Welcome to Gramene’s RiceCyc (Pathways) Tutorial RiceCyc allows biochemical pathways to be analyzed and visualized. This tutorial has been developed for first time and casual users of RiceCyc. These slides relate to Version 1.4 of RiceCyc.

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Introduction RiceCyc allows biochemical pathways to be analyzed and visualized. Gramene has incorporated the latest TIGR 4 genome into this release to create an Oryza sativa specific pathway dataset. Data is under development and subject to change. If you do see any errors in the dataset please feel free to contact us through the feedback provided at the top of Gramene webpages. RiceCyc allows biochemical pathways to be analyzed and visualized. It is based upon Pathway Tools version 9.5, which is maintained by Peter Karp’s Bioinformatics research group at SRI International in California. The biochemical pathways have been created automatically by use of the pathway tool that is incorporated within the Pathway Tools program. We have incorporated the latest TIGR 4 genome into this release to create an Oryza sativa specific pathway dataset. At this point in time very little manual curation has been performed upon the automatically generated pathways. It is expected that by the next Gramene release many of the RiceCyc pathways will have been manually reviewed and curated, and where relevant, new pathways added or removed. As this is an ongoing curation effort it is likely that many of the pathways may be incomplete or incorrect at this point in time. If you do see any errors in the dataset please feel free to contact us through our feedback pages. 4/25/2019

Click here to open the Pathways module Gramene Home Page www.gramene.org Click here to open the Pathways module 4/25/2019

Module Home-Page layout Module home pages provide the following information: Searching/Browsing – links to different types of searches. Other Tools – if applicable, links to different tools used in this module. Help – links to help pages, tutorials, release notes, FAQ and other helpful documentation. Download – information on where to download the database. Feedback – How to contact Gramene Acknowledgements – Other programs that contribute to this data. Quicklinks and external links – when appropriate these links are provided. 4/25/2019

RiceCyc and Biochemical Pathways Home Page List of other available species Click here to go to the search page with that species pre-selected. A short summary of RiceCyc Click here to begin your search The RiceCyc start page enables rapid access to the main features of RiceCyc Click to View your data in the overview (see slides 26-30) Click for overviews (see slides 23-25) For summary, see slide 32. Compare pathways between species (see slide 35) 4/25/2019

Searching and Browsing part 1 Search Options Select a dataset (see slide 9) 1) Term search (slides 10-11) and available data examples (slides -12-19) 2) Browse by RiceCyc ontology (slides 20-21) 3) Choose from a list (slide 22) Searching and Browsing part 1 This is what the main RiceCyc feature page looks like. From here you are able to:Select datasets, Make Queries, Browse Ontologies and Choose links to other RiceCyc Information Note: the RiceCyc ontology is separate from the other Gramene ontologies in the Ontologies Database. 4/25/2019

Other Search Page Options Use the Diagram to visualize cellular pathways (slides 23-25) use the Omics Viewer to integrate your data onto the overview (Slides 26- 30) Click to follow Summary links (Slides 31-34) Click to return to Pathways home Searching and Browsing part 1 This is what the main RiceCyc feature page looks like. From here you are able to:Select datasets, Make Queries, Browse Ontologies and Choose links to other RiceCyc Information Click to compare available species (slide 35) Submit a question or give feedback Click to access Help docs. 4/25/2019

(Image from search page, Slide 7) Select your organism (Image from search page, Slide 7) It is important that you choose the right dataset before starting your search. Rice is the default. In addition to the Rice dataset, RiceCyc also contains information on Arabidopsis thaliana and Escherichia coli. 4/25/2019

(Image from search page, Slide 7) 1. Searches in Pathways For this tutorial we will search by “all” and then explore the available information for these parameters to show you how to navigate between the information. However, you may search each parameter individually. RNA search is not currently available (Image from search page, Slide 7) Pathways can be searched by several parameters 4/25/2019

