The circadian clock and light signalling play central roles in plant physiology and development. As a consequence, massive amounts of omics data have been generated to characterize their individual components. Nonetheless, these data remain fragmented and researchers who want to explore the synergistic regulation exerted by the circadian clock and light signalling need to consult different papers and resources making imperative the use of molecular systems biology techniques to integrate and make easily accesible all the generated information.

ATTRACTOR, is a web based tool for the analysis of the synergistic transcriptional control exerted by the circadian clock and light signalling over genes exhibiting rhythmic expression profiles in the model plant Arabidopsis thaliana. ATTRACTOR, consists of a transcriptional network that integrates transcriptomic data collected over diurnal cycles with 12 hours of light and 12 hours of darkness with cistromic data generated using ChIP-seq for key transcriptional factors and regulators in the circadian clock and light signalling. Specifically, our network is composed of 5778 nodes or genes with diurnal rhythmic expression profiles and 14529 edges or transcriptional regulations. The transcription factors and regulators included in our network comprise the components of the morning and central loops CCA1, LHY, the pseudo response regulator family members TOC1,PRR5, PRR7 and PRR9; as well as some components of the evening loop such as LUX, ELF3 and ELF4. In order to capture synergistic regulations with light signalling we added the light sensors and transcriptional regulators phytochromes PHYA and PHYB, the cryptochrome CRY2 as well as the light transcriptional factors from the phytochrome interacting factor family PIF5, PIF4 and PIF3. Finally, the phytochrome interacting transcriptional factor FHY1 (Far-red elongated Hypocotyl 1) is also included in our network.

Use the navigation bar on the left to explore the different utilities in ATTRACTOR or alternatively view our video tutorial.

ATTRACTOR, is entirely developed using the R package shiny. The source code is released under GNU General Public License v3.0 and is hosted at GitHub. If you experience any problem using ATTRACTOR please create an issue in GitHub and we will address it.

ATTRACTOR at GitHub

We are strongly committed to open access software and open science. Following our philosophy we have deposited our GitHub code into Zenodo , a general-purpose open-access repository developed under the European OpenAIRE program. Meanwhile we publish our work in a journal if you find ATTRACTOR useful in your research we would be most grateful if you cite our GitHub repository with a, DOI as follows:

ATTRACTOR allows researchers to explore the coordinated regulation of several transcription factors or regulators over an individually selected gene as well as the effect observed in its expression profile. Follow the steps below:

1. Select a specific gene from our network using the Target Gene dropdown menu on the left below. You can enter either the AGI identifier or primary symbol for the gene of interest.
2. Select several transcription factors (TFs) to explore their regulation over the previously selected target gene using the Select Transcription Factors checkboxes on the left below.
3. Results will be depicted on the tabs below. The Clock Visualizer tab shows a circular representation of the diurnal cycle with the selected TFs and target gene located at the time point of their expression peak. Binding of TFs to the target gene and the observed effect over its expression are represented using colored arrows. The Expression Visualizer tab shows the target gene expression profile in a linear representation with the selected TFs located over the time point of their expression peak. The binding of the selected TFs to the target gene promoter and the observed effect is represented using colored arrows. The Peak Visualizer tab shows the selected target gene genomic location and the peaks detected in our analysis of the correspondig TFs ChIP-seq data. Here you can specify the length of the gene promoter and 3' region as well as DNA TFs binding motifs to search for in the detected peak regions with the specified score for identity.

ATTRACTOR allows researchers to explore the coordinated regulation of several transcription factors or regulators over their common targets. Follow the steps below:

1. Select your TFs of interest using the Select Transcription Factors checkbox menu on the left below.
2. You can also select a cluster of genes exhibiting a specific rhythmic pattern of expression by chosing the time point for their peak and trough using the dropdown menus Select a specific rhythmic gene expression pattern with peak at: ... and trough at:
3. Check the box Visualize Edges when you want to depict arrows from TFs to their target genes.
4. Click on the SELECT GENES to visualize your selected TFs common target genes exhibiting the specified rhythmic expression pattern in our transcriptional network. Explore the different tabs to download a table with the selected genes, perform a signficance analysis of the overlap between the selected TFs targets and the specified expression pattern as well as GO term, pathways and binding motifs enrichment analysis .