goa_gubbar

Copyright Notice

goa_gubbar is copyright (c) 2006 Magnus Palmblad

goa_gubbar is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

About goa_gubbar

goa_gubbar, or gene ontology annotation grouping under biochemical and biological activities and roles, is a tool for grouping protein hits under slim GOA terms, including all possible slim GOA for each protein and carrying forward abundance ratios and other statistical information on protein ratios in quantitative proteomics.

goa_gubbar takes as input a list of proteins, abundance ratios and standard deviations or uncertainty (from multiple peptides used in the relative protein quantitation).

The utility can be used to summarize protein identification datasets according to protein function or cellular location, as illustrated below.




Figure 1. Pie and donut charts of distributions of identified proteins according to biological process and biochemical activity, the donut chart comparing two sets of protein identifications.


Download goa_gubbar by clicking here. (Right-click and choose "Save Link As...".)

Compiling goa_gubbar

Compile goa_gubbar with: gcc -o goa_gubbar goa_gubbar.c

This is tested and works under Linux and Windows/Cygwin.

Using goa_gubbar

Usage: goa_gubbar <protein expression ratios> <species GOA file> <GOA slim map> <slim OBO file> <output>

where <protein expression ratios> is a space delimited list of identified proteins, abundance ratios and standard deviations.

For an example species GOA file, see gene_association.goa_arabidopsis. The suitable corresponding slim OBO file is goslim_goa.obo and GOA slim mapping goaslim.map. These are available from the EBI Gene Ontology Annotation (GOA) Database (http://www.ebi.ac.uk/GOA/).


magnus.palmblad@gmail.com