1 / 14

PIR Bio-defense Related Pathogen Data Mining

NIAID. PIR Bio-defense Related Pathogen Data Mining. November 19, 2007. Literature Mining of Pathogenesis-Related Proteins. Biodefense Proteomics Resource Center at PIR. Dengue Virus E Proteins Bioinformatics Analysis. US Army. Literature Mining of Pathogenesis-Related Proteins.

Download Presentation

PIR Bio-defense Related Pathogen Data Mining

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. NIAID PIR Bio-defense Related Pathogen Data Mining November 19, 2007 Literature Mining of Pathogenesis-Related Proteins Biodefense Proteomics Resource Center at PIR Dengue Virus E Proteins Bioinformatics Analysis US Army

  2. Literature Mining of Pathogenesis-Related Proteins • Objective: • To develop a text mining system for pathogenesis-related proteins in pathogens of military and biodefense relevance • To integrate the pathogenesis-related proteins into integrated protein databases for functional analysis • Priority pathogenic organisms: • Francisella tularensis – Gammaproteobacteria • Dengue virus – (+)ssRNA virus • Brucella – Alphaproteobacteria • Trypanosoma cruzi – Kinetoplastida • Integrated information for pathogenic proteins • UniProtKB • iProClass • Other pathway databases

  3. Functional pathway analysis iProClass Data integration Literature Mining of Pathogenesis-Related Proteins

  4. Literature Mining of Pathogenesis-Related Proteins Priority list of pathogens… 1 Document retrieval(Prioritizing) Name recognition Pathogenesis related papers 2 3 Passage highlighting n-1 System adjustment n

  5. http://pir.georgetown.edu/iprolink/rlimsp/

  6. BioThesaurus: Gene/protein name searches - synonyms, ambiguous names… http://pir.georgetown.edu/iprolink/biothesaurus/

  7. Exp. Data Gene ID Protein ID Peptide seq. UniProtKB AC/ID 1 Information 2 Function Pathway Family …… 3 Categorize, Statistics, Cross-dataset, Association Knowledge

  8. Organelle proteome data sets iProXpress– Pathway Profiling ER Mit • Protein information matrix: extensive annotations including protein name, family classification, function, protein-protein interaction, pathway… • Functional profiling: iterative categorization, sorting, cross-dataset comparison, coupled with manual examination. Mit ER KEGG pathway

  9. IP-MS Data from E2-treated breast cancer cells Gene Ontology: Molecular Process Transcriptional regulation chromatin interaction histone regulation

  10. NIAID • Albert Einstein College of MedicineT. gondii, C. parvum • Caprion Pharmaceuticals B. abortus • Harvard Institute of Proteomics V. cholerae, B. anthracis • Myriad Genetics B. anthracis, Y. pestis, F. tularensis, Vaccinia, Variola • Pacific Northwest National Laboratory S. typhimurium, S. typhi, Vaccinia, Monkeypox • ScrippsSARS CoV, Influenza • University of Michigan B. anthracis Albert Einstein PNNL U of Michigan Harvard Myriad DATA Scripps Caprion Resource Center PIR VBI SSS

  11. www.proteomicsresource.org

  12. Mouse proteins detected in B. anthracis and S. typhimurium infected macrophages

  13. Integrated Analysis:Selection Pressure, Entropy; Epitope Dengue DENV1 DENV3 DENV2 DENV4

  14. Dengue Interacting residues aa site variant exposed Interacting residues Additional Structure Analysis Exposed Result: identification of diagnostic and vaccine targets

More Related