Click on the appropriate selection Search Click Submit Enter term Results Click on the appropriate selection You can search for information on proteins by either name or EC number. The results page gives the name of the protein and any synonyms associated with it. It also shows the gene name associated with the protein and the reaction schematic of the gene. Information is also given on any reactions that are catalyzed by the enzyme. All pathways that contain the protein are also listed, by clicking on these links you will be taken to the relevant pathway page. 4/25/2019

Protein Information Click for Ensembl Gene Report info (see slide 18) Protein name and synonyms Gene associated with protein Reactions catalyzed by the enzyme (see slide 16) Reaction schematic of the gene - see slide 19 Pathways containing the enzyme. Click to access pathway (see slide 13) 4/25/2019

Pathway Information Detail Level 3 Click for more or less detail (next slide) Compound (red text). Click for more info (slide 17) EC number (click to go to reaction page, as in slide 16) Protein. Click for protein page (as in slide 12) You can search for information on pathways by entering the name in the query form. As the search has a wild card function it is not necessary to write the pathway’s full name. There are five levels of Pathway pages. This is the most basic. The blue lines represent reactions and clicking on them will take you to the reaction page; this wlil be covered later in this tutorial. Compounds are given in red. Further information on these compounds can be found by clicking on these links. By clicking on the more detail button, you will zoom into the pathway and be given more detailed information on it. If you are following this example please click the ‘More detail’ button twice. Gene, click to go view gene report in Ensembl (such as in Slide 18) Reaction (blue line) Click to go to reaction page (Slide 16) 4/25/2019

Pathway Detail Levels 1 & 2 Compounds Reactions In this view more compounds and reactions are being shown than in the previous view. Additionally it is now possible to see Information on genes and proteins. Information on proteins is given in orange text. If you click on this link you are taken to the protein page shown earlier in this presentation. The gene information is given in purple, by clicking on this you are taken to the Gramene Ensembl pages, where you can find detailed information on the gene in question. EC numbers are shown in light blue, clicking on these links will take you directly to the EC reaction pages. Level 2 4/25/2019

Move between levels with “more detail” and “less detail” buttons. Pathway Levels 4 & 5 Move between levels with “more detail” and “less detail” buttons. Level 4 Level 5 By using the ‘more detail’ button to zoom into the pathways the schematics of individual compounds can be seen. Clicking on the ‘Less detail’ button (Not shown) will take you to back to the previous view Clicking on a compound will give further information about it. 4/25/2019

Reaction Information Reaction Classification Other genes/enzymes that catalyze this reaction. Following a search for a reaction by EC number you will see a page similar to this. From here you will be able to see information on: The E.C. ontology category; Enzymes involved in catalyzing the reaction; Gene name; Associated pathways; Compounds and cofactors that play a role in the reaction. If you click on the Unification link you are taken to the ExPASy website; from here information on further gene products that catalyze the reaction is available. At bottom of screen, click unification link to go to ExPaSy for more gene products that catalyze the reaction. 4/25/2019

Compound Information Results 4/25/2019 You can search for information on compounds by entering their name in the query form. The compound results page gives information on the make up of a compound and its classification. Information is available about the formula of the compound, its molecular weight and its structure, where available. A unification link to KEGG Ligand is given. Any pathways in which a compound acts as a reactant or a product are shown at the bottom of the compound results page. 4/25/2019

Gene report links back to Pathways that this gene plays a role in. Gene Information Search by “gene” will take you out of Pathways and into the Gene report in Gramene’s Ensembl. You can search for information on genes by entering the name in the query form. As the search has a wild card function it is not necessary to write the genes full name. The gene result page gives information on the map position of the gene and its products and of any reactions that its protein may catalyze. Gene report links back to Pathways that this gene plays a role in. 4/25/2019

