Improved Methods to Query the LINCS L1000 Data
Avi Ma'ayan, PhD
LINCS Data Coordination Center and the CFDE Data Resource Center
The Library of Integrated Network-Based Cellular Signatures (LINCS) was an NIH Common Fund program that was established to catalog how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and gene expression signatures. The presentation will cover LINCS datasets, tools, and a newly developed method to query the LINCS L1000 data for better prioritization of drugs, small molecules and single gene perturbations.
Automatic Mining of Human and Mouse Gene Sets from GEO
Giacomo Marino
LINCS Data Coordination Center and the CFDE Data Resource Center
RummaGEO is a web server application that enables gene expression signature search against thousands of human and mouse RNA-seq studies deposited into GEO. To enable such a search engine, an offline automatic process was established to identify the experimental conditions from uniformly aligned GEO studies available from ARCHS4. Once conditions are identified, differential expression signatures are computed to extract gene sets from these signatures. In total, RummaGEO currently contains 135,264 human and 158,062 mouse gene sets from 23,395 GEO studies. Overall, RummaGEO provides an unprecedented resource for the biomedical research community enabling hypothesis generation for many future studies.
Hi @jeevangelista and @heesukim628 cc: @AviMaayan
The following summaries of the talks should be added to the webinar page: https://info.cfde.cloud/training_and_outreach/cfde-webinar-series
Improved Methods to Query the LINCS L1000 Data Avi Ma'ayan, PhD LINCS Data Coordination Center and the CFDE Data Resource Center
The Library of Integrated Network-Based Cellular Signatures (LINCS) was an NIH Common Fund program that was established to catalog how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and gene expression signatures. The presentation will cover LINCS datasets, tools, and a newly developed method to query the LINCS L1000 data for better prioritization of drugs, small molecules and single gene perturbations.
Relevant resources that will be discussed: Rummagene: https://rummagene.com/ SigCom LINCS: https://maayanlab.cloud/sigcom-lincs/ Playbook Workflow Builder: https://playbook-workflow-builder.cloud/
Automatic Mining of Human and Mouse Gene Sets from GEO Giacomo Marino LINCS Data Coordination Center and the CFDE Data Resource Center
RummaGEO is a web server application that enables gene expression signature search against thousands of human and mouse RNA-seq studies deposited into GEO. To enable such a search engine, an offline automatic process was established to identify the experimental conditions from uniformly aligned GEO studies available from ARCHS4. Once conditions are identified, differential expression signatures are computed to extract gene sets from these signatures. In total, RummaGEO currently contains 135,264 human and 158,062 mouse gene sets from 23,395 GEO studies. Overall, RummaGEO provides an unprecedented resource for the biomedical research community enabling hypothesis generation for many future studies.
Relevant resources that will be discussed: RummaGEO: https://rummageo.com/ ARCHS4: https://maayanlab.cloud/archs4/