An emerging cyberinfrastructure for biodefense pathogen and pathogen–host data

Zhang, C.; Crasta, O.; Cammer, S.; Will, R.; Kenyon, R.; Sullivan, D.; Yu, Q.; Sun, W.; Jha, R.; Liu, D.; Xue, T.; Zhang, Y.; Moore, M.; McGarvey, P.; Huang, H.; Chen, Y.; Zhang, J.; Mazumder, R.; Wu, C.; Sobral, B.

In the search page, http://pir.georgetown.edu/cgi-bin/ textsearch_cat.pl, the user can query the summarized gene/protein information across multiple experiments by entering any recognized gene/protein identifier (e.g. GenBank/EMBL/DDBJ, UniProtKB accession numbers), protein names, gene names or functional keyword(s). Searching over 40 fields across the tables in the database is supported. For example, by entering the text 'mitogen-activated', selecting 'protein name' in the category field and submitting the search, a summary table of mouse 'mitogen-activated' protein information is presented (Figure 2A ). The table can be customized with 'Display Options'. In the page of summarized mitogen-activated proteins, it is shown that 'mitogen-activated protein' was detected in the mass spectrometry experiment when the macrophage was infected by Bacillus anthracis ( Figure 2B ) or S. typhimurium ( Figure 2C ). Gene expression patterns of macrophage grown with different treatments were addressed as well ( Figure 2D ). By following the hyperlink on the iProClass image located at the left side of Figure 2A , the user can navigate to the comprehensive annotation data of the mitogen-activated protein, such as KEGG pathway description, KEGG ID, literature and so on.