ANALYSIS

Figure 1: Bacterial profile maps of HOMIMs of clinical samples.

Figure 1: Bacterial profiles of 461 bacterial taxa (representing about 300 species) comparing subgingival plaque from 105 healthy sites in periodontally healthy subjects (n=20) to 154 diseased sites from periodontally diseased subjects (n=47). Differences in profiles can be seen at a glance.

 

Figure 2: Bacterial profile maps of HOMIMs of clinical samples.

Figure 2: (A) Bacterial profiles of over 200 bacterial species comparing 10 samples from a single mouth. (B) Magnified from (A) illustrating dendrogram of cluster analysis and partial list of bacterial species tested. Band intensities represent relative bacterial proportions

Figure 2A illustrates data from individual HOMIM signals translated to a “bar code” format and normalized by comparing individual signal intensities to the average of signals from universal probes. The bands correspond to presence or absence and band intensities are scored as 0, 1+, 2+, 3+, 4+ or 5+. Thus more intense bands reflect higher proportions of a given species. Figure 2A represents a bacterial profile comparison of over 200 bacterial species of samples from 10 different sites in a single mouth. Differences or similarities in profiles can readily be seen. Samples are subsequently subjected to a variety of cluster analysis programs (Dr. George Chen, The Forsyth Institute). These analyses will also be available soon for online use at http://bioinformatics.forsyth.org/homim. The dendrogram of the cluster analysis is more clearly shown in Figure 2B. The cluster method used was UPGMA with a correlation distance function. Other cluster analyses such as single, complete, WPGMA, UPGMC, and WPGMC and other distance functions, such as Euclidean, Square, Offset, Spearman, and Jackknife can also be used. The cluster programs sort the samples into the appropriate clusters, but samples can also be analyzed without clustering. All data are also available in Excel tables.

 

Each registered user will have online access to a final report, raw data and analysis through a dedicated website. Details of data analysis can be found at http://bioinformatics.forsyth.org/homim. Data is cumulative so analyses of old data can be compared with new data. Data can also be shared upon agreement of registered users.