text: user976: I have a network which I clustered into 11 smaller clusters. I have a set of genes and I would like to check if statistically significant number of these genes fall on any specific cluster. One method which I thought of was to find which percentage of a total cluster were made up of my genes of interest. For example, say 60% of the genes in a cluster were the genes in my list. However, I was hoping that there was a better way to do this. This study on honey bees has done something of the kind.
  I would appreciate if there was a way to do something similar. I do not know how to replicate what they have done in the study. Any help is appreciated.
  
  user48: A hypergeometric test is related to the fisher test, in a table with one  dimension being some factors and the other one some other factors it is tested if they are independent. In R you con do this:
  data <- matrix(c(0, 1, 2, 5), ncol = 2, nro = 2)
  fisher.test(data)
  
  Or you can use the specific function phyper, to see the relation between them you can read this question and answer
  
original_text: 976: <p>I have a network which I clustered into 11 smaller clusters. I have a set of genes and I would like to check if statistically significant number of these genes fall on any specific cluster. One method which I thought of was to find which percentage of a total cluster were made up of my genes of interest. For example, say 60% of the genes in a cluster were the genes in my list. However, I was hoping that there was a better way to do this. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755009/" rel="nofollow noreferrer">This study on honey bees</a> has done something of the kind.</p>
  <p>I would appreciate if there was a way to do something similar. I do not know how to replicate what they have done in the study. Any help is appreciated.</p>
   48: <p>A hypergeometric test is related to the fisher test, in a table with one  dimension being some factors and the other one some other factors it is tested if they are independent. In R you con do this:</p>
  
  <pre><code>data &lt;- matrix(c(0, 1, 2, 5), ncol = 2, nro = 2)
  fisher.test(data)
  </code></pre>
  
  <p>Or you can use the specific function <a href="https://stackoverflow.com/q/8382806/2886003"><code>phyper</code></a>, to see the relation between them you can read this <a href="https://stats.stackexchange.com/q/82688/105234">question and answer</a></p>
  