Resources and data from publications

Resources and data from publications

Creation and implications of a phenome-genome network

Creation and implications of a phenome-genome network.
Butte AJ, Kohane IS
Nat Biotechnol24p55-62(2006 Jan)

GENOTEXT software and data

Evaluation and Integration of 49 Genome-wide Experiments and the Prediction of Previously Unknown Obesity-related Genes

Use of Bayesian networks to probabilistically model and improve the likelihood of validation of microarray findings by RT-PCR.
English SB, Shih SC, Ramoni MF, Smith LE, Butte AJ
J Biomed Informp(2008 Aug 26)

Source code and data files to regenerate table and figures

The "etiome": identification and clustering of human disease etiological factors

Selected Proceedings of the First Summit on Translational Bioinformatics 2008, BMC Bioinformatics.

Download disease-gene and disease-environmental factor association files. Use gzip and tar to uncompress and expand into two tab-delimited files, which can be read into R using the read.table command.

Dynamism in Gene Expression Across Multiple Studies

Download a table of the summary statistics of rank width, rank median, and expression variation ratio for human, rat, and mouse expression data from GEO and the data tables from the paper: alexmo-genedynamics-tables.zip.

Cell type-specific gene expression differences in complex tissues. Shen-Orr et al. Nature Methods, 2010.

csSAM Excel Add-in

Download the csSAM Excel Add-in! (Works only on Windows based machines or through virtual PC environments).

Academic users can receive a copy of csSAM Excel by filling in the software agreement, available here stanford_academic_software_agreement_s10-083.pdf, and emailing it back to Shai Shen-Orr ( shenorr at stanford dot edu ).

 If you are a commercial user, please contact Imelda Oropeza  ( imelda at stanford dot edu ) at Stanford's Office of Technology and Licensing for a commercial license of the csSAM Excel.
  add-in. Please do not contact Imelda Oropeza about downloading, technical questions etc. All she handles is commercial licensing!

csSAM R package

Download the latest csSAM package version 1.2: Executable for Windows cssam_1.2.zip or Source code (Mac/Unix/Linux) cssam_1.2.tar.gz

Older versions:

Download csSAM version 1.0: cssamv1p0.zip.

Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets

Suthram et al. PloS Computational Biology, 2010.

Download the set 4620 functional modules. The first column is the index, the second column is the Module name and the rest of the columns are the genes (Entrez Gene ID) in that module.: ModuleFile.txt

Butte Lab Medline Processing Code

Scripts and database schema for processing Medline XML source data files; unpublished.

tar file