Difference between revisions of "User Guide/SObA"

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(Created page with "== '''Summary of Ontology-based Annotations (SObA)''' == == Submit == Enter a gene list consisting of any accepted C. elegans gene names separated by spaces, colons or tabs...")
 
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== '''Summary of Ontology-based Annotations (SObA)''' ==
 
== '''Summary of Ontology-based Annotations (SObA)''' ==
  
== Submit ==
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== What is a SObA graph? ==
  
Enter a gene list consisting of any accepted C. elegans gene names separated by spaces, colons or tabs into the box. Alternatively, input a plain-text file of gene names separated by spaces, colons or tabs using the 'Choose file' button. Text files must be plain text (.txt).
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SObA is an abridged version of the ontology graph, trimmed based on annotations and hierarchical relationships.
The program returns enriched terms as assessed by a hypergeometric function, after FDR correction. A bar chart containing the top 15 (or less) enriched terms, sorted by increasing q-value and by decreasing fold-change is automatically generated. Bar coloring is intended to improve readability, and color does not convey information.
 
<p>Optionally, provide a background gene set as a csv (or simple text) file with a single column without a column name. Gene names must be in wbid format.
 
  
*<b>Sometimes the program's running time is longer than the set 'timeout' interval and it would cause a "504 Gateway Timeout" error. If that happens, please refresh the web page.</b>
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Starting with the full ontology graph, we trim the graph by:
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(A), removing all nodes (and their edges) that do not carry any (direct or inferred) annotations;
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(B), removing all nodes that do not have direct (as opposed to inferred) annotations unless they are the lowest common ancestral nodes of two or more descending nodes (lowest common ancestor, LCA);
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(C), applying transitive reduction by removing all paths between a pair of nodes unless they are the longest paths;
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(D), reducing hierarchy depth to focus on broader aspects of ontology (top slicing).
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(E), scaling node sizes based on the relative number of annotations that each node carries to indicate possible relative importance.
  
== Result ==
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SObA graph is drawn with Cytoscape. The graph may be manipulated in the following ways.
The Result table shows all significantly enriched terms, those that have a Q value < 0.1, sorted by their P values.
 
  
The bar chart displays up to 15 significantly enriched terms. Colors are meant to improve readability and do not convey information.
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1. zoom and move nodes around.
 
 
== Citation ==
 
 
 
[http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1229-9 David Angeles-Albores, Raymond Y. N. Lee, Juancarlos Chan and Paul W. Sternberg, 2016. "Tissue enrichment analysis for C. elegans genomics", BMC Bioinformatics 17:366]
 
 
 
[https://doi.org/10.17912/W25Q2N Angeles-Albores, D; Lee, RYN; Chan, J; Sternberg, PW (2018): Two new functions in the WormBase Enrichment Suite. Micropublication: biology. Dataset. https://doi.org/10.17912/W25Q2N]
 

Revision as of 19:11, 6 August 2019

Summary of Ontology-based Annotations (SObA)

What is a SObA graph?

SObA is an abridged version of the ontology graph, trimmed based on annotations and hierarchical relationships.

Starting with the full ontology graph, we trim the graph by: (A), removing all nodes (and their edges) that do not carry any (direct or inferred) annotations; (B), removing all nodes that do not have direct (as opposed to inferred) annotations unless they are the lowest common ancestral nodes of two or more descending nodes (lowest common ancestor, LCA); (C), applying transitive reduction by removing all paths between a pair of nodes unless they are the longest paths; (D), reducing hierarchy depth to focus on broader aspects of ontology (top slicing). (E), scaling node sizes based on the relative number of annotations that each node carries to indicate possible relative importance.

SObA graph is drawn with Cytoscape. The graph may be manipulated in the following ways.

1. zoom and move nodes around.