A P Francisco
Code and projects

TFRrank

A graph-based framework to prioritize regulatory players involved in transcriptional responses within the regulatory network of an organism, whereby every regulatory path containing genes of interest is explored and incorporated into the analysis. This tool was integrated in both YEASTRACT and regulatory snapshots prototype. Check our paper for algorithmic details and experimental results.

A prototype and yeast related files are available for evaluation purposes. Source code is available upon request.

Assuming that you have a Java environment available and that all files in the archive above are in your current directory, you can run our prototype as follows:

[aplf@darkstar ~]$ java -cp yrank.jar com.yeastract.rank.core.RankIt2 \
  orf2name.txt \
  gene_association.sgd \
  weighted_network.txt \
  0 0 0 1 \
  0.25 \
  100 \
  none \
  false \
  < sample_input.txt

Parameters are as follows:

We provide also two input examples in the archive above, sample_input.txt and sample_weighted_input.txt, where the latter includes expression weights for each gene in the input.

Please, let us know if you need help with anything.