A developmental lineage-based gene co-expression network for mouse pancreatic beta-cells
Each node in the meta-network represents a module of highly co-expressed genes. The meta-network is defined by correlations between module eigengenes and partitions modules into three distinct strongly connected module groups. See figure 1 in the manuscript for additional detail.
- Download large metanetwork image
- Download metanetwork Cytoscape file
- Browse/search gene expression data
- Browse/search module data
Please cite:
Anna B Osipovich, Karrie D Dudek, Emily Greenfest-Allen, Jean-Philippe Cartailler, Elisabetta Manduchi, Leah Potter Case, Eunyoung Choi, Austin G Chapman, Hannah Worchel Clayton, Guogiang Gu, Christian J Stoeckert, and Mark A Magnuson. A developmental lineage-based gene co-expression network for mouse pancreatic β-cells reveals a role for Zfp800 in pancreas development. Development 2021 .doi: 10.1242/dev.196964 (PDF)
For Biologists
We have prepared Cytoscape *session* files that you can download and simply open with Cytoscape to view and interact with the network meta-modules.
- Option 1 - Download Cytoscape file for all genes
- Option 2 - Download Cytoscape file for "TF" genes, filtered via transcription factor activity, sequence-specific DNA binding (GO:0003700)
For Bioinformaticians
For each meta-module, you will find below:
- Network image for "all genes" meta-modules
- Statistics about number of nodes and edges for "all genes" meta-modules
- Cytoscape JSON network file (compressed via ZIP) for all genes
- Cytoscape JSON network file (compressed via ZIP) for all genes filtered via **transcription factor activity, sequence-specific DNA binding** (GO:0003700)
| Meta-module | Image | # nodes1 | # of edges2 | All Genes | Transcription Factors Activity Genes |
|---|---|---|---|---|---|
| A |  |
103 | 732 | Download | Download |
| B |  |
1,039 | 64,306 | Download | Download |
| C |  |
3,070 | 546,028 | Download | Download |
| D |  |
1,096 | 65,970 | Download | Download |
| E |  |
30 | 56 | Download | Download |
| F |  |
869 | 42,414 | Download | Download |
| G |  |
54 | 177 | Download | Download |
| H |  |
226 | 2,927 | Download | Download |
| I |  |
246 | 3,549 | Download | Download |
| J |  |
1,078 | 62,768 | Download | Download |
| K |  |
42 | 145 | Download | Download |
Legend
- A node represents a gene
- An edge represents a connection between two nodes and the number of edges shown is representative of edges with correlations of greater than 0.5
FAQ
Where can I get Cytoscape?
You can download it here.
How do I load network files in Cytoscape?
In order to load a network from a local file you can select File → Import → Network → File... Choose the correct file in the file chooser dialog and press Open. After you choose a network file, another dialog will pop up. Here, you can choose either to create a new network collection for the new network, or load the new network into an existing network collection. When you choose the latter, make sure to choose the right mapping column to map the new network to the existing network collection.
Contact
If you have questions, please contact the corresponding author of the manuscript or post an issue in the GitHub issue tracker for this repository.