Formation of regulatory patterns during signal propagation in a Mammalian cellular network

Source: Science. 2005 Aug;309(5737):1078-83.

Authors: Ma'ayan A, Jenkins SL, Neves S, Hasseldine A, Grace E, Dubin-Thaler B, Eungdamrong NJ, Weng G, Ram PT, Rice JJ, Kershenbaum A, Stolovitzky GA, Blitzer RD, Iyengar R.

Supplementary Materials

File Name	Description
Text file S1	Network data in flat file format. Most recent updated version of the network.
Text file S2	Pajek format text file describing the network data and assigns 2D location for nodes on the map.
Text file S3	Raw output from the MFinder program searching for motifs of size 3.
Text file S4	Raw output from the MFinder program searching for motifs of size 4.
Text file S5	Raw output from the MFinder program searching for motifs of size 5.
Text file S6	Raw output from the MFinder program searching for motifs of size 6.
Code segment S7	Rules for sorting components into functional machines.
Code segment S8	Converts the network into a Pajek format text file.
Code segment S9	Creates sub-network where connectivity is propagated from ligands.
Code segment S10	Analysis for nodes, interactions, motifs, clustering and path-lengths of sub-networks starting at ligands.
Code segment S11	Implementation of the Floyd algorithm to compute the characteristic path-length.
Code segment S12	Implementation of the clustering coefficient algorithm.
Code segment S13	Implementation of the grid coefficient algorithm.
Code segment S14	Algorithm used to create 100 shuffled networks with the same connectivity distribution and one island.
Code segment S15	Code segment used to create sub-network from specified source node to specified target node.
Code segment S16	Code used to create sub-networks with gradual allowable nodal connectivity.
Code segment S17	Algorithm used to search for feedback loops.
Code segment S18	Algorithm used to search for feed-forward loops.
Code segment S19	Algorithm used to search for bi-fan motifs.
Movie S20	Illustration of the breadth-first concept.
Movie S21	Illustration of the sub-networks where the source and target are specified.
Movie S22	Illustration of the concept of gradual inclusion of nodes based on connectivity.
Spreadsheet S23	Connectivity propagation per step from all ligands.
Spreadsheet S24	Results of the number of nodes, interactions, motifs, computed clustering and path-lengths for sub-networks starting at ligands.
Spreadsheet S25	Connectivity distribution table.
Spreadsheet S26	Characteristic path-lengths, clustering coefficients and grid coefficients for the real network and for 100 shuffled networks with the same connectivity distribution.
Spreadsheet S27	Results of the analysis of sub-networks from source to target.
Spreadsheet S28	Analysis of sub-networks based on nodal connectivity.