The NEMO (NEtwork MOtif) language

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.

jlong@alaska.edu

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.