g:Profiler help

This document lists the query parameters accepted by the g:Profiler web service. All requests may be invoked as HTTP GET or HTTP POST. The data type of the parameter is specified in square brackets, one of

• string - a string value
• bool - a boolean value, 0 or 1 by convention
• int - an integer value
• float - a floating-point value

1. Parameters common for several tools

• organism - [string] Organism identifier consisting of the first character of the first part of the full Latin organism name and the second part, concatenated, lowercase (e.g. hsapiens, scerevisiae; all tools). The full list of organism IDs is available here.
• query - [string] Space-separated list of query symbols or a chromosomal range in the format chromosome:region_start:region end (all tools); see also "region_query" below
• output - [string] Parameter specifying output type, one of "html", "txt", "xls" or "mini". "txt" (textual output) and "mini" (tab-separated output without header) are most useful for programmatic access (all tools)
• prefix - [string] Treat numeric query symbols as belonging to the specified namespace (e.g. "WIKIGENE"; all tools)
• region_query - [bool] Interpret query as list of chromosomal ranges (g:GOSt, g:Cocoa, g:Convert, g:Orth)
• significant - [bool] Deliver only results deemed significant (g:GOSt, g:Cocoa)
• ordered_query - [bool] Ordered query (g:GOSt, g:Cocoa)
• no_iea - [bool] No electronic IEA annotations (g:GOSt, g:Cocoa)
• custbg_cb - [bool] Does not affect output. Documented here for historical/compatibility reasons. (g:GOSt, g:Cocoa)
• custbg - [string] A space-separated list of symbols to use as custom stat. background (g:GOSt, g:Cocoa)
• user_thr - [float] User-specified p-value threshold (g:GOSt, g:Cocoa)
• threshold_algo - [string] Parameter specifying the algorithm used for determining the significance threshold, one of "analytical", "bonferroni", "fdr" (g:GOSt, g:Cocoa)
• domain_size_type - [string] Parameter specifying the statistical domain size, one of "annotated" (only annotated genes) or "known" (all known genes) (g:GOSt, g:Cocoa)

2. g:GOSt-specific parameters

Request URL: http://biit.cs.ut.ee/gprofiler/

• term - [string] If used instead of "query", specifies a term ID to use as the query instead of a space-separated list of genes (e.g "GO:0009059")
• sort_by_structure - [bool] Hierarchical sorting, display parent-child relationships between terms

3. g:Cocoa-specific parameters

Request URL: http://biit.cs.ut.ee/gprofiler/gcocoa.cgi

• compare - [int] Parameter specifying the comparison method: 1 - order by appearance, 2 - order by similarity to first query, 3 - order by total significance

4. g:Convert-specific parameters

Request URL: http://biit.cs.ut.ee/gprofiler/gconvert.cgi

• target - [string] Target database (namespace) for conversion; for a full list, see http://biit.cs.ut.ee/gprofiler/gconvert.cgi

5. g:Sorter-specific parameters

Request URL: http://biit.cs.ut.ee/gprofiler/gsorter.cgi

• matrix - [sting] Microarray dataset, for a full list, see http://biit.cs.ut.ee/gprofiler/gsorter.cgi
• number - [int] Number of (most similar / dissimilar) probes to retrieve
• order - [string] One of "normal" (retieve similar probes), "reverse" (retrieve dissimilar probes), "mirror" (retrieve mirroring probes)
• distance - [string] Distance measure; one of "pear" (Pearson correlation), "abspear" (absolute Pearson correlation), "uncentcorrel" (uncentered correlation), "absuncentcorrel" (absolute uncentered correlation), "eucl" Euclidean distance), "maxdiff" (maximum difference)

6. g:Orth-specific parameters

Request URL: http://biit.cs.ut.ee/gprofiler/gorth.cgi

• target - [string] Target organism (see also "organism" above)