NEMO language examples:
G0 is up-regulated by transcription factors P1, P2, and P5 (P for protein) from G1, G2, and G5 respectively. It is down- regulated by P3 and P4.
The other genes are similarly described, and if they are not part of a motif, they are enclosed within a GLIST construct. Once the entire network is described, it is enclosed with square () brackets.
A Dense Overlapping Regulon (DOR) is a connected bipartite graph.
G0 up-regulates G1, G1 up-regulates G2, and G2 is up-regulated by G0.
G0 up-regulates G1, G1 up-regulates G2, G3, and G4, who are also up-regulated by G0.
G0 up-regulates G1, G2, and G3.
An example network with motifs other than DOR inside of a TMLIST (transcription motif list) construct. Click here for a listing of the SBML generated by the nemo2sbml compiler.
Same as above, except there is a specified input function for G10. Click here for a listing of the SBML generated by nemo2sbml.
RANGE/NEMO was developed while employed at the Biotechnology Computing Research Group, supported in part by Grant Number 5P20RR016466 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH), with prior support from 2P20RR016466-040005 and 2P20RR016466-049001, PI Thomas Marr.