Team:TrinityCollegeDublin/d3

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about

split view

TF regulatory
interactions

regulators of regulated by both selected genes only

cell type groups

paraxial mesoderm

primitive mesoderm

lymphoid

myeloid

endothelia

ectoderm

endoderm

primitive

welcome

The Transcription Factor Regulatory Networks browser facilitates the comparison and exploration of transcription factor interactions between a variety of cell types. You may select interaction types, genes and cell types, as well as export network graphs to text and SVG for downstream analysis and editing in Inkscape or Adobe Illustrator.

how to use

Pick one of four interaction types from the TF regulatory interactions section at the top of the screen:

regulators of - show factors of interest, along with those they regulate
regulated by - show factors, along with those which regulate them
both - show both of the aforementioned interaction types
selected genes - only show interactions between factors of interest (fastest)

Use the cell types button to select from one of 41 human cell types. Use the genes button to pick genes of interest associated with the selected cell type. Click on the graph button to render interactions for the selected genes.

usage tips

Move your mouse pointer over a gene-of-interest to highlight it and those genes it regulates.
Click and drag the graph to move it. You can also roll your mouse scrollwheel or trackpad up and down to zoom in and out of a graph (this is useful for more complex networks).
Click once on a node to bring up a gene detail panel. You can remove the gene from this panel, or add genes when exploring related genes through the panel browser.
To remove a gene-of-interest, double-click on the node. If it is a not gene-of-interest (i.e. "common" or "other") then double-clicking will add this as a gene-of-interest!
To export a text or SVG representation of the graph data, use the text or svg button.

about

We use genome-wide maps of in vivo DNaseI footprints to map an extensive core regulatory network comprising connections among hundreds of sequence-specific transcription factors, enabling exploration of unique characteristics that determine cellular identity and function. The networks displayed at this site will be updated as additional motif models and DNaseI footprinting maps become available. To access the networks presented at publication, please follow the link below:

Complete human networks (v09162013) (README)
Complete mouse networks (v12032013) (README)

citations

Shane Neph, Andrew B. Stergachis, Alex Reynolds, Richard Sandstrom, Elhanan Borenstein, and John A. Stamatoyannopoulos (2012). Circuitry and dynamics of human transcription factor regulatory networks. Cell doi:10.1016/j.cell.2012.04.040.
Andrew B. Stergachis, Shane Neph, Richard Sandstrom, Eric Haugen, Alex P. Reynolds, et al. (2014). Conservation of trans-acting circuitry during mammalian regulatory evolution. Nature doi:10.1038/nature13972.

credits

Site programming by Alex Reynolds
Network data generated by Shane Neph and Andrew Stergachis
Graph visualization uses the d3.js framework by Mike Bostock

questions and comments

Have questions about the site or want to leave bug reports or other feedback? Please contact us at: .

session

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