Support for Phenotype Microarray Data in Pathway Tools Suzanne - - PowerPoint PPT Presentation

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Mar 30, 2023 454 likes •603 views

Support for Phenotype Microarray Data in Pathway Tools Suzanne Paley March 2013 SRI International Bioinformatics 1 PM display on All Growth Media Page SRI International Bioinformatics 2 PM Growth Medium Representation

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SRI International Bioinformatics

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Support for Phenotype Microarray Data

in Pathway Tools

Suzanne Paley March 2013

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PM display on All Growth Media Page

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PM Growth Medium Representation

l Plate ID, Well ID l Constituents

 Concentration  Role: source of C, N, P or S

l Base medium l Name l Abbreviated name (just the added compound for

PM media)

l Citation, comment l pH l Osmolarity (computed from constituent

concentrations)

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Growth Observation Representation

l Growth media l Growth status: growth, no-growth, or low-growth

 No support for capturing quantitative data

l Citation, comment l Experimental variables

 Aerobic/anaerobic  Temperature  Wildtype or knocked out genes

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Conflicts

l Conflicts occur when multiple observations for

the same medium and conditions record different growth statuses

 We cannot detect conflicts when experiments use slightly

different but equivalent media.

l Conflict can be resolved by a curator

 This creates a new, privileged growth observation frame  Curator should record rationale with comment or citation  GUI will still show all primary observations

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Growth Medium Display

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PM Data in EcoCyc

l 5 Aerobic Datasets (4 for plates 2-4) Carbon Nitrogen Phosphorus Sulfur Total Total Wells 190 95 59 35 379 Observations 855 367 233 130 1585 Wells w/ conflicts 61 35 10 13 119 Resolved conflicts 53 10 6 5 74 Remaining unresolved 8 25 4 8 45 Remaining growth/no- growth conflicts 7 24 1 1 33

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Other Growth Observations in EcoCyc

l Low throughput data:

 Wildtype observations from literature for 23 media  Wildtype observations generated by our group for 21 media

l High throughput gene knockout data

 5 datasets

 2 on rich media  2 on glucose media  1 on glycerol media

 17,269 total knockout growth observations

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Navigating to All Growth Media Page

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Changing Display Conditions

l On All Growth Media page, can specify

different set of conditions

l Colors in display tables will update

accordingly

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Generating Heatmaps

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Importing PM Data

l File->Import->Phenotype Microarray Data from

Spreadsheet…

l Spreadsheet must be saved as tab-delimited text l One file per PM plate l Wells can be identified by either well ID or

compound name/ID

l Data values in spreadsheet can be either

quantitative or qualitative

 If quantitative, must specify cutoff values for no/low and low/

normal growth

 If qualitative, must specify what text values match normal/low/

no growth

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Importing PM Data

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Importing PM Growth Media

l Can either use base media from EcoCyc (or

ther PGDB) or create your own.