LIPID MAPS methodologies for pathway construction and analysis

Robert Byrnesa, Dawn Cottera, Eoin Fahya, Shakti Guptaa, Mano Mauryaa, Manish Suda, Shankar Subramaniama,b

aLIPID MAPS Bioinformatics Core, SDSC, UCSD, 9500 Gilman Dr, La Jolla, CA 92093; bDepartment of Bioengineering, UCSD, 9500, Gilman Dr, La Jolla, CA, 92093.

www.lipidmaps.org LIPID MAPS funded by Glue

Grant from :www.nigms.nih.gov

The LIPID MAPS bioinformatics group has developed several tools for managing, visualizing, and editing signaling and metabolic pathways related to lipid biology. These have been applied to the study of the extensive lipidomics and transcriptomic data generated from integrated studies on macrophages subjected to a variety of treatments. We present software and tools for display and analysis of lipid and gene array experimental data as well as construction and visualization of lipid-related pathways.

Pathways construction for eicosanoids

Introduction

LIPID MAPS experimental data

Pathways construction and analysis using VANTED1

Lipidomics experimental data

Gene array experimental data

Available lipidomics and gene array experimental data Lipidomics experimental data

[1] Junker. H. B.; Klukas C.; Schreiber F.; A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics. 2006, 7:109.

Pathways construction and analysis using Pathway Editor2

Pathway construction using VANTED

Lipids and genes experimental data mapping

Pathway analysis and images generation

Workflow for construction and analysis of pathways using VANTED

Bone marrow-derived macrophage treated with ATP and Kdo2-lipid A (8-timepoint study): Eicosanoids [media] (pmol/ug DNA) [Averaged DNA values]

RAW 264.7 cells treated with Compactin and Kdo2-lipid A (8-timepoint study): Eicosanoids [media]

Thioglycolate-elicited peritoneal macrophage treated with Compactin and Kdo2-lipid A (8-timepoint study): Sphingolipids (Lipids data shown for N-acyl chain C16)

Pathways construction for sterols

Design process

Input from Pathway databases: 1. Complete pathways (LIPID MAPS, KEGG) 2. Time course data (metabolomic, microarray, protein array) 3. Compound descriptions (analytes, gene symbols) 4. Links to on-line compound information databases

Input from files: 1. Complete pathways (LIPID MAPS .path, KEGG, SBML, BioPAX*) 2. Time course data (LIPID MAPS data format, CSV)

Design process

<=0.1 <=0.2 <=0.25 <=0.33 <=0.5 <=0.67 --- >=1.5 >=2 >=3 >=4 >=5 >=10 No value

Color:

Ratio values: First line:

Second line: Third line:

Compactin+Kdo2-lipid A/ Ctrl ratio Compactin/Ctrl ratio Kdo2-lipid A/Ctrl ratio

First line:

Second line: Third line:

ATP+Kdo2-lipid A/ Ctrl ratio ATP/Ctrl ratio Kdo2-lipid A/ Ctrl ratio

First line: Second line:

Third line:

Compactin+Kdo2-lipid A/Ctrl ratio Compactin/Ctrl ratio Kdo2-lipid A/Ctrl ratio

Download completed pathway Replace experimental data from database or file

Modify nodes, interactions, organelles, data presentation Add desired SBML (BioPAX*) features

[2] Byrnes R. W.; Cotter D.; Maer, A.; Li, J.; Nadeau, D.; An editor for pathway drawing and data visualization in the Biopathways Workbench. Subramaniam S. BMC Systems Biology 2009, 3:99.

Dialogs for SBML content Visual depiction of SBML model for eicosanoid metabolism in RAW 264.7 cells treated with Kdo2-lipid A