hi, I have a set of proteins from Neisseria bacteria one specific strain with their level of expression after rat infection in different anatomical location and need to know what of those proteins have significant importance? i need a guide to know how I could search these proteins and organize them in groups according to pathogensis ? beer in the mind many of these proteins are known their pathways and very popular protein like the proteins involved in the TCA cycle and glucogenesis!! so it is difficult for example to say this protein enzyme is involved in the attachment. how could I classify them? and i would be grateful if someone can give me bioinformatically new insights to do new research’s on those proteins? Thanks
Hi Barry
To classify Neisseria proteins by pathogenic significance, start with functional annotation using UniProt, KEGG, InterPro, and VFDB. Group proteins into categories like adhesion, immune evasion, iron acquisition, toxins, metabolism, and regulatory functions using GO terms and pathway data. Analyze expression patterns across anatomical sites using clustering (PCA or heatmaps) to identify location-specific expression. Integrate interaction data via STRING to highlight multifunctional or hub proteins. For novel insights, explore moonlighting roles of metabolic enzymes, conduct comparative genomics with non-pathogenic strains, and use reverse vaccinology tools (e.g., VaxiJen, IEDB) to identify potential antigens. Consider building a machine learning model to classify unknown proteins based on expression and features. Organize findings into tables and networks for interpretation. This integrative bioinformatics approach can reveal key virulence factors and uncover novel research directions.
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