Determination of hub genes in PPI network
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3.2 years ago

This might be a naive question, sorry. How are "hub genes" determined in a PPI network? Just determine the nodes degree and choose top 10 or so?

ppi hub genes • 4.3k views
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@catechize.2.learn: please do not delete posts, specially if they have good answers, as they are indexed by search engines and benefit people with questions similar to yours.

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thank you for the information.

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10
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3.2 years ago

A hub is a node that has a higher degree than other nodes in the graph. How this translates in practice seems to vary between papers. Some just use an arbitrary threshold either as a fixed number or as a percentage, others choose a threshold based on some statistical argument e.g. outliers in the distribution when assuming a scale-free graph.
As a side note, be careful about what you say about high-degree genes/proteins. Many of them have high degrees simply because they have been more studied (e.g. the historical oncogenes such as the RAS family, SRC, EGFR...) or because they belong to a particular class (e.g. ubiquitin-like families, chaperones) or because they are sticky proteins (some are well documented false-positives such as ferritin and ribosomal proteins for yeast two-hybrid or collagens in AP/MS, see also for example the crapome database for "contaminants" in AP/MS).
Finally, note that the scale-free assumption probably doesn't hold for many biological networks.

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Thank you @Jean-Karim Heriche. Nice and thorough response.

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3.2 years ago
h.mon 33k

Hub genes are highly interconnected genes. There are several methods and approaches for measuring interconnectedness, see for example the cyttoHubba paper for a list of methods.

While some papers just take the top X genes (following some interconnectedness score, or the intersection of several scores) as hub genes, ideally, a minimum requirement should also be required - I've seen often "genes with a connectivity degree of ≥ 8 were defined as hub genes" or "genes with a connectivity degree of ≥ 10 were defined as hub genes".

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Thank you @h.mon for your response and the article you introduced.

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