1 / 32

Building a Knowledge Discovery System: Integrating Bioinformatics for Drug and Disease Insights

This project focuses on developing a robust Knowledge Discovery System (KDS) that integrates bioinformatics data to elucidate the complex relationships between genes, proteins, miRNA, and their roles in diseases and therapeutics, particularly in Traditional Chinese Medicine (TCM). By utilizing analytical pipelines and databases such as KEGG and DrugBank, we aim to explore tissue-specific gene expressions and enhance drug discovery through data mining, integration, and translation, thereby fostering innovative approaches in diagnosing and treating diseases.

bao
Télécharger la présentation

Building a Knowledge Discovery System: Integrating Bioinformatics for Drug and Disease Insights

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. Building a Knowledge Discovery System

  2. Marcel Proust The real act of discovery consists not in finding new landsbut in seeing with new eyes - Marcel Proust Eying a picture is better than seeing a thousand words

  3. Uncover the hidden links Bioinformatics Data Knowledge Gene Protein miRNA SM Drug TCM Disease Symptom

  4. HT Analytical pipeline, database, algorithm, prediction/analytical tools Drug screening, TCM, Target ID, Diagnosis, Prognosis Omics, Annotation, Literature, Structure, Medical records/images Mining Clinical & HT data, Sequence, Literature etc. Focus Data Mining Data Integration Platform Building Translational Research

  5. Data Sources • KEGG • DrugBank • Locate • MGI • PubMed • iHOP • GO • OMIM Others Literature Structure HT data • NCBI - GEO • EBI – ArrayExpress • NextGen Sequencing • Connectivity Map • GWAS/SNP/aCGH • GenBank • Transfac • miRBase • InterPro • TarFisDock

  6. A Platform for Tissue-Specific Genes and beyond

  7. Gene X Gene Y Expression Profiling of TSG Tissue Specific Tissue Selective Tissue Types

  8. TSG Mining ~130 Tissues ~4000 Samples GeneLogic + Novartis

  9. liver COXPRESdb Novatis Human tissue compendium liver

  10. Drug-TSG Disease-TSG Disease-Drug Making the connection

  11. symptom Prescription Component TCM

  12. Functional Modules Batch View Multiple View Tissue View Gene View Title in here

  13. Discovery: From Diseases to Drug p < 1E-5 p < 1E-5 Enrichment (p < 1E-5)： immune response inflammatory response Cytokine-cytokine interaction Toll-like receptor signaling

  14. Discovery: From Diseases to Drug p < 0.05 TNF inhibitor： Etanercept Adalimumab Ortiz P, Bissada NFet al Periodontal therapy reduces the severity of active rheumatoid arthritis in patients treated with or without tumor necrosis factor inhibitors. J Periodontol 80: 535–540, 2009.

  15. Discovery：From Drug to Diseases p < 1E-5 Simvastatin： hypercholesterolemia cardiovascular disease

  16. Discovery：From Drug to Diseases p < 0.05 Bruner-Tran KL, Osteen KG, Duleba AJ. Simvastatin protects against the development of endometriosis in a nude mouse model. J Clin Endocrinol Metab 94: 2489–2494, 2009.

  17. Gene

  18. Literature mining Gene

  19. Disease Gene Drug 4324 – drugbank 562 – C-Map 544 – Compound 1305+ - TCM 3960 – drugbank 17119 – non-TSG 2741 – gene set 611 – miRNA 15188 – MeSH+OMIM 86 – TCM symptom 8703 – mammalian phenotype Pathway KDS 880 – KEGG + Reactome 38611 – gene ~ pathway Still growing Localiza- tion 3687 – TSG-related 52532 – gene ~ Go CC

  20. More development

  21. TFBS PFM

  22. TFBS Prediction 研究策略

  23. MAXLaps：TFBSPrediction Tool

  24. Human Gene TFBSPrediction

  25. TFBS Prediction for TSG TFBS PFM CRM1 . . . . . . . . . CRMk Tissue types CRM: T1 T2 T3

  26. Future Plan • More data collection & integration • Multiple verticals & prioritization • Mining capability & feature enrichment • Hypothesis generation & validation • Translational use • Collaboration

  27. Thanks! Xiaoqin Yang Xia Chen Guiping Wang Yun Ye Xuezhong Zhou NCBI KEGG Reactome MGI Locate Drugbank GO …… NSFC GD EA SMU

More Related