text: user9114: I have used WGCNA by integrating several datasets which are processed in a similar way. Identified 17 modules, followed by performed pathway analysis with the genes present in those modules.
  Among all the protein-coding genes,ncRNAs and other genes, I'm particularly interested in a specific lncRNA MALAT1.
  I found that MALAT1 is co-expressed with more than 800 genes in a module named blue. I have few questions, can anyone please help me in this?
  Questions:
  
  I would like to check which are the closest co-expressed genes to MALAT1. How can I know that?
  
  Once I get the closest genes to MALAT1, I would like to make a network with those genes and MALAT1. How to do this network?
  
  
  
  user851: The simplest way is to re-calculate (or load, if saved) the TOM matrix and find the genes with the highest TOM to MALAT1. If you have enough RAM to carry out WGCNA in a single block, you can use TOMsimilarityFromExpr, make sure you give it the same arguments as the ones you used in network construction, and select the appropriate column from the result. Then order the column and retain top genes, as many as you think is reasonable. You can also use adjacency instead of TOM, though TOM is a more natural quantity to use if you used in your network construction. Once you figure out which genes you want to retain, you can subset the TOM matrix (both rows and columns) to those genes and you have the sub-network among these genes.
  
original_text: 9114: <p>I have used WGCNA by integrating several datasets which are processed in a similar way. Identified 17 modules, followed by performed pathway analysis with the genes present in those modules.</p>
  <p>Among all the protein-coding genes,ncRNAs and other genes, I'm particularly interested in a specific lncRNA <code>MALAT1</code>.</p>
  <p>I found that <code>MALAT1</code> is co-expressed with more than 800 genes in a module named <code>blue</code>. I have few questions, can anyone please help me in this?</p>
  <p>Questions:</p>
  <ol>
  <li><p>I would like to check which are the closest co-expressed genes to <code>MALAT1</code>. How can I know that?</p>
  </li>
  <li><p>Once I get the closest genes to <code>MALAT1</code>, I would like to make a network with those genes and MALAT1. How to do this network?</p>
  </li>
  </ol>
   851: <p>The simplest way is to re-calculate (or load, if saved) the TOM matrix and find the genes with the highest TOM to MALAT1. If you have enough RAM to carry out WGCNA in a single block, you can use TOMsimilarityFromExpr, make sure you give it the same arguments as the ones you used in network construction, and select the appropriate column from the result. Then order the column and retain top genes, as many as you think is reasonable. You can also use adjacency instead of TOM, though TOM is a more natural quantity to use if you used in your network construction. Once you figure out which genes you want to retain, you can subset the TOM matrix (both rows and columns) to those genes and you have the sub-network among these genes.</p>
  