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