Human Gene Set: RIEGE_DELTANP63_DIRECT_TARGETS_UP


Standard name RIEGE_DELTANP63_DIRECT_TARGETS_UP
Systematic name M41739
Brief description Genes directly up-regulated by DeltaNp63, the p63 isoform that lacks the canonical transactivation domain and is predominantly expressed in stratifying epithelia, identified through a meta-analysis of both cell lines and primary cells.
Full description or abstract To identify genes commonly regulated by DeltaNp63 across cell types and tissues, we employed a previously established meta-analysis approach. From 11 genome-wide studies, 16 publicly available gene expression datasets were integrated to generate a specific p63 Expression Score (the number of datasets that identify a gene as significantly up-regulated minus the number of datasets that identify the genes as significantly down-regulated). The gene expression profiling datasets have been obtained from knockdown (n = 12) or overexpression experiments (n = 4) of p63 in primary keratinocytes (n = 3), the keratinocyte cell line HaCaT (n = 2), the foreskin fibroblast cell line BJ (n = 1), the breast epithelial cell line MCF10A (n = 4), the squamous carcinoma cell lines H226 (n = 2), KYSE70 (n = 1), and FaDu (n = 1), as well as the pancreatic ductal adenocarcinoma cell lines BxPC3 (n = 1) and SUIT2 (n = 1) In addition, we integrated 20 p63 ChIP-seq datasets. Given the large number of p63-binding sites identified and the high variance in p63-dependent gene regulation, we employed conservative thresholds to identify high-probability target genes of DeltaNp63. We only used p63-binding sites supported by at least half of the datasets (>=10) that are linked through TSS proximity (within 5 kb) or double-elite enhancer:gene associations to genes with a p63 Expression Score >= 8.
Collection C2: Curated
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 33263276   Authors: Riege K,Kretzmer H,Sahm A,McDade SS,Hoffmann S,Fischer M
Exact source Table 1 (positive p63 Expression Score)
Related gene sets (show 5 gene sets from the same authors)
External links https://doi.org/10.7554/elife.63266
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Source species Homo sapiens
Contributed by Martin Fischer (Leibniz Institute on Aging, Fritz Lipmann Institute (FLI))
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identifier namespace		 HUMAN_GENE_SYMBOL
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Version history 7.3: First Introduced.

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