1. Optionally start a Gaggle Boss
2. Microarray Data
   • DMV
   • Gaggle Web Application (ISB Internal only) More ways to explore data
   • Annotation
     • Halo (from TIGR)
     • Entrez annotations
     • sbeams+kegg annotations
   • Sequence Goose   (for use with BLASTP)
   • Networks
     • NRC-1 (Cytoscape 1.x)
     • NRC-1 (Cytoscape 2.6.0)
     • NRC-1 2006   (operons only, work in progress)
     • Tiles
     • Inferelator network (June 25, 2005)
     • Bicluster network (June 25, 2005)
     • EGRIN Bicluster and regulatory circuit viewer
     • Prolinks
     • IP
     • KEGG Reference Reactions
     • Halobacterium GTF protein-DNA interaction map (10202006) (Protein-DNA interaction data based on ChIP-chip experiments.)
     • ChIP-chip network based on MeDiChI (November 2007) (RESTRICTED ACCESS)

     MeDiChI network - cytoscape 1.x low confidence (pvalue < 0.2 )

     MeDiChI network - cytoscape 1.x high confidence (pvalue < 0.05 )

     Caveats/explanations regarding this network:

     1. The TFs are colored green.
     2. Some of the TFs (e.g. Bat and some of the tbp's) are probably bad IPs and will ultimately be removed.
     3. The network can (and should) be filtered to get any meaning out of it... For example, the top-level network has edges with a P-value of < 0.2, but the subnetwork was filtered to only include edges with p < 0.05.

     You might find it useful to further filter it using other edge attributes (and Cytoscape 2.6's nice filtering capabilities):

     • "Distance" (how far the hit was from the start-site of the gene)
     • "where.hit" (e.g. to only include "upstream" hits vs. downstream or in-gene) -- this is also used to set the edges' colors.
     • intensity (intensity ratio of IP vs. WCE of the peak)

   • Genome Browser (data available to Halo group only for now)
     • Tiling array -- Download halo tiling array dataset.
     • Growth curve -- Download halo growth dataset.
     • Trh and tfbd -- Download halo trh dataset.
     • 1451 knockout arrays -- Download dataset.
   • Translators
     • Halo to Haloarcula   (using COG membership)
     • Translator Goose: EC - VNG
     • Translator Goose: STRING to VNG   (use between STRING WBI & Cytoscape)
     • Translator Goose: VNG -> GI
     • Translator Goose: GI -> VNG
   • 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.

Reaction-Centered Cluster Explorations

1. Pyruvate

Utility Geese

• Sample Goose