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SmartTables & Enrichment Analysis

SmartTables & Enrichment Analysis. Richard Billington SRI Bioinformatics Research Group October 2018. SmartTables. Collect lists of database objects Genes, metabolites, pathways, sequence regions, … Transform them into related objects (eg: transform list of genes → list of pathways)

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SmartTables & Enrichment Analysis

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  1. SmartTables & Enrichment Analysis Richard Billington SRI Bioinformatics Research Group October 2018

  2. SmartTables • Collect lists of database objects • Genes, metabolites, pathways, sequence regions, … • Transform them into related objects (eg: transform list of genes → list of pathways) • Navigate • Filter and combine • Share with public or specific collaborators, publish • Export to spreadsheet • Omics analyses

  3. SmartTables Location • BioCyc.org, HumanCyc.org, EcoCyc.org… • To create saved SmartTables, create a (free) BioCyc account for yourself • From the web menu: • SmartTables->My SmartTables

  4. Three Types of SmartTables • Created by you • Public • Special • Most SmartTables associated with a single PGDB

  5. Creating SmartTables: User-Defined SmartTables • Create a SmartTable • Type in metabolite names • From search results • Upload a tab-delimited text file

  6. Creating SmartTables: User-Defined SmartTables • Create a SmartTable by typing in names • Operations -> New -> SmartTable of Objects from Text Entry • Names will be converted to rows of objects

  7. Creating SmartTables from Search Results • Turn into a SmartTable button appears on all search results

  8. Using SmartTables: Browsing Attributes

  9. SmartTable Columns • Object ID • Sort • Hide • Set display mode • First column: object ID vs common-name • Sequences • Delete

  10. SmartTable Transformations • Create new columns that are computed from existing columns • Those columns can be converted to new SmartTables via "+"

  11. Using SmartTables: SmartTable Transformations • Use Case: Find all genes that are regulated by a transcriptional regulator. • Step 1: Create a SmartTable that contains the transcription factor. • Step 2: In the “Transforms” menu, select “Regulation – genes regulated by polypeptide, complex, or RNA”. • A new column containing all genes regulated by the transcription factor is generated. • This SmartTable can be further transformed, e.g. into metabolic pathways. • The resulting lists can be exported.

  12. Using SmartTables: Attributes • Use Case: Find the chromosome positions of all genes encoding enzymes of a pathway, sort by position. Find regulators of those genes. • Step 1: Create a group that contains the pathway. • Step 2: In the “Transforms” menu, select “Genes of pathway”. • Step 3: Select gene column and select • Operations > New > Group from column OR • Click “+” at top of gene column • Step 4: Select “left-end-position” from “Add Property Column” menu and add. Sort by position by clicking on arrow in column header. • Step 5: Select “Direct regulators of gene” from “Add Transform Column” menu.

  13. Genes of Aspartate Superpathway

  14. Transforms

  15. Other Operations on SmartTables • Set union, intersection, difference among two SmartTables • Filter SmartTable rows to keep/reject all rows containing specified value or substring or regular expression • Share SmartTable with public or specified users • Freeze SmartTable for publication

  16. Genes, Sequences, Regions….

  17. Set Operations on SmartTables

  18. Alignment Viewer

  19. Frozen SmartTables

  20. Collapsible Columns, Select Rows By Number

  21. Enrichment Analysis * Statistical method to find classes of objects that have more or less objects than would be expected by chance * Based on the Hypergeometric Distribution * Can perform enrichment, depletion, or both * Multiple ontologies can be used in Pathway Tools * Multiple testing correction optional

  22. Enrichment Dialog

  23. Lab Exercise • Search for compounds that have 'glucose' in their name • Turn into SmartTable • Enrichment Analysis → Compounds Enriched for Pathways • Use defaults in Enrichment pop-up, click 'OK’ • Select ten most enriched pathways • Operations → New → From checked rows • Reactions of pathway • New SmartTable of reactions (green button on column) • Operations → Paint Data → On cellular overview

  24. Lab Exercise • Create a SmartTable containing all E. coli enzymes with a molecular weight greater than 500; determine the map positions of the genes encoding those enzymes • Determine which enzymes in E. coli are heteromultimers • Create a SmartTable of metabolites and determine what metabolic pathways those metabolites are involved in • Export a SmartTable to a file • Share a SmartTable with the person next to you

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