Authors: Jianhai Zhang, Jordan Hayes, Le Zhang, Bing Yang, Wolf B. Frommer, Julia Bailey-Serres, and Thomas Girke
Data source
brain_Prudencio: RNA-seq, Prudencio et al. 2015, accessed through the R package ExpressionAtlas (Keays 2019).
mouse_Merkin: RNA-seq, Merkin et al. 2012, accessed through the R package ExpressionAtlas (Keays 2019).
chicken_Cardoso.Moreira: RNA-seq, Cardoso-Moreira et al. 2019, accessed through the R package ExpressionAtlas (Keays 2019).
shoot_Mustroph/organ_Mustroph/root_Mustroph/shootRoot_Mustroph/rootRootTip_Mustroph: microarray, Mustroph et al. 2009, accessed through the R package GEOquery (S. Davis and Meltzer 2007).
multiDimensions_Attilio: Attilio et al. 2021, downloaded from GEO with access number GSE163415.
growthStage_Mustroph: random data.
Image source
brain_Prudencio/mouse_Merkin/chicken_Cardoso.Moreira: Expression Atlas-EMBL-EBI, https://github.com/ebi-gene-expression-group/anatomogram/tree/master/src/svg
shoot_Mustroph/organ_Mustroph/root_Mustroph/shootRoot_Mustroph/rootRootTip_Mustroph/growthStage_Mustroph: Mustroph et al. 2009.
multiDimensions_Attilio: Attilio et al. 2021
The network modules are identified using WGCNA (Langfelder and Horvath 2008), flashClust (Langfelder and Horvath 2012), dynamicTreeCut package (Langfelder, Zhang, and Steve Horvath 2016).
Fund source: this project has been funded by NSF awards: PGRP-1546879, PGRP-1810468, PGRP-1936492.
Reference
Keays, Maria. 2019. ExpressionAtlas: Download Datasets from EMBL-EBI Expression Atlas.
Prudencio, Mercedes, Veronique V Belzil, Ranjan Batra, Christian A Ross, Tania F Gendron, Luc J Pregent, Melissa E Murray, et al. 2015. “Distinct Brain Transcriptome Profiles in C9orf72-Associated and Sporadic ALS.” Nat. Neurosci. 18 (8): 1175–82
Merkin, Jason, Caitlin Russell, Ping Chen, and Christopher B Burge. 2012. “Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues.” Science 338 (6114): 1593–9
Cardoso-Moreira, Margarida, Jean Halbert, Delphine Valloton, Britta Velten, Chunyan Chen, Yi Shao, Angélica Liechti, et al. 2019. “Gene Expression Across Mammalian Organ Development.” Nature 571 (7766): 505–9
Davis, Sean, and Paul Meltzer. 2007. “GEOquery: A Bridge Between the Gene Expression Omnibus (GEO) and BioConductor.” Bioinformatics 14: 1846–7
Mustroph, Angelika, M Eugenia Zanetti, Charles J H Jang, Hans E Holtan, Peter P Repetti, David W Galbraith, Thomas Girke, and Julia Bailey-Serres. 2009. “Profiling Translatomes of Discrete Cell Populations Resolves Altered Cellular Priorities During Hypoxia in Arabidopsis.” Proc Natl Acad Sci U S A 106 (44): 18843–8 Attilio, Peter J, Dustin M Snapper, Milan Rusnak, Akira Isaac, Anthony R Soltis, Matthew D Wilkerson, Clifton L Dalgard, and Aviva J Symes. 2021. “Transcriptomic Analysis of Mouse Brain After Traumatic Brain Injury Reveals That the Angiotensin Receptor Blocker Candesartan Acts Through Novel Pathways.” Front. Neurosci. 15 (March): 636259 Langfelder, Peter, and Steve Horvath. 2008. “WGCNA: An R Package for Weighted Correlation Network Analysis.” BMC Bioinformatics 9 (December): 559
Peter Langfelder, Steve Horvath (2012). “Fast R Functions for Robust Correlations and Hierarchical Clustering.” Journal of Statistical Software 46 (11): 1–17. http://www.jstatsoft.org/v46/i11/
Langfelder, Peter, Bin Zhang, and with contributions from Steve Horvath. 2016. DynamicTreeCut: Methods for Detection of Clusters in Hierarchical Clustering Dendrograms. https://CRAN.R-project.org/package=dynamicTreeCut