Experiment level curation identifies high confidence transcriptional regulatory interactions in neurodevelopment Chu, Eric Ching-Pan
The capacity to computationally reconstruct gene regulatory networks using large-scale biological data is currently limited by the absence of a high confidence set of one-to-one regulatory interactions. Given the lengthy history of using small scale experimental assays to investigate individual interactions, we hypothesize that a reliable collection of gene regulatory interactions could be compiled by systematically inspecting the published literature. To this end, we developed a curation protocol to examine and record evidence of regulatory interactions at the individual experiment level. Focusing on the area of brain development, we applied our pipeline to 1,310 publications. We identified 3,601 individual experiments, providing detailed information about 1,499 regulatory interactions. Many of these interactions have verified activity specifically in the embryonic brain. By capturing reports of regulatory interactions at this level of granularity, we present a resource that is more interpretable than other similar resources.
List of Tables in TSV format:Supplementary Table S1. List of candidate papers Supplementary Table S2. List of TFs Supplementary Table S3. Curated records at the experiment level Supplementary Table S4. Curated records summarized at the DTRI level Supplementary Table S5. TF Perturbation experiment details Supplementary Table S6. TF-DNA Binding experiment details Supplementary Table S7. TF-reporter experiment details Supplementary Table S8. All DTRI records including those curated in external databases Supplementary Table S9. Records obtained from external databases Supplementary Table S10. List of differentially expressed genes following Pax6 perturbation Supplementary Table S11. Experiments with negative results