Table 1 Summary: the validity of current network analysis on static conglomerate networks

Topological Characteristics

Degree

No

Network statistics except average clustering coefficient are generally significantly different between the total network and stratified subnetworks

Betweenness

No

Clustering Coefficient

To some degree

Eccentricity

No

Functional Enrichment in Network

No

Proteins in different networks are enriched in context-specific functions

Network Hubs

Hubs in Conglomerate Networks

To some degree

16% hubs in the total network change into non-hubs in subnetworks on average

Non-hubs in Conglomerate Networks

Yes

0.8% hubs in subnetworks are non-hubs in the total network on average, which correspond to a trivial portion (< 0.1%) of non-hubs in the total network

Network Bottlenecks

Bottlenecks in Conglomerate Networks

To some degree

13% bottlenecks in the total network change into non-bottlenecks in subnetworks on average

Non-bottlenecks in Conglomerate Networks

Yes

9% bottlenecks in subnetworks are non-bottlenecks in the total network on average, which correspond to a trivial portion of non-bottlenecks in the total network

Modular Compatibility

No

Modules from the total network and those from subnetworks have low Modular Compatibility

Functional Enrichment in Modules

No

Modules from different networks differ in over-represented context-specific functions