All queries in By_Samples can be run by replacing "SAMPLE" in the files by the actual name of the sample.
Queries in By_Tissues can be run by replacing "TISSUE" by the name of the tissue, following formatting, and SAMPLE1 to SAMPLE15 by the names of the samples constituting the Tissue network. The number in the name of the query refer to the number of samples needed.
Change for tissues names:
| Original name | in graph name |
|---|---|
| " - " | "-" |
| " " | "_" |
| ", " | "-" |
| " (" | "-" |
| ") " | "-" |
| ")" | "" |
| "'" | "" |
| "." | "-" |
| "+" | "pos" |
A Virtuoso endpoint is available at https://regulatorycircuits-lod.genouest.org/sparql/ to run the queries.
Louarn, M., Chatonnet, F., Garnier, X., Fest, T., Siegel, A., Dameron, O.
Original data used are extracted from the paper: Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases. Marbach D, Lamparter D, Quon G, Kellis M, Kutalik Z, and Bergmann S. Nature Methods, 13, 366-370, 2016 (http://www.regulatorycircuits.org/) as of October 2021 the website is down but can accessed through Web archive the data can still be retrieve using: Supplementary_data.zip and FANTOM5_individual_networks.tar