Profiling of Sox4-dependent transcriptome in skin links tumour suppression and adult stem cell activation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26697322", "kind": "science-record", "revision": 8, "content_hash": "sha256:7d183abeff05bf1848f63d176a019f66bd7332862cf6275c2b2a801bdf803fdf", "created_at": "2026-11-01T15:40:14Z", "updated_at": "2026-11-01T22:42:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Profiling of Sox4-dependent transcriptome in skin links tumour suppression and adult stem cell activation.", "doi": "10.1016/j.gdata.2015.07.030", "pmid": "26697322", "authors": ["Miguel Foronda", "Lucia Morgado-Palacin", "Gonzalo Gómez-López", "Orlando Domínguez", "David G Pisano", "Maria A Blasco"], "journal": "Genomics data", "year": 2015, "abstract": "Adult stem cells (ASCs) reside in specific niches in a quiescent state in adult mammals. Upon specific cues they become activated and respond by self-renewing and differentiating into newly generated specialised cells that ensure appropriate tissue fitness. ASC quiescence also serves as a tumour suppression mechanism by hampering cellular transformation and expansion (White AC et al., 2014). Some genes restricted to early embryonic development and adult stem cell niches are often potent modulators of stem cell quiescence, and derailed expression of these is commonly associated to cancer (Vervoort SJ et al., 2013). Among them, it has been shown that recommissioned Sox4 expression facilitates proliferation, survival and migration of malignant cells. By generating a conditional Knockout mouse model in stratified epithelia (Sox4 (cKO) mice), we demonstrated a delayed plucking-induced Anagen in the absence of Sox4. Skin global transcriptome analysis revealed a prominent defect in the induction of transcriptional networks that control hair follicle stem cell (HFSC) activation such as those regulated by Wnt/Ctnnb1, Shh, Myc or Sox9, cell cycle and DNA damage response-associated pathways. Besides, Sox4 (cKO) mice are resistant to skin carcinogenesis, thus linking Sox4 to both normal and pathological HFSC activation (Foronda M et al., 2014). Here we provide additional details on the analysis of Sox4-regulated transcriptome in Telogen and Anagen skin. The raw and processed microarray data is deposited in GEO under GSE58155.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes were obtained by applying linear models with R limma package [10] (Bioconductor project, http://www.bioconductor.org).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697322", "locator": "sections[6] \"Gene expression analysis\" paragraph 2", "quote": "Differentially expressed genes were obtained by applying linear models with R limma package [10] (Bioconductor project, http://www.bioconductor.org)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw and processed microarray data is deposited in GEO under GSE58155.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697322", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The raw and processed microarray data is deposited in GEO under GSE58155."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Skin global transcriptome analysis revealed a prominent defect in the induction of transcriptional networks that control hair follicle stem cell (HFSC) activation in Sox4cKO mice; differential expression was assessed with linear models using R limma and Benjamini–Hochberg false discovery rate correction, while the raw and processed microarray data are available through GEO accession GSE58155 at \"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58155\".", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26697322", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Skin global transcriptome analysis revealed a prominent defect in the induction of transcriptional networks that control hair follicle stem cell (HFSC) activation such as those regulated by Wnt/Ctnnb1, Shh, Myc or Sox9, cell cycle and DNA damage response-associated pathways."}, {"asset": "source:pmid:26697322", "locator": "sections[6] \"Gene expression analysis\" paragraph 2", "quote": "Differentially expressed genes were obtained by applying linear models with R limma package [10] (Bioconductor project, http://www.bioconductor.org). To account for multiple hypothesis testing, the estimated significance level (p value) was adjusted using Benjamini & Hochberg false discovery rate (FDR) correction [11]. Those genes with FDR < 0.05 were selected as differentially expressed genes (DEGs)."}, {"asset": "source:pmid:26697322", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The raw and processed microarray data is deposited in GEO under GSE58155."}, {"asset": "source:pmid:26697322", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "The deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58155."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Skin global transcriptome analysis revealed a prominent defect in the induction of transcriptional networks that control hair follicle stem cell (HFSC) activation in Sox4cKO mice; differential expression was assessed with linear models using R limma and Benjamini–Hochberg false discovery rate correction, while the raw and processed microarray data are available through GEO accession GSE58155 at \"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58155\".", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26697322"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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