Table 1.
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 |
|
[42] |
Weighted Closeness Centrality† |
C |
|
[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 |
* ratio of the number of edges that exist between the k neighbors of gene i (Ei) and the number of potential edges between the neighbors, or ki(ki − 1).
† 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 dG 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].
‡ 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.