Q: Which identifiers does g:Profiler accept? Why are my identifiers not recognized?
A: g:Profiler relies on Ensembl to provide all identifier namespaces, hence it only recognizes identifiers present in Ensembl. To make sure that g:Profiler can parse your input list, you may pass it through the g:Convert tool. All available identifier namespaces are listed in the "Target database" dropdown menu in g:Convert.
Q: Can I use g:Profiler to analyse an organism that is not in the list? Can I use my own annotations as input to g:Profiler?
A: Unfortunately, this is not possible. g:Profiler is based on Ensembl and can only use organisms present in its database. The annotations have been built into static, high performance indexes backing g:Profiler and cannot be modified at runtime.
Q: I plug the population size, sample size, population successes
and sample successes into R's
phyper function, but receive a different
p-value than what g:Profiler outputs for the term. Why?
A: This is because g:GOSt runs multiple testing correction after the analysis to
discard false positives. After finding a significance threshold
using the selected multiple testing algorithm (the custom g:SCS by default), all p-values are scaled so the
threshold would be constant at 0.05:
for each p-value Px: Px_scaled = 0.05Px / T
Q: What are some of the columns in g:GOSt output?
n. of term genes(graphical) /
n. of query genes/
n. of common genes/
Q&T— These fields contain the number of genes in a term, number of recognized genes in the input query and in the overlap of the two. If a custom statistical background has been passed, these sets have been intersected with the background, resulting in a value smaller or equal than without a background.
t type— This field is mostly useful for GO results. It denotes the GO branch of the term - either BP (biological process), CC (cellular component) or MF (molecular function).
t group(textual only) — Subgraph number. Since the GO ontology is essentially a large DAC (directed acyclic graph), any g:Profiler result can be segmented into a number of subgraphs. Each is assigned a successive integer.