Omic Data Integration
Seralogix has implemented a MySQL-based relational database to store and organize user imported experimental data and a rich set of prior biological knowledge. The data ranges from time-resolved genome-wide gene expression arrays, rna next generation sequencing reads, and protein abundance measurements to physiological responses and symptomatic observations. Prior biological knowledge databases include KEGG, REACTOME, JASPER, Genbank, Gene Ontology, protein-protein interactome (NCBI), gene-chromosome mapping etc. The import process unifies synonyms based on standard ontologies (GO, NCBI) and utilized a comprehensive ID system to keep the semantics consistent between the data entities from the different resources. A set of custom developed utility tools supports importing and updating prior biological knowledge for all the data types employed in the analysis and modeling process such as the latest genome annotations from any available species or the custom creation of a hypothetical signaling pathway.
The data integration process currently supports the integration of genomic, metabolomic and proteomic data which can be merged with pathways for their integrated visualization. While omic data is becoming easier to collect, the ability to process and analyze this data in context with other omic data is basically non-existent. The Seralogix computational tools have the ability to merge omic data into the pathway and system models. The analysis tools enable the side-by-side comparison of protein abundance data with its encoding gene expression values. Protein measurements will be provided in table format and also included within the pathway visualization interface. For example, adjacent screen shot from the web reporting tool shows a magnification of the Regulation of Actin Cytoskeleton pathway where the proteins are shown with a unique icon identifier. Mouse cursor roll-over on the protein icon shows relevant information about the protein. The connected genes are those that encode the protein. Likewise, cursor roll-over of the gene node provides gene expression information at the given time point being interrogated.return to pipeline