Modulating the body's networks could become mainstream therapy for many health issues.
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Contributed by Steven P. Briggs, November 11, 2008
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↵1N.E.C., S.H.P., and Z.S. contributed equally to this work. (received for review June 19, 2008)
Article Figures & SI
Figures
- Fig. 1.
Work flow. All mass spectra are compared with three databases using Inspect. Spectra are filtered to a 1% false discovery rate and grouped into peptides. Novel peptides are separated from those that appear in TAIR7 and clustered. It is important to note that only a subset of the novel peptides appear in a peptide cluster. Novel peptide clusters are then segregated based on genome location. Those that overlap a current gene model (intragenic) are further classified by how they refine the model. Peptides that do not overlap a gene model (intergenic) are classified by whether they overlap a pseudogene. The peptide clusters, along with evidence from cDNA and current gene annotations, are given to the gene predictor AUGUSTUS to produce new gene models. Not all peptides in the peptide clusters are included in the final AUGUSTUS models.
- Fig. 2.
Novel gene supported discovered by proteogenomics. (A) A cluster of 13 uniquely located peptides that do not overlap a current gene model (Chr3). The prediction track shows the single exon gene model produced by AUGUSTUS. (B) The predicted sequence shows strong homology to a Thylakoid lumen family protein (sp|P82658|TL19_ARATH). It also shows strong similarity to proteins in both grapevine (emb|CAO40861.1 a hypothetical gene) and rice (Os08g0504500 a cDNA derived gene).
- Fig. 3.
Peptides overlapping a predicted transposable element gene. (A) 5 peptides, 4 unique, overlap locus AT4G07947, which is annotated as a transposable element gene. (B) Sequence alignment to an Arabidopsis Ulp1 (ubiquitin like protease) showing strong conservation (56% identity, e value 0.0). Observed peptides highlighted.
- Fig. 4.
Refined Gene Model. TAIR locus AT1G63500 encodes a protein kinase. (A) Four novel peptides map within the 5′ UTR and the first exon. (B) Zoom of the region shows that the current first exon (frame 3) is out of frame with the peptides (frame 2). (C) Sequence alignment with Arabidopsis and grapevine proteins supports translation in the frame supported by peptides (observed peptides highlighted in alignment).
Data supplements
Supporting Information
Files in this Data Supplement:
Discovery and revision of Arabidopsis genes by proteogenomics
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