BioSignatureG/P™ Comparative Genomic and Proteomic Analysis

BioSignatureG/P™ Comparative Genomic and Proteomic Analysis are used for the comparison of genomic and/or proteomic data sets. Our Biosignature analysis platform enables a computational methodology that implements a comparative data analysis flow from raw data to final output reports.   Ideal for the discovery of underlying disease and drug intervention mechanisms, the BioSignatureG/P™ Analysis includes:

Data Fusion:  The first step in BioSignatureG/P™ comparative genomics and proteomics analysis is data fusion (see methodology) . Here your experimental data sets are integrated. Data sets may include:

In this step, your experimental data is also fused with prior biological knowledge. Examples of prior knowledge that will be incorporated into your analysis include:

This data may then be fused with Seralogix’ existing knowledge base which includes metabolic and regulatory pathways, as well as biological functional ontologies. Seralogix’s knowledge database is continually updated with new information so that each analysis is the most comprehensive available.

Summary Comparative Analysis:   Expression data from multi-conditional gene and protein expression experiments are compared to identify only the elements showing relevant changes in expression. Figure 1 shows an analysis involving a three-way comparison of a set of genes in which a host is infected with three different pathogens (conditions). For gene expression analysis, all the pathways, biological functions, and genes that are both uniquely expressed or conserved, or those showing temporal differences in expression among each condition, are reported. Detailed descriptions of all genes including their gene ontology, chromosome mappings, and when possible, plots such as histograms, are all reported in an easy-to-navigate results table. Proteomic data can also be incorporated into the analysis with graphical visualization of protein expression overlaid with its corresponding gene expression patterns. The gene expression states over time of the different conditions can be visualized in tables (Figure 2) or in a pathway context as shown in Figure 3.


Figure 1. Example of a few selected comparative host gene expression profiles. CLICK ON IMAGE TO ENLARGE 
Figure 2. Example summary table of differential gene expression comparative results. 
Figure 3. Example pathway visulization for a comparative analysis.  
Pathway and Gene Ontology Comparative Analysis:  Not only are statistically significant changes in gene expression reported, but changes that are significant in the context of a gene-set or pathway are also identified. This new dimension of analysis decreases the false discovery rate and provides another level of results to better guide future experiments and increase the rate of discovery. Significant genes are mapped to known metabolic and regulatory pathways and presented in an interactive pathway format. Additionally, a listing of significantly changed genes with their appropriate Gene Ontology categories is provided. The genes in each category are ranked according to their overall amount of deviation from the control state. The results table compares activated Gene Ontology processes between conditions and time point. Figure 3 shows an analysis involving a three-way comparison, in which a host is infected with three different pathogens (conditions).


Figure 4. Example pathway activation comparison over time between three different infectious agents in a common host.
CLICK ON IMAGE TO ENLARGE 

Chromosome Comparative Mapping:   Significantly changed genes are mapped to their corresponding chromosomes for further understanding of disease mechanisms and differences in response to disease or treatment (Figure 5). The results are presented in a histogram. Additional results show a graphical representation of the gene loci along the relevant chromosome.


Figure 5. Example comparative analysis of chromosome mapping of significantly altered genes.
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Summary Comparative Analyses:   Each comparative analysis produces a high-level summary of the major findings of unique and common pathway, ontology, and gene modulations as a funciton of time. Information is provided in a secure web-based report that guides the end-users through all the analysis results. A summary table for a two-way comparison is shown in Figure 6.

Figure 6. Example summary comparative analysis page. CLICK ON IMAGE TO ENLARGE 

Cross-Species Comparative Analyses:   Comparative analysis across different species can be conducted if desired. Inquire for additional information.

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