Reviewer response for version 1
In principle the Expresso database will be useful to plant researchers. 
I would like to see a couple of things: what about mention of other databases like AGRIS at OSU and Cistome/ePlant at the BAR? 
Do these capture the kinds of interactions the authors are describing? 
Another is HRGRN (http://plantgrn.noble.org/hrgrn/). 
What are the disadvantages/limitations of these vis a vis Expresso?
Another thing that would a “nice-to-have” would be to include the Ecker Lab’s recent, extensive DAP-seq data set, which the authors ( https://www.ncbi.nlm.nih.gov/pubmed/27203113 ) show to be quite concordant with existing Chip-Seq data. 
These data are more extensive than the fairly limited number of Chip-seq data sets that Aghamirzaie et al. have collated.
I tried out the software, which worked as promised. 
The functionality was somewhat basic. 
It would be quite easy to use table.js or similar on the “Genes” search output page, or on the “Gene Expression” output page to be able to sort the table of favourite genes with their targets as a user expects to be able to do, or to sort by Pearson correlation. 
It might be nice to let users know how to download the “Genes” search results and load them into Cytoscape in a tutorial section. 
I was unable to download a file of TFs binding to my favourite genes (URL http://bioinformatics.cs.vt.edu/expresso/Expresso_Codes/getResFile_Genes.php ) – the page returned an error of “Unable to select database”.
“Run Demo” did not work on the “Gene Expression” page, or at least I thought it didn’t until I realized I had to scroll down to see the results, which appeared...b
but off the bottom of my screen…a
a little Javascript autoscroll to that section would be helpful after the calculation has finished.
Typos/grammar
In general: it’s ChIP-chip, not ChIP-ChIP (the first ChIP is for Chromatin Immuno-Precipitation, the second “chip” refers to microarray)
Be consistent: either ChIP-seq or ChIP-Seq (we see ChIP-seq, ChIP-Seq, and ChIP Seq in the paper)
Candidate target gene finding section: “the corresponding genomic sequences were extracted and trimmed” (“sequences” should be plural as multiple genomic sequences are analyzed, no?)
Candidate target gene finding section: 
“Otherwise, motif width was set to be between 5 to 30 bp” (“…to 5 to 30” is awkward)
Bottom of page 3: 
(“along with a link to TAIR10”) – TAIR10 refers to the 10th genome build. 
I’d say rather “along with a link to TAIR”. 
It might be nice to add a link to the Araport record for a given gene too.
Top of page 4: 
“…motifs in at least one peak located close to…” (missing “in”?)
Midway down page 4: “…the results are complete.” (instead of “get ready”)
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