This site contains supplementary information to the
paper:
V. Varadan, D. Miller III and
D. Anastassiou, “Computational
Inference of the Molecular Logic for Synaptic Connectivity in C. elegans,”
Bioinformatics, volume 22, issue 14 – ISMB 2006, pp. e497-506.
Please make reference to the above paper in any
publication for which you make use of any data or software from this website, which
will be updated and maintained to include newer versions of the matrices E,
A, B, as well as related software.
The ISMB 2006 paper connects the neural wiring diagram
with the single-neuron transcriptome of C. elegans using a systems-based
computational approach known as EMBP (entropy minimization and Boolean
parsimony). It also introduces an information-theoretic analysis of the
multivariate synergy of the joint expression levels of multiple genes with
respect to a phenotype, which provides insight into the structure of pathways
responsible for the phenotype.
V. Varadan and D. Anastassiou,
“Inference of
Disease-Related Molecular Logic from Systems-Based Microarray Analysis,” PLoS Computational Biology, Vol. 2, Issue 6, e68, June
2006, pp. 585-597.
The latest versions of the expression matrix are
available in the Mining
WormBase for Expression Data section along with a description of the
methodology used for creating it, as a result of our continuing
cross-disciplinary collaboration between
The adjacency matrices of the wiring diagram were
taken from the paper “Wiring
optimization can relate neuronal structure and function” by
B.L. Chen, D.H. Hall, and D.B. Chklovskii, PNAS,
Gap
Junction Neuronal Partners (Excel File)
Post
Synaptic Neuronal Partners (Excel File)
Pre Synaptic Neuronal Partners (Excel File)
You can download a simple “demo” version of nearest-neighbor
heuristic search entropy minimization software by clicking here.
Starting from a “seed” gene set, the program will iteratively produce new gene
sets of the same size with lower conditional entropy. Please type “help
iterate” for instructions. Following is an example output:
[pre_egl-3
pre_unc-129 ]; H = 0.991604
[pre_egl-3
post_glr-6 ]; H = 0.990541
[pre_egl-3
post_mgl-2 ]; H = 0.982978
[post_mgl-2
post_flp-18 ]; H = 0.981130
[pre_mig-1
post_mgl-2 ]; H = 0.969051
[pre_mig-1
post_glr-5 ]; H = 0.966375
[pre_mig-1
post_cam-1 ]; H = 0.966088
[pre_mig-1
post_F25B5.2]; H = 0.955069
[pre_unc-18
post_F25B5.2]; H = 0.954243
[pre_unc-18 post_glr-1
]; H = 0.952017