Avadis NGS provides the capability to learn how genes interact with each other using information extracted from the literature as well as from canonical pathways. Avadis NGS allows the user to ask and answer questions like: Which small molecules or other genes might interact with my list of genes? Interactions between genes and small molecules may provide insight into the functionality of the genes.
Extracting interaction data from literature
Much of human research results have been reported in scientific literature, and it has become increasingly difficult for any one researcher to read all the journal articles that are relevant to their research. Strand has developed a natural language processing (NLP) technology that understands the grammar of English sentences and can extract this interaction information from literature (in the life sciences). This information can be stored in a database and later used to infer relationships between genes, protein, small molecules, and processes.
When a journal article describes the result of a particular experiment such as: TLR-2 expression on monocytes was enhanced by macrophage colony-stimulating factor (M-CSF) and interleukin-10 (IL-10), but was reduced by transforming growth factor beta1, the NLP technology is able to extract the relationships between the gene products and record the information in a database. The NLP technology “knows” that transforming growth factor beta1 is the same as the protein with the gene name “TGFB1,” and this information can be used to construct interaction diagrams as shown below. The NLP tools are also made available so that users may add their own interactions to the database by parsing input text of their choosing (full-length articles, pdf files, html documents, Word documents, text files).
Download pathway interaction data
Strand has used this NLP technology to construct an Interaction Database for a wide variety of organisms. This database is freely available for Avadis NGS users and can be downloaded from the Strand Server using the menu option Annotations > Update Pathway Interactions > Update from Strand Server.
This will allow the user to select an organism for which to download the database. After the download process has completed, the database is ready for use.
Interaction networks and pathways can be shown in the main window and visualized in a number of ways as shown in the figure below. It shows the same pathways visualized in different styles. The cellular organization shows the location of the gene products with respect to the cellular location (if known).
Information can be overlaid on the networks. The image below shows the overlay of the abundance values from an RNA-Seq experiment (the bars on top of the proteins show the expression level for 4 conditions) as well as an indication of up- or down-regulation (blue is down-, and red is up-regulation). This allows for a very rich visual experience in Avadis NGS.
These interaction networks can be saved for future reuse and become pathways that can be used in future analysis to determine if a list of genes contains a statistically significant over-representation of genes belonging to the pre-existing, newly created pathway. Use the Workflow step Pathway Analysis or Find Significant Pathways (in the section Results Interpretation).