Galaxy: Integrative, Reproducible Analysis of Genomics Data

Genomic and Proteomic Approaches to Heart, Lung, Blood and Sleep Disorders

Jackson LaboratoriesRoss Hardison

September 10, 2008

Galaxy is developed and maintained by Anton Nekrutenko (PSU) and James Taylor (Emory U)

Types of data in genomics

• Sequences • Comparisons of DNA and protein sequences• Expression data• Chromosomes and chromatin data• Experimental manipulation• Variation and phenotypes• Protein structure and function• Stored in databases and browsers (e.g. UCSC

Genome Browser)• Many analysis tools (Galaxy)

Some major web resources in genomics

• UCSC Genome Browser and Table Browser– http://genome.ucsc.edu/

• Ensembl and EnsMart/BioMart– http://www.ensembl.org/

• TIGR Comprehensive Microbial Resource – http://cmr.tigr.org/

• NCBI for Blast server, PubMed, Gene Expression Omnibus, dbSNP, etc. – http://www.ncbi.nlm.nih.gov/

• dCode for alignments and other – http://dcode.org

• HapMap for haplotype and variation– http://hapmap.org

• Galaxy for data retrieval and analysis– http://galaxy.psu.edu

Sequences

• DNA sequences – Whole genomes and chromosomes– Genes

• Transcripts– Protein-coding and noncoding transcripts– Full-length or partial (expressed sequence tags or

ESTs)• Protein sequences

– Known– Predicted

• Repeats• Variants

Sequences from CFTR: Browser view

Regulation-related features around T2D risk variants

Reg Pot

Browsers vs Data Retrieval

• Browsers are designed to show selected information on one locus or region at a time.– UCSC Genome Browser– Ensembl

• Run on top of databases that record vast amounts of information.

• Sometimes need to retrieve one type of information for many genomics intervals or genome-wide.

• Access this by querying on the tables in the databases or “data marts”– UCSC Table Browser– EnsMart or BioMart

Retrieve all the protein-coding exons in humans

Challenges in genomic data analysis

• We have great browsers and data warehouses– But most lack facilities for performing

sophisticated analysis

• Many useful computational tools have been developed in bioinformatics– But they are not well integrated, they have

different user interfaces, different data formats, etc.

Some common solutions

• Glue it all together with Excel– Until you realize Excel cannot handle that

much data and the match isn’t coming out right anyway…

• Glue it all together with Perl– But that leads to duplication of effort,

duplication of bugs, ….

A better solution

• Build a framework that:– Defines a common format for describing the

interfaces of different computational tools and databases

– Provides the infrastructure to adapt those interfaces into standard form

– Defines common data types and standards for integrating the results

Two faces of Galaxy

• A web site where you can easily perform complex analysis integrating various data sources and computational tools

• A framework to easily build similar sites that integrate your choice of tools and data sources

Galaxy: Data retrieval and analysis

• Flexible data retrieval– From multiple external sources– Upload from user’s computer– Upload as URL from any site

• Hundreds of computational tools– Data editing, filter, sort– File format conversion– Extract sequences and alignments– Operations: merge, intersection, complement, cluster …– Get conservation and other scores for intervals– Statistics– Graphs and displays– EMBOSS tools for sequence analysis– HyPhy tools for molecular evolutionary analysis

• Workflows: run multiple steps reproducibly

Welcome to Galaxy

Welcome screen, changes periodically

News

When tools are invoked, displays information on the tool and allows user to chose parameters

Tool choice

Titles are toggles; more options are displayed when you click on them

History

Titles are toggles; more information is displayed when you click on them

Click on the “eye” to see all the data on another page

Click on the “pencil” to edit the attributes

Click on the “x” to delete

“Refresh” to get results if they have not appeared or to get status of query

Use “options” next to “History” to save, rename, move to or share histories. Must be logged in to do this.

Proxy based tools (e.g. UCSC Table Browser)

User makes request to Galaxy

Galaxy delegates request to external site

Proxy based tools

External site generates response - If data, Galaxy determines data type, processes it and adds it to the history - Otherwise, response is returned to user

Command line tools

Pick one of the programs from the left “Tools” bar

User chooses parameters for tool

Command is run

Background jobs in Galaxy

Web page with datasets on transcriptional regulation

Data uploads to Galaxy: use the URL

How many DHS overlap with high RP intervals?

Overlaps of DHS with high RP

segments (25%) and

highly constrained segments

(43%)

24,330/95,709 = 0.25441,000/95,709 = 0.428

Get constraint scores for intervals

Histogram of phastCons scores

Mean vs Maximum phastCons

Distribution of phastCons scores in DHS that are also occupied by CTCF

mean max

n=7000

Many thanks …

James Taylor, Anton Nekrutenko,

Funding from NIDDK, NHGRI, Huck Institutes of Life Sciences at PSU

Yong Cheng, Demesew Abebe, Christine Dorman, …, Ying Zhang, David King, Swathi Ashok Kumar