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readme.md

readme.md

Contained are the code and data needed to re-create the analyses and figures in:

Des Marais et al. (in press)

If you use any of the code, figures, analyses, or novel ideas, please cite the article below-- there's a preprint as well if you get stuck outside a paywall. If you use any of the data, please cite the appropriate manuscript(s).

Citation

Des Marais DL, Guerrero RF, Lasky JR, Scarpino SV. in press. Topological features of a gene co-expression network predict patterns of natural diversity in environmental response. Proceedings of the Royal Society B.

Preprint

Des Marais, D. L., Guerrero, R., Lasky, J. R., & Scarpino, S. V. (2016). Topological features of gene regulatory networks predict patterns of natural diversity in environmental response. bioRxiv, 080804.

Data

Cubillos ASE Cubillos, F. A., Stegle, O., Grondin, C., Canut, M., Tisné, S., Gy, I., & Loudet, O. (2014). Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis. The Plant Cell, 26(11), 4298-4310.

DaveAllGxTDrought Des Marais, D. L., McKay, J. K., Richards, J. H., Sen, S., Wayne, T., & Juenger, T. E. (2012). Physiological genomics of response to soil drying in diverse Arabidopsis accessions. The Plant Cell, 24(3), 893-914.

DaveAllTDrought Des Marais, D. L., McKay, J. K., Richards, J. H., Sen, S., Wayne, T., & Juenger, T. E. (2012). Physiological genomics of response to soil drying in diverse Arabidopsis accessions. The Plant Cell, 24(3), 893-914.

FDR0.1 Des Marais, D. L., McKay, J. K., Richards, J. H., Sen, S., Wayne, T., & Juenger, T. E. (2012). Physiological genomics of response to soil drying in diverse Arabidopsis accessions. The Plant Cell, 24(3), 893-914.

G&E Des Marais, D. L., McKay, J. K., Richards, J. H., Sen, S., Wayne, T., & Juenger, T. E. (2012). Physiological genomics of response to soil drying in diverse Arabidopsis accessions. The Plant Cell, 24(3), 893-914.

Splitting Drought Des Marais, D. L., McKay, J. K., Richards, J. H., Sen, S., Wayne, T., & Juenger, T. E. (2012). Physiological genomics of response to soil drying in diverse Arabidopsis accessions. The Plant Cell, 24(3), 893-914.

Expression Level Yang, L., & Gaut, B. S. (2011). Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Molecular biology and evolution, 28(8), 2359-2369.

Feltus_etal_AdditionalFile3_EdgeLists Feltus, F. A., Ficklin, S. P., Gibson, S. M., & Smith, M. C. (2013). Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study. BMC systems biology, 7(1), 44.

gene_expression_net_feltus_main Feltus, F. A., Ficklin, S. P., Gibson, S. M., & Smith, M. C. (2013). Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study. BMC systems biology, 7(1), 44.

HannahAllGxTCold Hannah, M. A., Wiese, D., Freund, S., Fiehn, O., Heyer, A. G., & Hincha, D. K. (2006). Natural genetic variation of freezing tolerance in Arabidopsis. Plant physiology, 142(1), 98-112.

HannahAllTCold Hannah, M. A., Wiese, D., Freund, S., Fiehn, O., Heyer, A. G., & Hincha, D. K. (2006). Natural genetic variation of freezing tolerance in Arabidopsis. Plant physiology, 142(1), 98-112.

TPC2015_00910 Bechtold, U., Penfold, C. A., Jenkins, D. J., Legaie, R., Moore, J. D., Lawson, T., ... & Hickman, R. (2016). Time-series transcriptomics reveals that AGAMOUS-LIKE22 links primary metabolism to developmental processes in drought-stressed Arabidopsis. The Plant Cell, TPC2015-00910.

comm_props_raw_21Jan16 Des Marais DL, Guerrero RF, Lasky JR, Scarpino SV. in press. Topological features of a gene co-expression network predict patterns of natural diversity in environmental response. Proceedings of the Royal Society B.

Legal

The data aren't all ours, but we did write a lot of the code. Obviously everything, e.g., code, data, etc., are provided without any guarantee about accuracy, quality, or the impact factor of the journal you can publish them in. Please cite the appropriate paper for each data set and the appropriate paper for any internal code (e.g., if you use any R libraries).

License

GPL (>= 3.0), where applicable.