Av2, U74Bv2, U74Cv2, 430 2.0, 430A 2.0, Mu11KA/B.
Rat Affymetrix chips: U34A, 230A/B/2.0.
Fly Affymetrix chips: Genome 2.0.
GATHER accepts IDs from the following Operon chips: Human v3, v4; Mouse v3, v4; Drosophila V1.
If your favorite database or microarray chip is not included in this list, please let us know. If it's a common ID that many people request, we'll try to add it.
A positive Bayes factor indicates that the evidence supports the hypothesis that the annotation is more related to your list of genes than other genes in the genome. A negative Bayes factor indicates that the evidence suggests that the annotation is more strongly associated with other genes in the genome.
It is hard to choose an appropriate cutoff for Bayes factors. It measures the amount of evidence supporting the annotation, so the cutoff depends on what you intend to do with the information. If you need to prove an association beyond a shadow of doubt, you need to have a high Bayes factor cutoff. On the other hand, if you can accept annotations upon a preponderance of evidence, you can use a lower Bayes factor cutoff.
Still want a cutoff? OK, we recommend 6, as that cutoff appears to balance false positives with false negatives (see Chang and Nevins, accepted for publication).
1. GO:0007049 : cell cycleThe GO:0007049 is the unique identifier and cell cycle is the description for this GO annotation.  indicates the depth of that annotation. GO terms are structured as a tree such that deeper terms are refinements of their parents. For example, "cell cycle" at depth 5 is a refinement of "cellular physiological process," which is at depth 4.
The resultant table contains the following columns:
|#||An index to number the annotations.|
|Annotation||The name of the annotation.|
|Total Genes With Ann||The number of genes from your list that have the annotation. If the Include Homologs inference is used, then this number will also include the homologous genes with the annotation from other organisms.|
|Your Genes (With Ann)||The number of genes from your list with the annotation.|
|Your Genes (No Ann)||The number of genes from your list without the annotation.|
|Genome (With Ann)||The number of genes in the genome (excluding those in your list) with the annotation.|
|Genome (No Ann)||The number of genes in the genome (excluding those in your list) without the annotation.|
|ln(Bayes factor)||The Bayes factor quantifying the amount of evidence supporting the hypothesis that the annotation is associated with your gene list. This is the same number that is shown on the website, but here, it is not rounded -- it contains more significant digits.|
|neg ln(p value)||The negative logarithm of the p value calculated from the Bayes factor (see Supplementary materials for the publication). The website shows the actual p values, but here, they are reported as logarithms for a more compact representation.|
|FE: neg ln(p value)||The negative logarithm of the p value calculated using a Fisher's exact test.|
|FE: neg ln(FDR)||The false discovery rate based on the Fisher's exact p value.|
|Genes||The symbols of the genes that have the annotation. If the Include Homologs inference is used, the homologous genes that have the annotation will also appear, but with a :H suffix. Similarly, if the Infer from Network inference is used, the genes that were included based on the network inference, and also have the annotation, will have a :N suffix.|
The server will return the results as a tab-delimited text file. Please add a 2s delay between queries so that the server is not saturated with requests. We do monitor for excessive use and will throttle or cut off a connection if it is degrading the quality of service for others. If you need to run a large batch of queries, contact us.