Building Regulatory Networks with CyTargetLinker

Martina Kutmonmartina.kutmon@maastrichtuniversity.nl

NetBio SIG: July 19, 2013

Outline

• Background

• CyTargetLinker walkthrough

• Biological applications

• Next steps

Background

• Our initial use case: biological pathways

o Graphical representation of a biological processo Intuitiveo Signaling pathways, metabolic pathwayso Contains gene products, proteins, metabolites,

different reactions and interactions

o WikiPathways, Reactome, KEGG, ...

Background

http://wikipathways.org/index.php/Pathway:WP197

Background

• Regulatory elements are often missing in pathways

o transcription factorso microRNAso drugso ...

• Why?o Is the specific regulator really involved in this pathway?o Often it makes the pathway to big and cluttered.

Basic Idea

microRNA

miRecords database

miRTarBase database

TFe database

transcription factor

target gene

proteins/existing network

Goal

• Integration of regulatory elements in network analysis

• Using multiple datasources in parallel

• Flexibility and extensibility

• Different regulatory interactions, e.g. TF-target or miRNA-target

• Integrate functionality in the Cytoscape framework

Goal

User-friendly for biologists and bioinformaticians

Development of a Cytoscape app to integrate regulatory interactions into network analysis

Cytoscape app CyTargetLinkerprojects.bigcat.unimaas.nl/cytargetlinker

CyTargetLinker Walkthrough

Where does the data come from?

• Regulatory interactions are loaded from RINs

o RIN = Regulatory Interaction Networks

o RINs support multiple identifier systems (BridgeDb)o Existing regulatory interaction databases or user

generatedo Conversion scripts are open source and available on

github o RINs for different species and interaction types are

available on the CyTargetLinker website

RINs

http://mirtarbase.mbc.nctu.edu.tw

XGMML file with microRNA -> gene interactions from miRTarBase 3.5

CyTargetLinker workflow

Initial network

Protein-protein network, biological pathway, single nodes, ...

Gene set from MSigDBGNF2_MKI67 - cancer gene neighborhoods

CyTargetLinker workflow

CyTargetLinker workflow

Extension of the initial network with microRNA-target information

predicted and validated miRNA targets from 4 different resources

CyTargetLinker workflow

CyTargetLinker workflow

Show/Hide functionalityonly interactions from validated resources are shown

CyTargetLinker workflow

only interactions supported by at least two resources are shown

Overlap threshold functionality

CyTargetLinker workflow

• CyTargetLinker extracts the regulatory interactions from all RINs relevant for the initial network

• CyTargetLinker for Cytoscape 3 in pre-release status (downloadable from website)

• CyTargetLinker for Cytoscape 2.8 can be installed through the plugin manager

Biological Applications

microRNAs in breast cancer

199 interactions from miRecords443 interactions from miRTarBase

Heneghan, H. M., et al. "MicroRNAs as novel biomarkers for breast cancer."Journal of oncology 2010 (2009).

BCL2 --> target of 4 miRNAsCDKN1A --> target of 4 miRNAsRB1 --> target of 2 miRNAsERBB2 --> target of 2 miRNAs...

Identify target genes of specific miRNAs and start building hypotheses

Pathway Extension

ENCODE: the Encyclopedia Of DNA Elements

•Goal: identify all functional elements in the human genome sequence

•Paper: Architecture of the human regulatory network derived from ENCODE data --> proximal and distal transcription factor regulation

•Data is provided as networks

•RINs are provided on the website

Pathway Extension

DNA damage response pathway

127 proximal interactions (blue)82 distal interactions (red)

BRCA1 - distal regulationABL1 - proximal regulation

Next steps

Next steps

• Conversion of more resources to RINs

• Data retrieval through other services (webservices, RDF, Neo4j databases)

• Export function to show which interactions were added in which extension step

• Statistical output - VENN diagram showing overlapping interactions

• Improved result visualization options (shape and color of added nodes)

Summary

• User-friendly Cytoscape app to integrate regulatory interactions into network analysis in a flexible and extensible way

• RINs and tutorials can be found on http://projects.bigcat.unimaas.nl/cytargetlinker

• CyTargetLinker is Open Source:o http://github.com/mkutmon/cytargetlinkero http://github.com/mkutmon/rin-creation

Acknowledgements

• Thomas Kelder

• Susan Coort

• Chris Evelo

Students:

• Pooja Mandaviya

• Naïme Douallin

Thank you for your attention!Questions?