Apart from those involved in secondary metabolism (see above), the others include a cluster of function-unknown genes whose expression was particularly strongly dependent on bldA at the mRNA (SCO4246, SCO4252-3, SCO4256 and SCO4262; Fig. 5A) and protein levels (SCO4251-3; Fig. 5B) [ 9].
We do not find the same clustering of functions with the FKBPs as were found with the cyclophilins.
The top five clusters of functions were protein transport, protein catabolic process, vehicle-mediated transport, protein modification/ubiquitination, and regulation of translation (see Table 3 DAVID cluster scores > 5).
Response: We still believe that displaying both depictions has some value because the first reflect the "natural" clustering based on the Kamada-Kawai algorithm, whereas the second is the knowledge-based manual clustering of functions.
These include such clusters of functions classified with the Ingenuity Pathway Analysis program, as impaired psychological processes, coordination and memory, pre-pulse inhibition and long term and synaptic depression.
In order to probe the functional significance of the genes regulated by Enh or PrL, we investigated functional enrichment in these categories using DAVID [ 42, 43] followed by clustering of functions with significant numbers of shared genes using Enrichment map [ 44].
Interestingly, one EST (AI843903) that is classified to a UniGene cluster of unknown function (as of October 2005) was predicted in Biozon to have similarity to protocadherins.
The third ppk2 homologue (MLP_23310) was relatively similar to both ppk2 and pap, but was located in a distinct cluster of undetermined function (Fig. 2a).
Concepts presented here may be useful for objective clustering of protein functions and deriving a comprehensive protein interaction map.
Several approaches propose an encapsulation and clustering of related functions to accomplish the changed requirements.
Our method consists of six steps: (i) land-use inventory; (ii) energy demand inventory; (iii) local renewable/residual energy potential analysis; (iv) clusters of spatial functions exploration; (v) energetic linkages analysis; (vi) network patterns exploration.
