what is the meaning of semantic x space in REVIGO scatterplot?
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3.8 years ago
maple964 • 0

Dear all,

Very simple question, what is the meaning of semantic x space and y space in REVIGO?

It is known that "REVIGO enriched terms remaining after the redundancy reduction are represented as scatterplots in a two dimensional space which summarize GO terms’ semantic similarities."

"The guiding principle is that semantically similar GO terms should remain close together in the plot, but the semantic space units have no intrinsic meaning. Bubble color indicates the p-value for the false discovery rates; circle size indicates the frequency of the GO term in the underlying GO database (bubbles of more general terms are larger)"

However, when professors asked "what's the meaning of semantic x space and y space?" or "If the semantic space units have no intrinsic meaning, what do the numbers on the x and y space represent?" or "How does REVIGO plot those semantic similarities on the x and y space?", I failed to answer...

Looking forward to the answers from your help

Thank you all in advance

R Revigo • 3.0k views
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There's a paper that describes their method in detail: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021800

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