Gene Schematic Protein complexes EC number of catalyzing enzyme Gene The gene-reaction schematic is a visual representation of the relationship among a set of genes, enzymes, and reactions. The boxes on the left hand side represent the reactions, the boxes on the right hand side represent genes, and the circles in the middle represent polypeptides or protein complexes. A line from a gene to a circle means the gene codes for the protein When two circles are linked together - a gene product is a subunit of a protein complex When the Circle is connected to reaction -reaction is catalyzed by enzyme. Schematic models the relationship among reactions, genes and proteins. The left hand side represents a reaction and shows the corresponding EC number. The central circle is representative of protein complexes and the right hand side represents the gene. Clicking within the gene schematic will take you to the RiceCyc reaction or protein pages, or to the Gramene ensemble page Lines between objects represent relationships. A line from a gene to a circle shows that the gene codes for the protein; if two circles are linked together then this indicates that a gene product is a subunit of a protein complex; when a circle is connected to a reaction, it shows that the reaction is catalyzed by the enzyme. 4/25/2019

2. Browse RiceCyc Ontology (Image from search page, Slide 7) In addition to carrying out searches RiceCyc allows you to browse Pathways, EC reactions, genes and compounds ontology's. This is a very useful aspect of RiceCyc as the names of many biochemical compounds and enzymatic reactions are often long and easily misspelled. To browse to a relevant pathway simply choose from the menu shown above The following slides will give you an overview of this useful function; please choose browse by pathways and click submit. Select your ontology Click “submit” 4/25/2019

Browse RiceCyc Ontologies We are browsing Pathways. - Indicates term is expanded. Click to collapse. Click parent term for more information on other relationships After clicking on the browse by pathways screen this is the page that you will see The pathways in RiceCyc are arranged into hierarchies. By clicking on a pathway you will open up a further branch of the tree. Once you reach the furthest branch, clicking on the link will take you directly to the pathway (as in slides 14-18) + indicates term is collapsed, Click to expand ontology tree. Click terms at end of tree to go to Pathway (as in slides 13-15) 4/25/2019

3. Choose from a List We have a list of Pathways. Click term to open pathway (as in slides 13-15) Select your list type Click “submit” 4/25/2019

4a. Cellular Overview Diagram (Image from search page, Slide 7) Biosynthetic pathways TCA Cycle Catabolic Orphan All of the Oryza sativa biochemical pathways and reactions that have been created for RiceCyc are shown in this ‘overview’ page In the metabolic overview the TCA cycle is shown in the centre of the diagram, to the left of it are biosynthetic pathways, whilst catabolic pathways are on the right hand side. Any reactions that are part of orphan pathways are shown on the far right. . Different shapes represent different classes of metabolic compounds and the key is given on the right hand side of the metabolic map overview. The blue lines that connect the metabolic compounds are representative of reactions that have an associated gene product. Any reactions that do not have an associated gene product are greyed out. The flow of the pathway is from the top of the page to the bottom 4/25/2019

Metabolic Map Overview Mouse over compound to see compound name and pathway. (requires javascript browser) If you mouse over a compound, the name of the compound and the pathway it is in will appear on the bottom of your browser window. This will only work for Javascript-enabled browsers. 4/25/2019

Metabolic Map Overview Click a compound to access details and pathways . Mouse-over to close pop-up Click links to navigate If you click on a metabolic compound a pop up box will be displayed. This will enable you to navigate to any pathways that the compound is associated with or to details on the compound itself Click to print out a diagram of pathway 4/25/2019

4b. Omics viewer data selection Visualize your Microarray Expression data, Proteomics data, Metabolomics data, Reaction Flux data, or other experimental data on the Metabolic Overview diagram. (Image from search page, Slide 7) Select dataset Select data to upload The Omics viewer makes use of the Metabolic Overview to globally display the results of high throughput experiments. The viewer enables genes or proteins that play a role in metabolism to be mapped upon the reaction steps of the Metabolic Overview. Any changes in expression level can be visualized by a range of different colors; this enables the user to instantly tell if pathways are activated or deactivated under the experimental conditions.. Identify terms Select values 4/25/2019

