shuang liang ● southern medical university building a knowledge discovery system
TRANSCRIPT
Shuang Liang ● Southern Medical UniversityShuang Liang ● Southern Medical University
Building a Knowledge Discovery System
Building a Knowledge Discovery System
The real act of discovery consists not in finding new lands but in seeing with new eyes - Marcel Proust
Marcel ProustMarcel Proust
Eying a picture is better than seeing a thousand words
Uncover the hidden linksUncover the hidden links
DiseaseSymptom
GeneProteinmiRNA
SM DrugTCM
Data Knowledge
Bioinformatics
FocusFocus
Data Mining
Data Integration
Platform Building
TranslationalResearch
Mining Clinicaldata, Sequence, Literature etc.
Omics, Annotation, Literature,Structure, Medical records/images
HT Analytical pipeline, database, algorithm, prediction/analytical tools
Drug screening, TCM, Target ID, Diagnosis, Prognosis
NCBI - GEO EBI – ArrayExpress NextGen Sequencing Connectivity Map GWAS/SNP/aCGH
HT data Literature Structure Others
KEGG DrugBank Locate MGI
PubMed iHOP GO OMIM
GenBank Transfac miRBase InterPro TarFisDock
Data SourcesData Sources
Gene Y
Expression Profiling of TSGExpression Profiling of TSGGene X
Tissue Types
Tissue Specific
Tissue Selective
~130 Tissues~4000 Samples
TSG Mining
GeneLogic+ Novartis
liverCOXPRESdb
liver
Novatis Human tissue compendium
Disease-TSG
Drug-TSG
Disease-Drug
Making the connection
symptom
Prescription
TCM
Component
Data Type Number
Tissue/Cell types 127
TSGs 3960
TSG - Disease relationships 5672
TSG - Drug relationships 2171
TSG - Subcellular Localization 3687
TSG - GO annotation 47418
TSG - Pathway 6359
TSG - Mammalian Phenotype 32397
Functional ModulesFunctional Modules
Batch View
Tissue View Multiple View
Title in hereGene View
Discovery: From Diseases to DrugDiscovery: From Diseases to Drug
Enrichment (p < 1E-5):immune responseinflammatory responseCytokine-cytokine interactionToll-like receptor signaling
p < 1E-5
p < 1E-5
Discovery: From Diseases to DrugDiscovery: From Diseases to Drug
TNF inhibitor :EtanerceptAdalimumab
Ortiz P, Bissada NF et 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.
p < 0.05
Discovery : From Drug to Diseases Discovery : From Drug to Diseases
Simvastatin:hypercholesterolemiacardiovascular disease
p < 1E-5
Discovery : From Drug to Diseases Discovery : From Drug to Diseases
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.
p < 0.05
Gene
Literature mining
Gene
Drug
Pathway
Localiza-tion
Disease
Gene
KDS
– drugbank562 – C-Map544 – Compound1305+ TCM
– drugbank17119 – non-TSG2741 – gene set611 – miRNA
– MeSH+OMIM86 – TCM symptom8703 – mammalian phenotype
– TSG-related52532 – gene ~ Go CC
– KEGG + Reactome38611 – gene ~ pathway
Still growing
PFM
TFBSTFBS
TFBS PredictionTFBS Prediction
研究策略
MAXLaps : TFBS Prediction ToolMAXLaps : TFBS Prediction Tool
Motif MEME NMICA this study
HLF200 bp Yes Yes Yes
800 bp No No Yes
C-FOS200 bp Yes Yes Yes
600 bp No No Yes
HFH-1800 bp Yes Yes Yes
1400 bp No No Yes
Human Gene TFBS PredictionHuman Gene TFBS Prediction
T1 T2 T3
TFBS PFMCRM1.........CRMk
TFBS Prediction for TSGTFBS Prediction for TSG
CRM:
Tis
sue
type
s
Future PlanFuture Plan
More data collection & integration
Multiple verticals & prioritization
Mining capability & feature enrichment
Hypothesis generation & validation
Translational use
Collaboration
Shuang Liang ● Southern Medical UniversityShuang Liang ● Southern Medical University
Xiaoqin Yang
Xia ChenGuiping WangYun Ye
Xuezhong Zhou
NCBIKEGGReactomeMGILocateDrugbankGO……
NSFC
GD EA
SMU