Skypainter is a tool to determine which events (reactions and/or pathways) are statistically overrepresented in a set of genes as specified by submitted list of identifiers. In other words, given a list of genes, Skypainter can identify common events for these genes.

Given a set of M genes which participate in an event, the total of X genes (for the given species) that Reactome is aware of, and given the submitted list of K genes of which N genes participate in the given event, skypainter calculates (by performing the hypergeometric test) the probability of picking N or more genes involved in the given event purely by chance. Hence a low probability suggests that participation in a given event is what the genes in the submitted list have in common. Note, however, that the probabilities as reported by Skypainter are not corrected for multiple testing arising from evaluating the submitted list of genes against every event for the given species.

Identifiers which can be used are UniProt accession numbers and ids, GenBank/EMBL/DDBJ protein ids, RefPep, RefSeq, EntrezGene, MIM, InterPro, Affymetrix, Agilent and Ensembl protein, transcript and gene identifiers. All purely numeric identifiers, such as from MIM and EntrezGene have to have the abbreviated database name and colon prepended to them, i.e. MIM:602544, EntrezGene:55718.

The colour of each reaction arrow on the reaction map indicates the the number of genes in the submitted list that participates in the reaction.

Similar functionality, i.e colouring reactions according to the number of times the reaction is hit by the identifiers in the submitted list, is also available for small molecule identifiers from ChEBI and KEGG COMPOUND identifiers (e.g. ChEBI:2359, C00002), Enzyme Commission (EC) numbers (e.g. 1.1.1.1) and Gene Ontology (GO) accession numbers (e.g. GO:0004672). GO cellular component accession numbers can be used to highlight reactions involving molecules localized to that compartment or which themselves correspond to the given GO cellular component term. GO molecular function accession numbers highlight reactions which are catalysed by the activities they specify. GO biological process accession numbers highlight reactions which either correspond or are components of pathways corresponding to the given GO biological processes. Please note that the overrepresentation analysis is not performed for those identifiers.

If the identifiers are followed (separated by space or tab) by a numeric value, the colouring will be done according to the average of the numeric values of all identifiers linked to the reaction. A time series can be displayed as an animation by providing multiple values (on the same line, separated by a single space or tab) for each identifier. This feature can be used, for example, to produce a "movie" on the basis of micro-array expression analysis a time series.To see an example of the Reactome reaction map painted using a test set of identifiers, click on the hyper-linked word "identifiers" in the data entry box above. To see an example of the reaction map painted using a test set of identifiers with values (producing a "movie") click on the words "identifiers with values" in the data entry box. Please note that the overrepresentation analysis is not performed in this case.