Omics viewer display selection Enter column numbers Select color scheme The next step in entering your data is to enter the column number from which to extract data from. E.g. if you have multiple columns of data then enter them as shown in the example on the left. If using a denominator column for a ratio calculation it should be entered into the second column The Omics viewer gives you the choice of three color schemes in which to display your data. The default output ranges over the entire spectrum and makes comparison across experiments difficult. As a Signal Log Ratio of 1 (a 2 fold induction) is usually used as a cut off value in microarray experiments. It is recommended that you choose the three color display; this will enable you to easily see if a gene is upregulated (red), downregulated (yellow) or relatively unchanged (blue). It is also possible to generate tables of data above a threshold of your choice as an alternative to painting the data on top of the cellular overview chart. Select display type Click “submit” 4/25/2019

Caution: Requires 5-30 minutes to process! Omics Viewer display Red lines represent upregulated processes. Blue lines represent unchanged processes. The output will be displayed similar to this: Red lines represent upregulated processes. Blue lines represent unchanged processes. Yellow lines represent downregulated processes. The Cellular overview can take a long time to be created. The small example set of 480 genes available on RiceCyc typically takes 5 to 10 minutes to be created. A set of 10,000 genes may take as long as three hours to be mapped onto the Omics viewer. Yellow lines represent downregulated processes. Caution: Requires 5-30 minutes to process! 4/25/2019

Omics viewer pathway regulation Regulation of a pathway can be followed over a timecourse. In this example the carotenoid pathway becomes switched on over time. Hovering over a reaction will tell you the name of the compound affected and the influenced pathway. 4/25/2019

Omics Viewer Table Details of differentially regulated genes in pathway Pathway display This is an example of what the ‘table’ form of data generated by the Omics viewer looks like. The left hand side displays the Pathway, the center section gives details of any differentially regulated genes in the pathway, and the right hand side gives the names of the genes that are involved in the pathway. Gene names 4/25/2019

(Image from search page, Slide 7) 5. Summary Information (Image from search page, Slide 7) Summary for RiceCyc in table form (Slide 32). Species shown will match dataset selected on search page (slide #7) History of updates to dataset (see slide 33) The PathoLogic program creates a new Pathway/Genome Database for an organism that contains a prediction of the metabolic-pathway complement of the organism. PathoLogic uses the MetaCyc pathway DB to interpret the annotated genome of the organism by matching enzymes in the annotated genome against enzymes in the MetaCyc DB. (see slide 34) 4/25/2019

RiceCyc Summary To view a different species, from the search page (slide #7) select a dataset and then click on “Summary Page for Dataset” 4/25/2019

History of Updates History of updates on Gramene For RiceCyc there is a of curated (added or deleted) pathways 4/25/2019

PathoLogic Pathway Analysis Lists the evidence for the presence of each pathway in terms of the number of enzymes for each pathway that were found in the genome Reports pathway holes -- reactions missing that would complete its partial pathways, as well as former pathway holes for which enzymes have been identified using the Pathway Hole Filler (PHFiller) 4/25/2019

(Image from search page, Slide 7) 6. Comparative Analysis (Image from search page, Slide 7) Select analysis to make A useful feature of RiceCyc is the ability to compare metabolic networks across different organisms. In addition to the information on Oryza sativa, RiceCyc also holds data on Arabidopsis thaliana and Escherichia coli. The comparison analysis page allows you to select datasets and organisms that you are interested in. Select organisms to compare Click “submit” 4/25/2019

FAQs Feedback: Submit a question to Gramene Search FAQ Click category to expand or collapse a question or answer 4/25/2019

Use Feedback to ask questions or make comments to Gramene Help Use Feedback to ask questions or make comments to Gramene Help documents assist in how to conduct a search and to define your results. 4/25/2019

Email Gramene List-serve at gramene@gramene.org Contact Gramene Use the feedback button, located at the top of every page, to provide feedback or to ask questions about Gramene. or Email Gramene List-serve at gramene@gramene.org