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Table 1 Measures of expression and network topology that potentially characterize the essentiality of a transcription factor in a gene-regulatory network

From: Stat and interferon genes identified by network analysis differentially regulate primitive and definitive erythropoiesis

Topological property Abbrev. Description Reference
Global Connectivity GC number of local networks in which gene is found  
Degree k number of edges incident to a gene, normalized by size of the neighborhood (k/N)  
Proportion Predicted Targets T proportion of incident edges annotated by predicted binding  
Weighted Clustering Coefficient* CCw C C i = E i k i k i 1 [42]
Weighted Closeness Centrality C C i = n 1 Σ j V i d G i , j [43]
Absolute Expression    
Proerythroblast P Average expression across replicates  
Basophilic Erythroblast B Average expression across replicates  
Polyorthochromatic Erythroblast O Average expression across replicates  
Reticulocyte R Average expression across replicates  
Differential Expression    
Profile Shape PS Best-fit vector mapped to the average expression profile  
Maximum Ratio MR Ratio of maximum to minimum expression during developmental series  
  1. * ratio of the number of edges that exist between the k neighbors of gene i (E i ) and the number of potential edges between the neighbors, or k i (k i  − 1).
  2. reciprocal of the mean shortest path length between a gene i and all other genes that can be reached from it, where V is the set of all possible genes and d G is the shortest path length between genes i and j. Path lengths were estimated using the Dijkstra distance [44] as implemented in the Boost Graph Library [45].
  3. Average expression profiles mapped to 28 templates using vector projection. The best-fit profile (PS) was used as an indicator of the trend in expression during erythropoiesis.