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.

2. Expression Profiling of Response to Cold, Drought and Salinity
Stress in Thellungiella salsuginea
 aka. T. halophila
 ~90-95% sequence identity with Arabidopsis
 8045 ESTs from Cold, Drought and Salinity stressed libraries
 6578 after cleaning
 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