|
Sign In to gain access to subscriptions and/or personal tools.
|
Tools for Interpreting Large-scale Protein Profiling in Microbiology
E.L. Hendrickson1,2,
R.J. Lamont3 and
M. Hackett1,*
1 Departments of Chemical Engineering
2 Microbiology, University of Washington, Box 355014, Seattle, WA 98195, USA
3 Department of Oral Biology and Center for Molecular Microbiology, College of Dentistry, Box 100424 JHMHSC, University of Florida, Gainesville, FL 32610, USA
View larger version (91K):
[in this window]
[in a new window]
|
Figure 1. Examples of different approaches to visualizing quantitative proteomics data. (A) Pseudo-abundance ratio measurement (M) vs. overall signal strength (A) plot of 791 P. gingivalis proteins determined by spectral counting. Green indicates under-expression when P. gingivalis was co-incubated with S. gordonii and F. nucleatum; red, over-expression; black, no change in abundance. The solid black lines, LOWESS curves (Cleveland, 1981), indicate boundaries for the region of expected random error about an abundance change of zero, and can also be used to estimate the power to detect abundance change as a function of total spectral counts at any point on the x-axis. (B) An example of proteomics data displayed in genome order, P. gingivalis’ response to co-incubation with S. gordonii by spectral counting. Each circle represents an annotated protein-encoding ORF in the order that it is encoded in the genome. Colored circles show the results of the quantitative proteomic analysis. Green indicates under-expression in P. gingivalis cells co-incubated with S. gordonii compared with P. gingivalis alone; red, over-expression; yellow, proteins that were identified, but showed no statistically significant abundance change; grey, no protein was detected. Blacked out regions indicate ORF numbers for which there is no TIGR annotation. (C) A section of the genomic representation of three M. maripaludis proteome experiments displayed in MEV (Multi-experiment Viewer, www.tm4.org/mev.html). Each row represents an ORF in the order that it is encoded in the genome (MMP1662-1680). Undetected proteins in this range are not shown. The annotation of each ORF is listed at the end of the row. The columns represent experimental conditions. NH4/H2, ammonia-limiting compared with H2-limiting growth conditions; P/H2, phosphate-limiting compared with H2-limiting growth conditions; P/NH4, phosphate-limiting compared with ammonia-limiting growth conditions. The colors represent a gradient of differential abundance between the conditions, from green for over-expression to red for under-expression, with black showing no change in abundance.
|
|
View larger version (71K):
[in this window]
[in a new window]
|
Figure 2. The P. gingivalis metabolic pathway map from BioCyc (www.biocyc.org). This is the metabolic map prior to the overlaying of any data onto the pathways. The name ‘Calvin cycle’ was added to the map to highlight the location of this metabolic pathway. Color examples of individual metabolic pathways with accompanying proteomics data can be found in the APPENDIX.
|
|
View larger version (32K):
[in this window]
[in a new window]
|
Figure 3. The absence of natural clusters in protein abundance ratio data. (A) P. gingivalis proteomic data displayed as the log 2 of the spectral counts for internalized (y-axis) against control cells (x-axis). (B) As in (A), but displaying only points with at least a two-fold difference between internalized and control cells. (C) M. maripaludis proteomics data plotting the protein ratios of phosphate-limited/ammonia-limited samples (y-axis) against the ratios of phosphate-limited/H2-limited samples (x-axis). In this display, proteins regulated by phosphate limitation fall along the diagonal. (D) As in (C), but displaying only points with at least a 1.4-fold difference between conditions for both phosphate/ammonia limitation and phosphate/H2 limitation.
|
|
View larger version (51K):
[in this window]
[in a new window]
|
Figure 4. Classification and clustering of the M. mairpaludis proteome. Each row represents an ORF from M. maripaludis. The annotation of each ORF is listed at the end of the row. The columns represent experimental conditions. NH4/H2, ammonia-limiting compared with H2-limiting growth conditions; P/H2, phosphate-limiting compared with H2-limiting growth conditions; P/NH4, phosphate-limiting compared with ammonia-limiting growth conditions. The abundance changes are shown in gray scale, with black showing no change in abundance. A color version of the figure can be found in the APPENDIX. (A) Flagella protein expression class. Proteins were classified as matching the abundance pattern of flagella proteins by means of the ‘K nearest neighbor’ algorithm in MEV (www.tm4.org/mev.html). A leave-one-out validation was conducted for the classification (Theilhaber et al., 2002). The procedure involves re-running the classification, leaving out one of the original training group proteins, and doing this for all of the members of the original training group. Proteins that were present in the class across the entire leave-one-out validation are indicated in bold. (B) A subsection of the agglomerative hierarchical clustering of the M. maripaludis proteome in MEV. The dendrogram shows the protein relationships in the clusters.
|
|
View larger version (40K):
[in this window]
[in a new window]
|
Figure 5. Ontology diagrams of proteins from P. gingivalis and M. maripaludis. (A) Ontology of the 60-kDa chaperonin GroEL (PG0520) from P. gingivalis. The position of GroEL is shown for two of the three ontologies in the Gene Ontology (http://www.geneontology.org/), Biological process and Molecular function. The light gray box represents the protein. All other boxes represent ontology terms. The arrows indicate category relationships. (B) Ontology of the protein N5-methyltetrahydromethanopterin: methyl transferase A (MtrA) (MMP1564) from M. maripaludis. The position of the methanogenesis protein MtrA, as given in GoMiner (http://discover.nci.nih.gov/gominer/), is shown for two of the three ontologies in the Gene Ontology, Biological process and Molecular function. The light gray box represents the protein. All other boxes represent ontology terms. The arrows indicate category relationships. Dashed lines and circled crosses indicate categories to which the protein was not assigned (see text discussion).
|
|
Journal of Dental Research, Vol. 87, No. 11,
1004-1015 (2008)
DOI: 10.1177/154405910808701113
 CiteULike  Complore  Connotea  Del.icio.us  Digg  Reddit  Technorati  Twitter What's this?
|
|
