Content Pathway Studio overview Pathway Studio usage Methods and tools used by Pathway Studio

1. Lecture 8: Pathway Development Tool III: Pathway Studio: Software for Visualization and Analysis of Biological PathwaysY.Z. ChenDepartment of PharmacyNational University of SingaporeTel: 65-6616-6877; Email: phacyz@nus.edu.sg ; Web: http://bidd.nus.edu.sg • Content • Pathway Studio overview • Pathway Studio usage • Methods and tools used by Pathway Studio

2. Pathway Studio Overview • Pathway Studio pathways analysis software helps you to: • Interpret biological meaning from gene expression, molecular interaction and other high throughput data • Build, expand and analyze pathways • Find relationships among genes, proteins, cell processes and diseases • Draw publication-quality pathway diagrams • Website: • http://www.ariadnegenomics.com/products/pathway-studio/ • Publication: • Nikitin et al. Bioinformatics 19, 2155-2157 (2003)

3. Pathway Studio Features • Desktop software • Build and visualize pathways • Analyze and curate pathways • Import and analyze gene & protein lists • Interpret microarray gene expression data • Analyze proteomics and metabolomics data • Website: • http://www.ariadnegenomics.com/products/pathway-studio/ • Publication: • Nikitin et al. Bioinformatics 19, 2155-2157 (2003)

4. Pathway Studio Features • MedScan Technology • Search and mine the literature • Extract interactions from the literature • Build targeted data content • Database management system • ResNet database • Interrogate different species, multiple genomes • Supports public and commercial databases

5. Pathway Studio Features • Pathway Visualization • Graphical user interface for drawing, coloring, viewing, editing and annotation of pathway and relationship maps • Automatic layout algorithms revealing pathway organization • Publication-quality illustrations in all major image file formats • Export of pathways as clickable HTML or XML files

6. Pathway Studio Features • Pathway Analysis and Curation • Create your own pathways and produce publication quality graphics and diagrams • Optimize views by filtering, pathway expansion, and protein classification • Build pathways for gene lists imported from microarray and other experiments • Display specific upstream and downstream events • Find interaction paths among molecules, cell objects and processes • Determine and identify common targets and regulators for a group of proteins

7. Pathway Studio Features • Molecular Interaction Networks from the Literature • Analyze pathways with ResNet database, compiled from PubMed abstracts and articles • Access more than 1,000,000 facts of regulation, interaction and modification • Validate the facts by clicking on the link to an original sentence, abstract or source

8. Pathway Studio Features • Pathway Reconstruction Algorithms • "Build Pathway" is a search tool with flexible options to navigate the network database and build pathways. Choose from multiple algorithms for assembling a pathway such as "find only direct interactions", "find shortest paths", "find common targets" or "find common regulators". • "Find relevant networks" - finds pathways related to a list of molecules • Find differentially expressed networks (pathways) for a microarray experiment

9. Pathway Studio Features • Data Mining and Searches • Find all interacting molecules for a protein or other biological entity • Find all networks/pathways for a query protein • Use context and field-specific database searches • Filter to see only specific types of biological objects to be included in your pathway, such as proteins, complexes, small molecules, cellular processes etc. • Filter to see only specific types of biological interactions such as binding interactions, post-translational regulation, expression regulation, enzymatic activity, molecular synthesis, transport, and others. • Review original literature sources for every relation within a pathway via direct links to PubMed abstract and exact source sentence where each finding is referenced

10. Pathway Studio Features • Import and Analysis of Gene & Protein Lists • Import/export gene and protein lists • Map gene lists on signaling and metabolic pathways, and GO groups • Build and analyze pathways from imported lists • Work with protein IDs, names or aliases from various sources: Unigene IDs, Accession Numbers, LocusLink, Swiss-Prot, Affymetrix GeneChip® IDs, Gene Names and Gene Symbols

11. Pathway Studio Features • Literature Mining • Use integrated MedScan software to extract biological interactions from scientific text • Mine PubMed and build pathways from extracted facts • Update pathways using data from recent publications

