Biology Reference
In-Depth Information
Center for Biotechnology Information non-reduntant
(NCBInr) protein database ( http://www.ncbi.nlm.nih.gov/).
Sequences are retrieved using the keyword search enquiry
“organism,” adding potentially contaminating proteins retrieved
using the keyword search enquiry “trypsin” OR “keratin.”
34. Check manually one by one each protein description one to
one all the loaded sequences within the project. The descrip-
tions can be modifi ed by clicking right button of the mouse
over the protein entry and selecting “change annotation and
description.”
35. Revise manually the GO terms associated to all the sequences
loaded to the project. Once the Blast, mapping, and annota-
tion processes are fi nished, the application offers the possibility
of direct statistical analysis on protein function information.
A common analysis is the statistical assessment of GO term
enrichments in a group of interesting proteins when com-
pared with a reference group [ 47 ]. This enrichment analysis is
based on the Fisher's Exact Test applying a robust false discov-
ery rate (FDR) correction for multiple testing and returns a list
of signifi cant GO terms ranked by their corrected or one-test
p -values. B2G performs various statistical charts which allow
visualization of the results obtained at blasting, mapping, or
annotation.
Acknowledgements
This work has been supported by research grants from MICINN-
FEDER (BIO2008-2941, BFU2009-08151, and BIO2011-
29856-C02-02). ABSJ and AL held a grant from the Ministerio de
Ciencia e Innovación. MJME acknowledges a grant from Fundación
Caja Murcia-University of Alicante. University of Alicante
Proteomics Facility is a member of Proteored (ISCIII). JCV
acknowledges support from Red Temática de Investigacion
Cooperativa de Cáncer (RTICC).
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