PathwayExplorer Tutorial - IOGMA® 3.8

Description

IOGMA® 3.8
PathwayExplorer Tutorial
www.genostar.comPathwayExplorer Tutorial
Contact
Genostar
Miniparc Chartreuse
60, rue Lavoisier
38330 Montbonnot
http://www.genostar.com
[e-mail]
PathwayExplorer Tutorial, 17 December 2010 © Genostar 2/49Table of Contents
1. Introduction ............................................................................................................... 6
1.1. PathwayExplorer help .......................................................................................... 6
1.2. PTutorial ...................................................................................... 6
Comparative Analysis .......................................................................................... 6
Data Sources .................................................................................................... 6
1.3. What's new in IOGMA 3.8 ...................................................................................... 7
Metabolic Pathway Builder / MicroB ........................................................................ 7
Reporting facilities ............................................................................................. 7
Genome annotation ............................................................................................ 7
Comparative analysis .......................................................................................... 7
Multiple alignment .................................................... ...

Sujets

• Maple
• Limonade
• Visionneuse d'images
• Réaction de Wurtz
• Enzyme de restriction
• Chromosome 1 humain

Informations

• Publié par: Vaem
• Nombre de lectures: 147
• Langue: English
• Poids de l'ouvrage: 3 Mo

Extrait

IOGMA® 3.8

PathwayExplorer Tutorial

www.genostar.com

Contact Genostar Miniparc Chartreuse 60, rue Lavoisier 38330 Montbonnot

PathwayExplorer Tutorial

http://www.genostar.com

[e-mail]

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Table of Contents 1. Introduction ............................................................................................................... 6 1.1. PathwayExplorer help .......................................................................................... 6 1.2. PathwayExplorer Tutorial ...................................................................................... 6 Comparative Analysis .......................................................................................... 6 Data Sources .................................................................................................... 6 1.3. What's new in IOGMA 3.8 ...................................................................................... 7 Metabolic Pathway Builder / MicroB ........................................................................ 7 Reporting facilities ............................................................................................. 7 Genome annotation ............................................................................................ 7 Comparative analysis .......................................................................................... 7 Multiple alignment ............................................................................................. 7 Data transfer between modules ............................................................................. 8 Documentation .................................................................................................. 8 Installation ....................................................................................................... 8 2. Starting IOGMA® ......................................................................................................... 9 2.1. Welcome Page ................................................................................................... 9 2.2. Data Manager .................................................................................................... 9 3. Loading a Workspace .................................................................................................. 11 4. Computing Homologies and Syntenies .............................................................................. 15 5. Visualizing Chromosomes .............................................................................................. 18 6. Viewing CDS Properties ................................................................................................ 24 7. Finding CDSs Specific to an Organism .............................................................................. 28 8. Mapping a Specific CDS ............................................................................................... 29 9. Analyzing a Virulence Gene Cluster ................................................................................. 32 10. Characterizing Specific CDSs ........................................................................................ 34 10.1. Linking CDSs to Enzymes .................................................................................... 34 10.2. Linking CDSs to Metabolic Pathways ...................................................................... 37 The Biosynthesis of Terpenoid backbone Pathway ....................................................... 38 CompareLIMONCDSs andLIINNCDSs in the Biosynthesis of Terpenoid backbone Pathway ....... 40 11. Showing CDSs active in the KEGG map on the genomic map .................................................. 46

