Download Interpreting Gene Lists from Omics Studies

NCRI Cancer Conference
November 1, 2015
www.bioinformatics.ca
Module #: Title of Module
2
The ICGC Data Portal
Part 1: Data submission, processing and release
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ICGC Data Release Cycle
Data
files
Data
files
Open
Sign off
Submission and
Validation
Portal
Release Open
Data
Annotation &
ETL
Sign off
Submission and
Validation
Release 1
Portal
Release
Data
Annotation &
ETL
Release 2
Time
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Data Type Submitted
• To the Data Coordination Center (DCC)
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Simple somatic and germline mutation
Somatic copy number variation
Somatic structural mutation
Methylation
Gene expression (RNAseq, Arrays)
Protein expression
miRNA
Exon junctions
• To the European Genome Archive (EGA) and cgHub
– Sequencing raw data (Fastq, BAM)
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Data Validation at Submission
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Data Annotation & ETL Pipeline
• Annotation
– Mutation frequencies
– Mutation gene consequences
• Amino Acid changes and their consequences for all gene & transcripts
(e.g. frameshift)
– Mutation functional impact
– Gene Ontology terms, Reactome pathways, Cancer Gene
Census
– Germline mutations masking
• ETL pipeline
– Annotated data indexed using an ElasticSearch cluster of 16
nodes
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THE ICGC Data Portal
Part 2: Portal features highlights
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ICGC Data Portal
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Top 20 mutated genes with high functional
impact SSMs in selected cancer projects
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Simple somatic mutation rate per donor across
selected cancer projects
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Project Entity Page
ALSO
• Most frequent mutations
• Most affected donors
• Publications
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Workshop
2015
• Filter
on high impact
mutations
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Gene Entity Page
Frequencies by cancer projects
Pfam domains for all transcripts
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Reactome Pathway Entity Page
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Mutation Entity Page
Permanent ID across releases
Consequences for all transcripts
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Genome Viewer
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Current filters
Affected donors, mutated genes and
mutations found simultaneously
Search data of interest by
applying filters at Donor,
Gene, and/or Mutation
Download data files for filtered donors only
Export table
Search for donor files in external
repositories (e.g. raw data)
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Customized saved donor, gene and mutation sets
Analyses:
• Enrichment Analysis
• Phenotype Comparison
• Set Operation
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File filters: Repository, Data Type, Experimental
Strategy, File format, Access
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Acknowledgment
• Principal Investigator
– Vincent Ferretti
• Project Manager
– Francois Gerthoffert
• Lead bioinformatician
– Junjun Zhang
• Software Architect and Tech Lead
• Business Analyst
– Phuong-My Do
• Software Developer
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Dusan Andric
Terry Lin
Michael Moncada
Vitalii Slobodianyk
– Bob Tiernay
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The ICGC Data Portal
Part 3: Live demo
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