12. Pathway Studio Features • Microarray Gene Expression Data Analysis • Import data from all popular microarray analysis software packages • Reconstruct molecular networks from gene expression and proteomics data • View how genes in a pathway are up or down regulated through various biological states to identify key regulators or targets of interest

13. Pathway Studio Features

14. Pathway Studio Usage: Creating pathway from Input Protein or Other Info • Step 1: Downloading of a local database • The Download Database dialog box is displayed automatically during the first start of the application (including demo installations); it will be displayed in each start of the application until a user successfully opens a local database. • To download the latest version of the ResNet database from the Ariadne web site, select the menu Database>Download Database and choose the Download Database from the Internet option. Select the ResNet database from the list and press OK. The latest version of the ResNet database will be downloaded to your computer. 5

15. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info • Step 2: Open a Local Database • Open Pathway Studio. To open a database: • Open Local Database ; Call the Database>Manage Databases>Open Local Database • In the Open Local Database dialog box that appears, select a database and press Open; • The next time you start Pathway Studio, the last opened database opens automatically.

16. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info • Step 3: Importing data • Importing Lists of Proteins • Protein lists exported from several standalone • programs or received from an expression experiment can be imported into Pathway Studio. • The software provides two tools that help you to import a list of genes and find functional links and regulations between proteins in the list. • The Import Protein List tool is available via the Tools>Import Protein List menu. This tool helps you to import the list of genes from your experiment and save it in the database as a functional group

17. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info • Step 3: Importing data • Importing Lists of Proteins

18. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info • Step 3: Importing data • To import a list of genes, do the following steps: • Create a one column list of genes in Notepad • Copy the list into Clipboard • Call Tools>Import Protein List menu (Import Protein List dialog box appears) • Press Paste (The list appears in the dialog box) • Specify the appropriate ID types (LocusLink ID or another ID type) • Press the Lookup button to map these proteins to the IDs in the database (descriptions appear for successfully mapped proteins, proteins not found are shown as not found) • Press Import (List Pane opens and the list of proteins appears as a new group)

19. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info • Step 3: Importing data

20. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info • Step 3: Importing data • Supported gene IDs: • Pathway Studio supports the identification strings (IDs) from the following databases: • LocusLink from NCBI2 • HGNC (HUGO Gene Nomenclature Committee3) • GenBank IDs • Affymetrix Probe IDs • UniGene from NCBI4 • In addition, you can import the list of protein names and aliases. While • importing, the software searches the ResNet protein database to match the • specified field to the record in the imported ID list. If the record has not been • found in the database, the program marks it as not found. Current ResNet • protein database contains records from human, mouse, and rat genomes. • Proteins from other organisms cannot be found in ResNet

21. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info • Step 3: Importing data • Importing Protein Network • The Importing of Protein Network tool is designed to store your experiment data results and display a graphical representation of them • Examples of uses for this tool include a list of genes from your expression experiment or a list of proteins from a scientific article. • The Import Protein Network can help you develop a hypothesis that explains the molecular mechanisms of the protein regulation. • It searches the database of biological association networks to find functional links and regulations between proteins in the list.

22. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info • Step 3: Importing data • Importing Protein Network • Menu: Tools>Import Protein Network • Create the two column list of protein IDs in MS Excel • Copy the list into Clipboard • Call the Tools>Import Protein Network menu (Import Protein Network dialog box appears) • Press Paste (list appears in the dialog box windows, one column per window) • In the ID field, specify the appropriate ID types • In the Relation Type field, specify the relation type (You can specify one relation type per importing session) • In the Direction field, choose the link direction (<–, —, –>) • In the Effect field, select the effect type (negative, positive, unknown) • Press the Lookup button to create a pathway (relation description appears for those successfully Mapped relations) • Press the Import button (The pathway appears in the Pathway Pane)

23. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info Step 3: Importing data

24. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info Step 3: Importing data Import Wizard

25. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info Step 3: Importing data Import Wizard

26. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info Step 3: Importing data Import Wizard

27. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info • Step 3: Importing data • Importing Pathway • Call the Database>Import Wizard menu • In the Data Source dialog box, choose the Other Data option • In the Data Format dialog box, specify ResNet format as the type of import you want to use • In the Data Files dialog box, press the Add button. Select the name and location of the pathway file, and press the Next button • In the Preview dialog box, review the data designated for importing, and press the Next button to start the import process (The imported pathway appears as a new folder in the Database Pane with the pathway’s name corresponding to the name of the file)

28. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info • Step 3: Importing data • Importing KEGG Pathway • KEGG files can be obtained from: • ftp://ftp.genome.ad.jp/pub/kegg/ligand/enzyme (Enzyme file) • ftp://ftp.genome.ad.jp/pub/kegg/ligand/compound (Compound file) • ftp://ftp.genome.ad.jp/pub/kegg/ligand/reaction (Reaction file) • ftp://ftp.genome.ad.jp/pub/kegg/ligand/glycan (Glycan file) • ftp://ftp.genome.ad.jp/pub/kegg/ligand/drug (Drug file) • To import the KEGG pathways in Pathway Studio, you should import all these files (the Enzyme file, Compound file, Glycan file, Drug file ,and Reaction file). After importing, the software creates the KEGG Pathways folder in the Database Pane.

29. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info • Importing KEGG • Pathway: • It is recommend to not using the Pathway Studio Download KEGG from ftp option Instead, download the KEGG data from the KEGG ftp site and then use the ImportWizard to import the data to your database.

30. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info • Step 3: Importing data • Importing Expression and Other Microarray Numerical Data • The data file can be in Plain Text or MS Excel, CEL1, or GPR2 format.3 • To import your data, call Expression>Import Expression Experiment menu and choose format. Then, specify the location of the data file. • The imported data will be opened in the Import Expression Wizard. Follow the steps provided with the Wizard system.

31. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info • Step 3: Importing data • Importing Expression and Other Microarray Numerical Data • In the window that appears next: 1) specify the column of the • data file that contains the Gene IDs, 2) specify the ID types used • in your experiment, and 3) press the Next button. By default, the selections offered are either the Microarray ID or LocusLink ID type

32. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info • Step 4: Creating Pathway • Choose Database>New Pathway from the Main Menu, or press the Create New Pathway button on the Database Pane Toolbar • The Pathway named "New Pathway" appears in the User Pathways Folder • To save a pathway, choose Pathway>Save Pathway

33. Pathway Studio Usage: Creating pathway from Input Proteins or Other Info • Step 5: Analyzing Pathway

34. Pathway Studio Usage: Pathway Analysis

35. Pathway Studio Usage: Pathway Analysis

36. Pathway Studio Usage: Pathway Analysis

37. Methods and Tools used by Pathway Studio: MEDSCAN for Literature Search

38. Methods and Tools used by Pathway Studio: MEDSCAN for Literature Search

39. Methods and Tools used by Pathway Studio: MEDSCAN for Literature Search

40. Methods and Tools used by Pathway Studio: MEDSCAN for Literature Search

41. Methods and Tools used by Pathway Studio: MEDSCAN for Literature Search

42. Methods and Technology used by Pathway Studio: MEDSCAN for Literature Search

45. Methods and Tools used by Pathway Studio: RESNET Databases • The ResNet Databases represent different sets of pre-compiled information on biological relationships and associations, interactions and facts which have been extracted from the biomedical literature using MedScan. There are several available ResNet databases: • ResNet 5 Mammalian Database - for Human, Rat and Mouse • ResNet Plant Database - download through Pathway Studio software • ResNet Targeted Databases - available from the Download Center

46. Methods and Tools used by Pathway Studio: RESNET Databases • RESNET Features • All extracted relations have linked access to the original article or abstract • Synonyms and homologs are included to maintain gene identity and to obviate redundancy in search results • Users can update ResNet as often as required using the MedScan technology built into all Ariadne products • Updates are made available by Ariadne every quarter

47. Methods and Tools used by Pathway Studio: RESNET Databases RESNET Features

48. Methods and Tools used by Pathway Studio: RESNET Databases RESNET Features

49. Methods and Tools used by Pathway Studio: RESNET Databases RESNET Features

50. Methods and Tools used by Pathway Studio: RESNET Databases RESNET Features