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PROMETRA – MULTI OMICS VIEWER
Heiko Neuweger
Introduction to Integrative Bioinformatics MCB research school course Bergen November 24th, 2009
Overview
ProMeTra Concept & System Design
Application Examples GenomeMaps for Transcriptomics Experiments C.glutamicum metabolic pathway map
Summary
HowTos
Motivation
Provide method to visualize results of multi-omics experiments
Flexibility and modularity with respect to data and visualization concepts transcriptomics, metabolomics, proteomics M-values, levels, pool sizes, fluxes, … Metabolic pathways, gene lists, compound classes
User driven & platform independent
Design Concepts
SaaS (Software as a Service)
Integration of heterogeneous datasources using Web Services
SVG - open vector based image format Combination of layout and mark-up User defined pathway maps Animations possible
SBML support
ProMeTra Architecture
Web based user interface
Upload/select pathway map
Select experimental data from MeltDB, QuPE, EMMA2
Upload your own data (CSV, XLS)
Specify rendering approach & color palette
Application examples
GenomeMaps
Converted all replicons available at NCBI Genomes DB to ProMeTra Images
Genes are represented as rectangles in a grid Order determined by stop codon
Locus tags used as identifiers
Gene names used as labels if available
GenomeMaps Example
Genome map with relative gene expression data
GenomeMaps Example
C. glutamicum fermentation experiment
Transcriptomics measurements obtained at six timepoints
Visualization of transcriptional changes
Timepoints 2 to 6 compared to timepoint 1
M-values for the reporters of all genes are shown
Operons can be verified
PathwayMaps
Design metabolic pathways using Inkscape / CorelDraw
Add ProMeTra MarkUp for Metabolites, Proteins and/or Transcripts
Upload to ProMeTra webserver
Map quantitative datasets
PathwayMaps Example
CellDesigner & SBML Support
ProMeTra server converts SBML pathway maps
SVG images incl. ProMeTra MarkUp
Can be combined with KEGG2SBML
SBML Converter
Summary
High quality pathway images coupled with multi-omics quantitative data
Web based - platform independent More flexible compared to KEGG pathway maps
GenomeMaps for operon confirmation WebServices & Input formats
MeltDB, QuPE, EMMA2 CSV & XLS supported
Thank you
CellDesigner HowTos
Review your KEGG2SBML results
Start CellDesigner & open .xml file from KEGG2SBML
Change positioning of proteins & metabolites
Correct & improve the layout interactively Remove enzymes or metabolites Save updated version
ProMeTra HowTos
Login & Session Management
http://prometra.cebitec.uni-bielefeld.de
Public access via ‚prometra‘ user Click main logo
User session expires after one hour inactivity Uploaded data is stored only temporarily Pathways can be stored permanently
Login & Session Management
ProMeTra Start page
Access Main ProMeTra Functions Data upload & retrieval Data visualization ...
Left Menu List of available contexts (A) List of available actions (B)
Top Menu Overview of already imported Omics datasets (C ) Fulltext search function (D) Help (E)
Context Home always brings you back to this page
ProMeTra Start page
b
a
c d
e
Convert existing SBML files to SVG
Select the Convert SBML action from the start page
Specify a unique name and SBML file in the dialog
Convert existing SBML files to SVG
Click Create and check the result
Parsed protein, metabolite & transcript identifiers listed below the SVG image
Download SVG image & optionally edit in Inkscape
Optional: Add design elements via Inkscape
Start Inkscape and open the downloaded SVG image
Use the Inkscape drawing functionality to add additional graphical elements
http://www.inkscape.org
Upload and register SVG Pathways
Select the Import SVG action from the start page
Specify unique name, description and your SVG file
Click Create and check the result
Upload and register SVG Pathways
Parsed protein, metabolite & transcript listed below the SVG image
Update or delete your pathway using the actions listed in the menu bar
Select Upload CSV action from the start page
Submit your merged CSV file from J-Express
Specify type Protein
Visualize your data on pathway map
Visualize your data on pathway map
Check your uploaded data
Click Map data to pathway
...
Visualize your data on pathway map
Select your pathway map
Click Process Pathway Map
Review and download enriched pathway map