75 Integrating Membrane Transport with Male Gametophyte ... - TAIR

103 Proteomic services at the European Bioinformatics Institute
D Thorneycroft, J Khadake, S Orchard, L Montecchi-Palazzi, S Kerrin, C Leroy, B Aranda, M Kleen, P Jones, R Cote,
L Martens, A Quinn, W Derache, C Taylor, A Fleischmann, M Darsow, K Degtyarenko, W Fleischmann, S Boyce, K
Axelsen, J Risse, M Ennis, N Vinod, P de Matos, S Klie, H Hemjakob, R Apweiler
European Bioinformatics Institute
Proteome analysis is becoming a powerful tool in the functional characterization of plants and has been applied to processes such
as photomorphogenesis, flower development, protein degradation systems, signal transduction and plant-microbe protein interactions.
These studies have expanded and refined understanding of the plant proteome and interactome in both model and crop species.
The European Bioinformatics Institute (EBI) is the European node for globally coordinated efforts to collect and disseminate
biological data. The Proteomics Services Team (EBI) provides databases and tools for the deposition, distribution and analysis of
proteomics and proteomics-related data. PRIDE, the 'PRoteomics IDEntifications database' (http://www.ebi.ac.uk/pride) is a database
of protein and peptide identifications that have been described in the scientific literature. These identifications may be annotated
with supporting mass spectra. PRIDE is a web application, so submission, searching and data retrieval can all be performed using an
internet browser. The Intact database (http://www.ebi.ac.uk/intact/index.jsp) provides a freely available, open source database system
and tools for the storage and analysis of protein interaction data. The IntAct toolkit provides textural and graphical representation of
the data and allows the user to explore protein interaction networks using a web-based interface. The database contains an increasing
amount of protein interaction data derived from model and crop plants.
The Proteomics Services team coordinates HUPO’s Proteomics Standards Initiative (PSI). , which is developing data standards
for protein-protein interactions, mass spectrometry and general proteomics. The proteomics team also provides biochemical reference
databases such as IntEnz, the Integrated relational Enzyme database which is the most up-to-date version of the Enzyme Nomenclature
and ChEBI, the Chemical Entities of Biological Interest database, a freely available dictionary of molecular entities focused on ‘small’
chemical compounds. The Proteomics Services Team seeks to constantly evolve to meet the needs of its users and play its part in the
development and adoption of proteomic standards by the scientific community. For more information visit http://www.ebi.ac.uk.
PRIDE: a public repository of protein and peptide identifications for the proteomics community. P Jones et al. Nucleic Acids Research Vol 1
Issue 34 (Database issue) D659-D663. IntAct - an open source molecular interaction database. H. Hermjakob et al. Nucl. Acids. Res. 2004 32:
D452-D455. IntEnz, the integrated relational enzyme database. Fleischmann A et al. Nucleic Acids Res. 2004 Jan 1;32(Database issue)D434-
7. Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6,
2005. S. Orchard et al. Proteomics. 2006 Feb;6(3):738-41. The European Bioinformatics Institute's data resources: towards systems biology.
Brooksbank C et al. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D46-53.
104 New Gene Discovery in Unannotated Regions of the Arabidopsis Genome
Yongli Xiao, William Moskal, Hank Wu, Beverly Underwood, Wei Wang, Erin Monaghan, Christopher Town
The Institute for Genomic Research, Rockville MD, USA.
The whole genome sequence of Arabidopsis with its annotation was completed at the end of 2000. Since then,
four versions of genome re-annotation were released sequentially based on new experimental evidence and improved
computational analysis. Evidence based mainly on sequence conservation indicated the existence of yet more genes
in un-annotated regions of the genome. TwinScan and EuGene are two relatively new gene prediction programs that
incorporate comparative genomic information. Compared with the TIGRv5 annotation, EuGene predicts 1,559 and
TwinScan predicts 1,440 genes in intergenic regions of the Arabidopsis genome with 365 predictions in common. In order
to verify the novel genes predicted by EuGene and TwinScan, a high throughput method of rapid amplification of cDNA
ends (RACE) using cDNA from 11 diverse RNA populations was applied to 918 predictions in intergenic regions. We
recovered transcripts from 429 predictions that yielded 323 novel full-length cDNAs. In addition, a comparative study
of Arabidopsis and Brassica yielded a number of Conserved Arabidopsis Genome Sequences (CAGS), 28% of which
aligned to un-annotated regions suggesting the presence of un-annotated novel genes. We similarly targeted 192 intergenic
CAGS by the RACE pipeline and found an additional 25 un-annotated genes. Thus, a total 454 of novel genes in the
intergenic regions of Arabidopsis has been recovered. We have implemented a streamlined Gateway® cloning protocol
that permits simultaneous generation of ORF clones with and without stop codons with little additional cost. To date, we
have generated ORF clones in Gateway® entry vectors for over 2,000 Arabidopsis genes, including the novel intergenic
structures described above, that are expressed at very low levels and thus absent from current EST/cDNA collections.
Research supported by the NSF 2010 Project.