Protocol for generation of a time-resolved cellular interactome during tissue remodeling in adult mice

Groppa, 2023, Spatial compartmentalization of signaling imparts source-specific functions on secreted factors, Cell Rep., 42, 112051, 10.1016/j.celrep.2023.112051

Lemos, 2015, Nilotinib reduces muscle fibrosis in chronic muscle injury by promoting TNF-mediated apoptosis of fibro/adipogenic progenitors, Nat. Med., 21, 786, 10.1038/nm.3869

R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

Risso, 2014, Normalization of RNA-seq data using factor analysis of control genes or samples, Nat. Biotechnol., 32, 896, 10.1038/nbt.2931

Robinson, 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139, 10.1093/bioinformatics/btp616

Csardi G, Nepusz T (2006). “The igraph software package for complex network research.” InterJournal, Complex Systems, 1695. https://igraph.org.

Wu, 2021, clusterProfiler 4.0: A universal enrichment tool for interpreting omics data, The Innovation, 2, 100141, 10.1016/j.xinn.2021.100141

Martini, 2014, timeClip: pathway analysis for time course data without replicates, BMC Bioinf., 15, S3, 10.1186/1471-2105-15-S5-S3

Joe, 2010, Muscle injury activates resident fibro/adipogenic progenitors that facilitate myogenesis, Nat. Cell Biol., 12, 153, 10.1038/ncb2015

Crisan, 2008, A Perivascular Origin for Mesenchymal Stem Cells in Multiple Human Organs, Cell Stem Cell, 3, 301, 10.1016/j.stem.2008.07.003

Rezza, 2016, Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles, Cell Rep., 14, 3001, 10.1016/j.celrep.2016.02.078

Yu, 2012, clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters, OMICS A J. Integr. Biol., 16, 284, 10.1089/omi.2011.0118

Sales, 2012, graphite - a Bioconductor package to convert pathway topology to gene network, BMC Bioinf., 13, 20, 10.1186/1471-2105-13-20

Sales, 2019, meta Graphite–a new layer of pathway annotation to get metabolite networks, Bioinformatics, 35, 1258, 10.1093/bioinformatics/bty719

Dmitrijeva, 2018, Tissue-specific DNA methylation loss during ageing and carcinogenesis is linked to chromosome structure, replication timing and cell division rates, Nucleic Acids Res., 46, 7022, 10.1093/nar/gky498

Charrad, 2014, Nbclust: An R package for determining the relevant number of clusters in a data set, J. Stat. Softw., 61, 1

Brock, 2008, ClValid: An R package for cluster validation, J. Stat. Softw., 25, 1

Alvarez, 2016, Functional characterization of somatic mutations in cancer using network-based inference of protein activity, Nat. Genet., 48, 838, 10.1038/ng.3593

Kinsella, 2011, Ensembl BioMarts: A Hub for Data Retrieval across Taxonomic Space, Database, 2011, 10.1093/database/bar030