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Table 1 Proportion of Hepatitis C virus-binding proteins in top ranked gene seeds

From: Dynamic protein interaction modules in human hepatocellular carcinoma progression

Top levela Gene set HCC transitionb
   N-C C-D D-E E-A
0.1% DEG 0/11 1/11 0/11 1/11
  DCG 7/63* 9/65*** 10/60*** 4/63
0.5% DEG 3/55 2/55 2/55 4/55
  DCG 25/290*** 36/279*** 27/287*** 27/288***
1.0% DEG 6/110 3/110 5/110 6/110
  DCG 47/524*** 51/538*** 36/523*** 41/559***
  1. In each cell, the proportion is shown as ″x/y″, with y for top-ranked genes and × for genes of interest. Enrichment p-value < 0.01 (*) or < 0.0001 (***) are marked.
  2. aTop-level is the fraction of the top-ranked genes/pairs in the total network nodes/edges. For differential expression genes (DEG), we used the node-wise fraction; for differential co-expression genes (DCGs) deriving from pairs, we used the edge-wise fraction. A same fraction of pairs involve a greater number of genes.
  3. bTransition names: Normal to Cirrhosis (N-C), Cirrhosis to Dysplasia (C-D), Dysplasia to Early HCC (D-E), and Early HCC to Advanced HCC (E-A).