This repository supports data associated with our studies of a co-expression network for mouse pancreatic beta-cells.

Please cite:

Anna B Osipovich, et al, manuscript in preparation

URL to manuscript

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Explore

Please explore the data here.

Sample summary

Expression profiles were determined at the following timepoints and genotypes:

TABLE or IMAGE here

Meta-module network

Each node (numbered) in the meta-network represents a module of highly co-expressed genes. The meta-network is defined by correlations between module eigengenes, which partitions modules into several distinct and strongly connected groups of modules.

Meta-module	Color	Image	# of nodes	# of edges	All Genes	TF
A	#5778A4		2110	1831174	metamodule-A.filterLevel-any.cyjs.zst
B	#E49444		319	67374	metamodule-B.filterLevel-any.cyjs.zst
C	#85B6B2		1159	1173480	metamodule-C.filterLevel-any.cyjs.zst
D	#E7CA60		257	34882	metamodule-D.filterLevel-any.cyjs.zst
E	#A87C9F		3237	4041196	metamodule-E.filterLevel-any.cyjs.zst
F	#F1A2A9		334	63296	metamodule-F.filterLevel-any.cyjs.zst

Data preparation & methods

1. Create new git repo, downloaded ZIP for original IsletDynamics-gcn as baseline. Did not fork intentionally to avoid history and accidental contributions to upstream repo.

2. Setup LFS for large file storage for Cytoscape files, git lfs track 'cysjs/**'

3. To create images, open Cytoscape

   1. Import file .cys
   2. Layout > Prefuse Force Directed Layout
   3. Layout > yFiles Remove Overlaps
   4. Export image

4. Created a Cytoscape-all-modules-filterLevel-high.cys which contains extracted networks for all metamodules, both with "All" genes and "TF only" genes.