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

Thank You Ph.ali.kishk@gmail.com

linked-in : https://eg.linkedin.com/in/ali-kishk-997423a9