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List of Figures 2.1. IOGMA Welcome page ................................................................................................ 9 2.2. PathwayExplorer Data Manager (empty) ......................................................................... 10 3.1. Open the tutorial workspace ...................................................................................... 11 3.2. Collections in PathwayExplorer tutorial workspace ............................................................ 11 3.3. Successfully loaded Workspace with Objects listed in Object Collections .................................. 12 3.4. UsePropagateObject's properties in the Properties Viewer .................................... 13to view an 3.5. The Properties Viewer (and the Navigation Panel) shows information about the CDS highlighted ....... 14 4.1. Apply a task to compute homologies betweenLIMONandLIIN 15CDSs ........................................ 4.2. Choose parameters of the homology computation ............................................................. 15 4.3. The homology computation task is running ..................................................................... 16 4.4. Some CDss ignored for the homology computation ............................................................. 16 4.5. Name the new Collection of homologies ......................................................................... 16 4.6. Apply a task to compute syntenies betweenLIMONandLIINN............................................... 17 4.7. Choose parameters of the syntenies computation and name the new Collection"Syntons"........... 17 5.1. Display all replicons on a genomic map ......................................................................... 18 5.2. Map Viewer appears in the bottom half of the Data Manager ................................................ 19 5.3. Initial view ofLIMONandLIINN 19in Map Viewer ................................................................. 5.4. The enlargedLIMONMap shows the CDSssodA,ispG, andispH. ............................................ 20 5.5. Synchronizing the zoom on 2 maps ............................................................................... 21 5.6. The 2 maps in MapViewer are now synchronized to the same scale ......................................... 21 5.7. Maps of the two chromosomes synchronized by the homology relation between CDSs ................... 22 5.8. Synchronize the homologous CDSs ................................................................................ 22 5.9. Visualize syntenies ................................................................................................... 23 6.1. Properties for theispGCDS in the Properties Viewer after propagation from Map Viewer ............... 24 6.2. Explore the characteristics of theispG 25CDS in the Navigation Panel ........................................ 6.3. The Navigation Panel shows the data connections to the PolypeptidePP_P58668......................... 26 6.4. TheispGis part of the Terpenoid backbone biosynthesis pathway ............................CDS (gene)  26 6.5. TheispH 27gene is also part of the Terpenoid backbone biosynthesis pathway .............................. 7.1. Apply a task to find CDSs inLIMON 28with no homologies in the workspace ................................. 7.2. Name the new Collection of LIMON specific CDSs .............................................................. 28 8.1. Map theLIMONspecific CDSs onto theLIMON 29genome map .................................................. 8.2. Selected Objects are now outlined on theLIMONgenome ................................................... 29 8.3. Change the shape of unique CDSs to see them more easily .................................................. 29 8.4. Increase the CDS arrow shape to the maximum possible ..................................................... 30 8.5. EnlargedLIMON 30see even after they are no longer selected Objects.....-unique CDSs are now easy to 8.6. Visualize the chromosome in a circular view ................................................................... 31 9.1. Use theSelect (0)...feature to find a CDS of interest ....................................................... 32 9.2.glmUis now highlighted and centered on the Map Viewer ................................................... 32 9.3. Propagate the CDS to see its properties in the Properties Viewer ........................................... 33 9.4. Virulence cluster ..................................................................................................... 33 10.1. Select the CDSs unique toLIMONand use theSearchfunction to find corresponding enzymes ........ 35 10.2. Add the Objects returned by the search to a new Collection ............................................... 35 10.3. Explore the connections of Objects in the Navigation panel ................................................ 36 10.4. EC 1.17.1.2 is linked to theispH 36 .......................................................................... CDS 10.5. Find metabolic pathways linked to CDSs via EC numbers .................................................... 37 10.6. Add the Objects returned by the search to a new Collection ............................................... 38 10.7. Use the Specialized Viewers window to see the KEGG map of this metabolic pathway ................. 38 10.8. Select the enzyme and compound and propagate them in other Specialized Viewers ................... 39 10.9. The 2D Structure Viewer .......................................................................................... 39 10.10. The Reaction Viewer ............................................................................................. 40 10.11. Use the propagate function to highlight the reactions catalyzed by CDSs specific toLIMON.......... 41 10.12. Choose blue to highlight the reactions catalyzed by enzymes specific toLIMONin this pathway..... 41 10.13. Choose red to highlight all reactions catalyzed by enzymes ofLIMON 42in this pathway ................ 10.14. The KEGG map now showsLIMON-specific reactions among allLIMON 43reactions ....................... 10.15. Choose green to highlight all reactions Catalyzed byLIINNin this pathway ............................. 44

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10.16. Contrasting colors allow easy visual differentiation between reactions .................................. 44 11.1. Select CDSs to show in genomic map and make a Collection of CDSs fromLIMON....................... 46 11.2. SelectLIMONCDSs specific to MAP 900 to display in genomic map ........................................ 47 11.3. CDSs which result in reactions active in this metabolic pathway are outlined in the genomic m a..p. 47 11.4. Color the selected CDSs in red ................................................................................... 48 11.5. Change the color of the two CDSs in the Map 100 pathway ................................................. 48

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Part 1. Introduction

PathwayExplorer is a module of Genostar’s IOGMA® environment. Use PathwayExplorer to explore the relation between genes, products of genes as enzymes, reactions catalyzed by enzymes, and metabolic pathways in which these reactions appear. PathwayExplorer integrates and classifies different kinds of biological data, provides several viewers which provide a clear view of data and their relations, and contains powerful functionalities to search, navigate and highlight entities. 1.1. PathwayExplorer help

PathwayExplorer has an expanded on-line help function. Look for: • theHelplink on the upper right of the Data Manager, which will open the entire help section; • the  buttons located throughout the software, which will open the help section pertinent to its location. 1.2. PathwayExplorer Tutorial

The purpose of this tutorial is to guide the user through a comparative analysis of the two speciesListeria monocytogenesandListeria innocuafamiliar with a variety of PathwayExplorer functions and tasks.to become Comparative Analysis You will start this comparative analysis by loading data on these two species (referred to throughout this tutorial asLIMONandLIINN) into PathwayExplorer from a previously prepared Tutorial Workspace. With this tutorial, you will: • visually explore genomes of both species; • use (pre-calculated) homology relations between genes to navigate between species and visually inves- tigate differences; • identify CDSs specific to the pathogenic strainListeria monocytogenes; • map CDSs specific toListeria monocytogenes; • find the CDSs specific toListeria monocytogeneswhich produce enzymes; • find and visualize the reactions catalyzed by these enzymes; • find and visualize the metabolic pathways in which these reactions are involved, using the interactive functions of KEGG maps in PathwayExplorer. Through investigations such as the one illustrated in this tutorial, PathwayExplorer helps to answer such ques- tions as:is this metabolic pathway specific to this species? Data Sources The data of the Workspace used in this tutorial come from several databases: GenomeReviews (EBI), UniPro- tKB, Enzyme, GeneOntology, KEGG, NCBI Taxonomy, and HAMAP. The data have been checked, corrected or completed if necessary, linked and integrated.

