We are working on converting our R code into a package for network inference.
Yeast gene expression data
ArrayExpress
accession number E-MTAB-412.
Time series gene expression data consisting of genotyped
yeast segregants under a drug(rapamycin) perturbation.
This data was generated in the
Bumgarner Lab, with
significant contributions from Drs.
Eric Schadt,
Jun Zhu at SAGE, and Kenneth Dombek at UW.
The Array Express entry consists of all the CEL files and the RMA normalized data for all genes on the arrays. We are working on getting the subset of 3556
genes available as a separate Array Express entry.
ArrayExpress
accession number E-MTAB-446.
Gene expression data of yeast ARO80, DAT1 and RTG3 deletion mutants after
rapamycin perturbation.
This data was generated in the
Bumgarner Lab, with
significant contributions from Dr.
Kenneth Dombek at UW.
Again, this Array Express entry consists of all the CEL files and RMA normalized
files.
Networks in the paper: The edge lists reported in the paper are
available as tab-delimited text files. Column 1 contains the systematic
names of the regulators, column 2 is the systematic names of the
target gene, and column 3 is the posterior probabilities from iBMA.
Network A: 65122 edges thresholded at 50% posterior probabilities. This network
was constructed using iBMA with exernal data sources (nbest=10, p=100).
Network B: 63026 edges thresholded at 50% posterior probabilities. This network
was constructed using iBMA using array data only (nbest=10, p=100).
Yeastract documented regulatory relationships used to assess
networks A and B in the paper. This tab-delimited text file was retrieved
from the YEASTRACT database.
Only documented evidence was used.
The systematic names of the transcription factor and target genes are
in columns 2 and 4 respectively.
Note that this file contains the TF-gene relationships for the 3556-subset
only, and the hard-coded gene pairs have already been subtracted.
Hard-coded TF-gene pairs.
Known TF-gene regulatory relationships were hard-coded in our regression-based
method. This tab-delimited text file was constructed using YPD and SCPD.
The systematic names of the TF and target genes are in columns 1 and 4.