GenBank and beyond Yanli Wang San Diego California March 13th17th 2016 251st American Chemical Society National Meeting 2 Public Data Repository at NCBI ID: 780187
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Slide1
PubChem BioAssay: Link chemical research to GenBank and beyond
Yanli Wang
San Diego, CaliforniaMarch 13th-17th, 2016
251st American Chemical Society National Meeting
Slide22Public Data Repository at NCBIOpen Research DatabaseSmall Molecule Bioactivity DataRNAi Screening
Connect to PubChem Substance
Integrated with Other Biomedical Resources
PubChem
BioAssay
…
Slide33Chemical BiologyChemgenomicsMedicinal Chemistry
Drug DiscoveryFunctional Genomics
PubChem BioAssay
… support multiple research areas
Slide4PubChem BioAssay … data standard Meta dataProtocolTargetCell lineComment / Categorized commentGrant numberEmbargo dateCross reference publication taxonomy related assays gene, nucleotide etc.Test results
Sample ID / SIDBioactivity outcome / score/potency/dose responsePhenotype annotation
Bioactivity readoutCross referenceTarget ReplicateAttributes
Slide5PubChem BioAssay … data content Statistics1,000, 000 records3,000,000 tested substances220,000,000 bioactivity outcomes1,000,000,000 data points200 chemical probesData typeHTS experimentLiterature curationBioactivityToxicitySelectivity Profiling
Slide66Links to many other databasesOMIM
Depositor website
GEO
Taxonomy
3000
BioSystems
a pathway db
PubMed
50,000
research
data
Structure
a mirror of Protein Data Bank (PDB)
CDD
conserved protein family domain
MeSH
Protein
10,000
assay target
Gene
50,000
assay target
Nucleotide
assay target
drug annotation
Literature claasifiication
Slide7Link Research Data to Molecular Target … 7BioAssay targetsall test results
specific to test reagentspecific readout
Slide88Chemical Probe F2RL3 antagonistsIC50: 0.139 uM(CID: 2333)CHRM5 antagonistsIC50: 0.44uM(CID: 42519285)mGlu5 positive allosteric PotentiatorEC50: 2.411 uM(CID: 1318633)EGFR inhibitor
IC50: 0.7079 uM
(CID: 2303746)
Thyroid Hormone Receptor /Steroid Receptor Coregulator 2interaction inhibitor
Potency: 1.4uM(CID: 5184800)STAR inhibitorIC50: 2.12 uM
(CID: 45100448)
MRGPRX1
allosteric activator
EC50: 0.19
uM
(CID:71598556)
mGluR3 modulator
IC50: 2.611
uM
(CID: 60210836)
…
200 more
Slide9Protein BioAssay Target …
Slide10Biological Pathways for Protein Target … BioSystems nameKEGG id (conserved pathway)Count of genesNeuroactive ligand-receptor interactionko04080623Calcium signaling pathwayko04020
329
cAMP signaling pathway
ko04024
299PI3K-Akt signaling pathway
ko04151
279
MAPK signaling pathway
ko04010
252
Ribosome
ko03010
220
Proteoglycans in cancer
ko05205
194
cGMP-PKG signaling pathway
ko04022
190
Focal adhesion
ko04510
189
Rap1 signaling pathway
ko04015
186
Oxytocin signaling pathway
ko04921
181
Retrograde endocannabinoid signaling
ko04723
168
Inflammatory mediator regulation of TRP channels
ko04750
168
HTLV-I infection
ko05166
165
Vascular smooth muscle contraction
ko04270
165
Chemokine signaling pathway
ko04062
163
Alzheimer's disease
ko05010
161
Epstein-Barr virus infection
ko05169
155
Adrenergic signaling in cardiomyocytes
ko04261
155
Dopaminergic synapse
ko04728
153
Slide11OrganismAssay CountRattus norvegicus391714Homo sapiens260507Mus musculus118398Staphylococcus aureus17767
Canis lupus familiaris
16884
Escherichia coli
13513Cavia porcellus
12341
Human immunodeficiency virus 1
9075
Pseudomonas aeruginosa
6654
Oryctolagus cuniculus
6574
Candida albicans
6206
Bos taurus
5277
Plasmodium falciparum
5037
Macaca mulatta
4412
Streptococcus pneumoniae
3604
Mycobacterium tuberculosis
3562
Macaca fascicularis
3244
Klebsiella pneumoniae
3031
Saccharomyces cerevisiae
2900
Cricetulus griseus
2889
Organisms …
Slide12Gene Target and its relevance to disease …
Slide13BioAssay Descriptions & Data …https://pubchem.ncbi.nlm.nih.gov/bioassay/1202
Slide14A RNAi BioAssay Record…http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=720703Gene target
Slide15Kinase selectivity profiling assay…
Slide16BioAssay Search … - classification tool for research data https://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi
Slide17BioAssay Target Search …
Slide18Link BioAssay data to Entrez Gene …18
Identify drugs & chemical modulators
Verify gene functions with RNAi data
Slide19Summary Repository of chemistry & functional genomics research data Cross link chemical biology data to genomic resources providing access to chemical tools Identify gene functions Predict target and off-targets Evaluate selectivity, promiscuity, toxicity Construct drug target network Drug repositioning
Slide20PubChem … Open & Public Resourcehttp://pubchem.ncbi.nlm.nih.gov Send questions to: pubchem-help@ncbi.nlm.nih.govpubchem-deposit-help@ncbi.nlm.nih.govywang@ncbi.nlm.nih.gov
Slide21Steve BryantEvan BoltonJie ChenTiejun ChengGang FuHaehnke Volker Lewis GeerRenata GeerAsta GindulyteLianyi HanJane HeSiqian He
Sunghwan Kim
Ben Shoemaker
Paul Thiessen
Jiyao WangBo Yu
Jian Zhang
Acknowledgement