Functional Genomics Resources in Thellungiella and Sinorhizobium
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The document describes a study that analyzed expression profiling of the plant species Thellungiella salsuginea in response to cold, drought, and salinity stress. 8045 ESTs were obtained from stressed libraries and 6578 remained after cleaning. 3628 assemblies resulted after gene clustering. The study found little overlap in gene expression between the different stresses.
Functional Genomics Resources in Thellungiella and Sinorhizobium
- 2. Expression Profiling of Response to Cold, Drought and Salinity Stress in Thellungiella salsuginea ï‚ž aka. T. halophila ï‚ž ~90-95% sequence identity with Arabidopsis ï‚ž 8045 ESTs from Cold, Drought and Salinity stressed libraries ï‚ž 6578 after cleaning ï‚ž 3628 assemblies after gene-index-style clustering Wong, C.E., Li, Y., Whitty, B.R., Diaz-Camino, C., Akhter, S.R., Brandle, J.E., Golding, G.B., Weretilnyk, E.A., Moffatt, B.A. and M. Griffith, "Expressed Sequence Tags from the Yukon Ecotype of Thellungiella salsuginea Reveal That Gene Expression in Response to Cold, Drought and Salinity Shows Little Overlap", Plant Molecular Biology 2005 Jul;58(4):561-74. Wong, C.E., Li, Y., Labbe, A., Guevara, D., Nuin, P., Whitty, B., Diaz, C., Golding, G.B., Gray, G.R., Weretilnyk, E.A., Griffith, M. and B.A. Moffatt, "Transcriptional Profiling Implicates Novel Interactions Between Abiotic Stress and Hormonal Responses in Thellungiella, a Close Relative of Arabidopsis", Plant Physiology 2006 Feb 24. Working towards a yet uncompleted M.Sc. @McMaster, 2002-2005
- 6. Phylogenetic Profiles for Protein Functional Prediction in Sinorhizobium meliloti Working towards a yet uncompleted M.Sc. @McMaster, 2002-2005
- 7. Phylogenetic Profiles • A phylogenetic profile is an array representing the presence or absence of an ortholog of a query protein within a set of subject proteomes. • The phylogenetic profiles method assumes if two proteins have a functional association, they will be conserved together through evolution. Working towards a yet uncompleted M.Sc. @McMaster, 2002-2005
- 9. KEGG Pathway Assignment More Genomes! TIGR Gene Pairs
- 10. Query Protein: Complete archaeal/eubacterial proteomes SMc03019 / fliG Flagellar motor switch protein Increasing distance between profiles Below average homology Above average homology Nearest neighbours to the query protein’s profile. Each square in a protein’s profile represents the presence of a homolog of Functional relationships are predicted based on profile distance, that protein in a given proteome not any measure of similarity between the proteins sequence/structure. ***In this case all are flagellum-associated proteins***
- 12. Creating the Profiles • Putative orthologs are now identified using the ‘reciprocal shortest distance’ algorithm. – Statistically significant reciprocal top hits are collected between a query protein and a subject genome. – A multiple alignment is performed on the top hits (CLUSTALW), followed by maximum likelihood estimation of the number of amino acid substitutions between the proteins (PAML). – If a query and subject protein are found to have a reciprocal shortest evolutionary distance relationship, then the pair is assumed to be truly orthologous. Working towards a yet uncompleted M.Sc. @McMaster, 2002-2005
Editor's Notes
- #11: This is a general example of what the display of the phylogenetic profile web page looks like. In this case, the query protein is SMc03019 (fliG) --- a flagellar protein. All of the closest neighbours shown here are also flagellar proteins, reinforcing the idea that this method can identify functionally related proteins. Predicted relationships between proteins DO NOT depend on any sequence or structural similarity (this is a key point), but are determined by the measure of distance between the profiles for each protein. These profiles themselves ARE determined by identifying the presence or absence of homologs for each protein of the Sinorhizobium proteome across all the other complete proteomes of the fully sequenced bacterial genomes currently available from GenBank (in the horizontal direction along the length of the profile); but, again the predicted relationships between Sinorhizobium proteins (profile neighbours --- in the vertical direction moving downwards) are based ONLY on profile similarity. Normalized homology scores are a measure of homology relative to the average level of homology for all homologs of Sinorhizobium proteins within a given bacterial genome; and are based on the alignment scores of a Smith-Waterman alignment of the query Sinorhizobium protein with the bi-directional best-hit (BLASTP) within the target genome --- they are also normalized for length of the alignment. Sinorhizobium against itself appears as a column of yellow spots (1.0 score) all the way down.
- #12: This slide shows an example of a query protein, SMc01915 (nuoD1), for which the nearest neighbour is a ‘Conserved Hypothetical Protein’, and other nearest neightbours have a KNOWN RELATED FUNCTION to the query protein (in this case there are THREE unknowns amongst the known neighbours --- they are indicated by the arrows)