1. The Maize Inflorescence Project Website Tutorial Nov 7, 2014

2. To access the data, you must login first http://www.maizeinflorescence.org Click to login Navigation panel to unrestricted pages.

3. To access the data, you must login first http://www.maizeinflorescence.org/ Username Password Click to login

4. Click on user’s name to edit user information Click to log out Your name appears after your login Access Profile page Navigation panel changed

5. You may change your password

6. Click on “Tools” tab to see the list of tools. Click on the buttons above to visit respective tool page. You can only see the list of “tools” after you login

7. Select experiments to be displayed for each Gene id. (default: all) Filter the Gene ids by RPKM value in the selected experiment. (optional) Specify a list of gene ids or gene description in each line of the query box. (default: none) Click on “sample text” to fill the query box with a small set of gene ids and description as shown. Click “Search” to extract list of genes in tabular format. Profile Display – slide# 1

8. Information on count of entries present in the database. To navigate to the next 20 entries and previous 20 entries Self descriptive table with Gene id, Gene description and RPKM values. Click anywhere within the row of the first Gene id “GRMZM2G176394”. The RPKM values for this gene is plotted against the selected experiments. The plot is at the bottom of the table. NOTE: The checkboxes in the table and “Combine Graph” button above the plot is explained on next slide. Profile Display – slide# 2

9. Use checkbox to select two or more Gene ids to merge their profile in a single chart. Click “Combine graph” to generate the chart. Profile Display – slide# 3

10. Provide a gene id for profile search. (required) Select correlation method “Pearson”, “Spearman” and “Kendall”. (default: pearson) Set the cutoff value for the correlation method. (default: >= 0.9) Select the experiments for consideration. (default: all experiments) Click on “Search”. Profile Search – slide# 1 The profile search takes considerable amount of time, an URL link to search results page will be emailed to you. This is the email sent to the user, providing link to search results page.

11. Table of Gene ids whose profile correlates with query gene “GRMZM2G32875” Select all the genes. Click on “Combine graph” to merge the profiles of selected genes. The chart is shown below the table. Profile Search – slide# 2

12. Select experiments to be considered while performing cluster analysis. Provide a list of Gene ids to be clustered. Select the Agglomeration method e.g. ward, single, complete, average, mcquitty, median and centroid. (default: complete). Click on “Run” to execute clustering analysis. Profile Clustering – Hierarchical Clustering Slide# 1

13. Output: Cluster Dendrogram Profile Clustering – Hierarchical Clustering Slide# 2

14. Select experiments to be considered while performing cluster analysis. Provide a list of Gene ids to be clustered. Click on “Run” to execute clustering analysis. Profile Clustering – Heatmap Slide# 1

15. Output: Heatmap Profile Clustering – Heatmap Slide# 2

16. This part of the webpage is for available tracks. This part of the webpage is for visualizing the Chromosome along with the tracks. Genome Browser (Jbrowse)

17. Select or Unselect the tracks from the “Available Tracks” to visualize in “Genome Browser” region. Controls to browse through a selected Chromosome Click on “X” to remove the track from “Genome Browser” and place it in “Available Tracks” region. GFF track QTL track RNAseq tracks Genome Browser (Jbrowse) More info available at http://gmod.org/mediawiki/images/0/0c/JBrowse_bioit_world_apr2013.pdf

18. Click on the coordinates in the table to perform interval search. QTL Regions Data obtained regarding QTL

19. Promoter Analysis (Query) Select the upstream basepairs for the gene ids. Use sample text to insert a sample list, or list them in the box

20. Promoter Analysis(Gene list) Select the Gene ids and click on “Get Motifs” This button appears after generation MEME output. Click on it to see MEME output.

21. Promoter Analysis(Meme Output)

22. Gene Ontology Term Enrichment (goatools)

23. Select from the gene list files and lookup for GO terms Use the text box to list the ids to get GO terms. Minimum ids: 25

24. Gene Ontology Term Enrichment (goatools) The output from goatools tool, in tabular format. The “e” in enrichment column means “enriched”.

25. BLAST search Perform BLAST. All the genomes that are available at GRAMENE.ORG

26. Gene Network Search Results Select gene ids of interest and take carry these ids to Profile Display page.

27. Interval Query (1. Search) Use drop down to select the Chromosome and enter the start and end coordinates. Now click “Search”

28. Interval Query (2. Genes) The genes are linked to JBrowse for visualization. Ortholog information from Arabidopsis thaliana and Setaria italica. The gene in black and gene description in dark red

29. Interval Query (2. Genes) Profile Display: To load the gene ids onto “Profile Display” tool input box. RNAseq: To know whether the selected genes are differentially expressed. ChIPseq: To query for presence of Peak summits within 2kb of the gene. SNPs: To know if there is any SNPs within 2kb of the gene. Orthologs: To get the Orthologs Save list: To save list of gene ids in a file

30. Interval Query (3. RNAseq results) On mouseover on the column header, a tooltip with detailed description of the column headers appear. In this example, “log fold change” appears on mouse over column header “ln_fc” RNAseq results can be filtered by selecting a series “Tassel development”, “Ear development” or “Mutant” The subject 1 and subject 2 comparisons update based on the series selected.

31. Interval Query (4. Filter RNAseq results) RNAseq results can be filtered by selecting a series “Tassel development”, “Ear development” or “Mutant” The subject 1 and subject 2 comparisons update based on the series selected. Click “Filter” to filter the RNAseq output. A new tab called “RNAseq (filter)” appears on the top, and that tab holds the filtered results.

32. Interval Query (4. Filter RNAseq results)

33. Interval Query (6. ChIPseq search) Default is 2000 bp, define the interval and click “Change Interval”. Results will appear in a new tab. At the end of above table is a column called “Summit difference”. It is the difference between Peak summit and start position of gene.

34. Interval Query (7. SNPs) Distance from start position of the gene to position of SNP.

35. Interval Query (8: Orthologs) Ortholog gene id in black. Ortholog gene description in red. List of available orthologs in the database Select and click to get addional Orthologs

36. Interval Query (9: Save list) Click on “Save list” to save the gene ids into a file for further analysis. Name the list and click on “Save”.

37. Keyword search (Gene description or GO description) The database output. List the keywords and click “Search”

38. MyGene (1. List) Lists the your files so far. Maximum limit is 10. Upload a list of gene ids in a file. Maximum limit: 100 gene ids Show: To see contents of the file Edit: To change name and gene ids Delete: To delete the file.

39. MyGene (2. Upload)

40. MyGene (3. Show) Clicked “Show” and the contents are listed. To perform further analysis on the given list of gene ids.

41. MyGene (4. Edit) Click on the “Edit” link to access the list and click “Update” to save the changes to the list.

42. MyGene (5. Delete) Click on “Delete” the list and it has to confirmed before deleting.

43. Data Download Click on the “Download” link to go to data download web page Data is categorized based on the date we received the data. Click on the links to download