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1.3. What's new in IOGMA 3.8

Genostar has developed and integrated many exciting new features in Metabolic Pathway Builder 3.8. New methods for data analysis and improvements in reporting, sharing and data transfer features are only part of the picture. With MPB 3.8, you can now easily expand and manage your internal knowledge base. Metabolic Pathway Builder / MicroB With decreases in the cost of sequencing, the quantity of data being generated and analyzed is increasing rapidly. We’ve made it easier to centralize and manage your results in a traceable way. In addition to drawing on the wealth of data in MicroB for your comparative analyses, you can now connect, integrate and save your analyzed genomes in your dedicated MicroB, augmenting and consolidating your knowledge base. Your data is easy to access, and you can visualize, explore, share and export it anytime. Reporting facilities Metabolic Pathway Builder 3.8 has new click and copy features for your reports and publications. We’ve im- proved the copy features so that you can copy any kind of object or graphical image from your workspace and paste it directly into your favorite programs as text or in Fasta format. Genome annotation Blast databank manager.that enables you to easily add,We have a new graphical Blast databank manager delete and share Blast databanks. Manual CDS creation.Take advantage of additional ways to manually create CDSs: from specified bounds, along a whole sequence, from selected features. Frameshift detection.a new frameshift detection task. Frameshifts can be either a resultGenoAnnot has of mutation or a consequence of sequencing misreads. Some frameshifts generate artificial insertions and deletions of nucleotides. This can lead to errors in predicted protein sequences and compromise analysis of the genome sequence. With the new “Detect Frameshifts” task, you can detect putative frameshift locations in a sequence and visualize them on a map, improving the accuracy of their annotations. The task is based on the comparison of the targeted sequence against a protein database. Comparative analysis We’ve added a new task in GenoAnnot that allows you to detect single-nucleotide polymorphisms and dele- tion-insertion polymorphisms (SNPs and DIPs). When polymorphisms occur in coding regions of DNA sequences, they may change the amino acid sequence of the protein that is produced. Such polymorphisms can be useful in understanding how species develop diseases or respond to drugs, pathogens or other agents. Polymorphisms that occur outside coding regions may have consequences for gene splicing, transcription factor binding or the sequence of non-coding RNA. The Compute SNPs and DIPs tool in GenoAnnot compares a sequence or contigs against a closely related reference sequence and detects single-nucleotide and deletion-insertion polymorphisms. The SNPs and DIPs are easily visualized in a table and can be explored graphically using the genomic viewer. PathwayExplorer also includes a new task that enables you to compute homologies between organisms, taking replicons and plasmids into account. Multiple alignment We’ve integrated the MAFT program into ProteoAnnot for high speed computation of multiple alignments. This complements the ClustalW and Muscle programs already present.

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Data transfer between modules

Data transfer between GenoAnnot and PathwayExplorer has been improved. You can now indicate the type and shape of your replicon.

Documentation

HOW-TO documentation is now available in the on-line help

Installation

IOGMA provides a new simple way to specify where your personal files will be stored.

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Part 2. Starting IOGMA® 2.1. Welcome Page

The first window to open when you launch IOGMA is the Welcome page. Here you can select a module to open. You can also launch IOGMA modules and services (viewers) via the top-left corner menu ( ).

Fig. 2.1. IOGMA Welcome page Click on PathwayExplorer in the Welcome page to launch the module. After a few seconds, an empty Data Manager appears. 2.2. Data Manager

The Data Manager in PathwayExplorer allows you to organize, consult, save and query data. More formally, the Data Manager allows you to manipulate Objects and Collections of Objects in the Workspace. The Workspace also contains the underlying data model and a set of tasks.

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Fig. 2.2. PathwayExplorer Data Manager (empty)

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Part 3. Loading a Workspace Load the ready-to-use Workspace containing the data from the two species ofListeriaby clicking onFile| Open tutorial workspace.

Fig. 3.1. Open the tutorial workspace After a few minutes of data loading, PathwayExplorer classifies the data into 7 different Collections. The number in parentheses following the Collection name indicates how many Objects the Collection contains.

Fig. 3.2. Collections in PathwayExplorer tutorial workspace These Collections include data on: • Biochemical Reactions; • Compounds;

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