Arabidopsis has undergone massive expansion of TF families, and many members of the same family are capable of binding to the same motifs (conserved cis-regulatory boxes). This makes it difficult to identify which TF influences which downstream genes.
This website allows you to look through and download data related to how bHLHs and bZIPs (which are expressed in seedlings) regulate genes downstream of perfect G-boxes (CACGTG).
Please e-mail daphne.ezer@slcu.cam.ac.uk for any assistance and please cite https://doi.org/10.1101/128371 when using this website.Observe patterns in the complete network:
Search for a particular gene in the network:
Search for a set of genes to find i) which subset of genes are in the network ii) what time of day these genes are expressed iii) which genes are frequently upstream (TFs) or downstream (genes near G-boxes) of the genes in this set:
Important Note 1: By TAIR ID, we mean a gene in this format: ATxGxxxxx. For instance, PIF4 would be labelled as AT2G43010, PIF3 would be AT1G09530, and PYE (the example shown in the manuscript) would be AT3G47640. It is fine to use lower-case or upper-case, and to include trailing spaces. If you still can't get it to work, it may be because you are copying a hidden character and it would be better to use a different text editor or type in the gene names straight into the box.
Important Note 2: Some of the users of the website have suggested expanding the distance we search for G-boxes from the TSS to 1000bp (up from 500bp) or to include non-perfect G-boxes (such as CAGGTG, etc.). By incorporating these criteria, the number of genes in the network expands to more than 14,000 genes, but we expect to end up with a much larger proportion of false-positive edges. In addition, due to the size of the network, we estimate it using only Genie3 instead of using an ensemble machine learning approach used in the manuscript, which will also reduces this network's accuracy. Note that it can take several minutes to compute statistics, and shorter gene descriptions are used than in the previous Ara-BOX-cis network.