Yeast Bicluster Gaggle (2007-04)

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The Gaggle paper in BMC Bioinformatics

Yeast Bicluster Gaggle (2007-04)

Boss
DMV (6209 genes x 567 conditions, from SMD)
NOTE: In this viewer, all NaN's have been changed to 0 so that the correlation finder will work. If you like, you can download the original matrix data (22MB).
Networks
- Protein-DNA interactions (from ???) 2416 nodes, 4358 edges
- Protein-Protein interactions (from ???) 3756 nodes, 5614 edges
- Biclusters D.Reiss & R.Bonneau, September 13, 2005
- Cluster Information
- Prolinks Association Network
Translator
- Yeast SDG to GI translator
Genome Browser
- ChIP-chip Ranish lab (password required)
- ChIP-chip Ranish lab plus perocci_2007 (password required)
Analysis Tools
- MeV MultiExperiment Viewer microarray data analysis tool.
  - For general information on MeV see the TM4 website.
- R statistics package
  - If R and the Gaggle package are not installed, see these instructions.
  - Connect R to the Gaggle, as described in 'Startup'.
    - At the R prompt, type these commands (in R 2.4.x):
```
library(gaggle)
source("http://gaggle.systemsbiology.net/R/gaggleUtil.R")
gaggleInit()
```
  - See the cribsheet for quick instructions on how to accomplish common tasks using R and the R goose.
- Firegoose
  - If the Firegoose extension is not installed, see these instructions.
  - Start the Firefox browser.
  - Use the Paster Application to paste data into Firegoose.
- Genome Browser
  - The genome browser is a way of visualizing data plotted against coordinates on the genome. Tiling arrays and ChIP-chip data are a couple use cases.