This collection stores the input files for ExpressOrtho, a method to confidently predict transient transcription factor or other protein binding sites on the genome. ExpressOrtho is based on the observation that tens to hundreds of thousands of gene pairs are tightly co-expressed across thousands of RNA-seq or gene expression microarray samples. We have shown statistically highly significant co-expression coincides with the binding of similar sets of transcription factors, histone remodeling enzymes, and the presence of similar histone modifications. Regulatory sites are also tested in the orthologous mouse (or human) gene.
Please also see our Git page at https://git.unl.edu/sladunga2/ExpressOrtho.
We also submitted a manuscript for publication by:
Istvan Ladunga, Avi C. Knecht, Adam Caprez, Natasha Pavlovikj,
Timothy L. Bailey, Tao Liu6, Pedro Madrigal, and David R. Swanson:
The “terra incognita” of gene regulation:
predicting transient transcriptional regulatory sites
based on orthologous and co-expressed genes