systems pharmacology 3: predicting drug side effects
TRANSCRIPT
Side effect Prediction
Based on L1000 data
By: Ali Kishk
SEP-L1000 serves the results of the predicted ADRs for the drugs and small-molecule compounds profiled in the LINCS L1000 project.
Used Data :1. L1000 transcriptomic profiles “gene-list”2. Chemical Structure fragments “Great for
integrating Structural Biology data”3. Morphological features of 812 cell line4. Enrichment Profiles
SEP-L1000
Other used data : FAERS• On-label ADRs of FDA-approved drugs were downloaded
from SIDER , which covers :• 996 marketed drugs,
4,192 ADRs99,423 drug-ADR associations.
Off-label ADRs were retrieved from the Offside table [2], which has processed data from the post-market ADR reports within the FDA Adverse Event Report System (FAERS), covering:
• 1,322 drugs10,097 ADRs438,801 drug-ADR associations.
SEP-L1000 Workflow (A) Venn diagram shows the overlap between drugs and small molecule compounds across different data sources.
(B)use of drug-feature matrices of different types to predict adverse drug reactions using multi-label classification.
Zichen Wang, Neil R. Clark, and Avi Ma'ayan (2016) Drug Induced Adverse Events Prediction with the LINCS L1000 DataBioinformatics doi:10.1093/bioinformatics/btw168
Site interface
A) How to predict the unreported Adverse side effects of a drug / small molecule ??
1-Open SEP-L1000 site : http://maayanlab.net/SEP-L1000/ 2-Search the search box up right with :
• your drug name “eg : Paracetamol” • or with the PubChem Aliases of the small molecule “can be retrieved using
PubChem Compound site https://www.ncbi.nlm.nih.gov/pccompound “ 3-Click on your result. 4-You can rank the prediction by clicking “Already Labeled” to use “No” result for further investigation.5-Copy the result of download as PDF.
Output
Ranked list of side effects.
Try it out:
with Colistin “Our last defense Antibiotic”
Demo 1
Now ranking according to already labelled
A) How to predict a list of drugs / small molecules related to unreported Adverse side effect??
1-Open SEP-L1000 site : http://maayanlab.net/SEP-L1000/ 2-Search the search box in the center with the side effect “eg :
Nausea” • 3-You can rank the prediction by clicking “Filter” next to
“already known to cause this side effect” result for further investigation.
• 4-Copy the result of download as PDF.
Note : You can browse the Adverse effects
by “System organ classes of side effects” using the home website.
Try it out with :
Memory impairment
Ranking to predicted only
