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Integrative analysis of mRNA-miRNA-TFs reveals the key regulatory connections involved in basal cell carcinoma


Basal cell carcinoma (BCC) is one of the most common skin cancers worldwide and contributes substantially to global morbidity, but its tumorigenesis and pathogenesis remain largely unknown. To investigate the crosstalk between microRNAs (miRNAs), mRNAs and transcription factors (TFs) and the regulatory processes underlying BCC, we have constructed an integrative miRNA-mRNA-TFs network based on RNA-sequencing datasets. In this study, two RNA-sequencing datasets and matched miRNA expression datasets of selected differentially-expressed genes (DEGs) were used to infer potential miRNA regulatory and TFs activities in BCC. A total of 1247 DEGs were identified by combining two BCC RNA-sequencing profiles. Furthermore, by integrating network interaction construction, we found 37 important dysregulated genes (ING3, VEGFA, TP63, MMP11, NRP1, HIF1A, APC, PTCH1, etc.) that are significantly associated with BCC, as well as a few novel potential miRNAs (miR-203, miR-29b, miR-141, miR-7b, miR-9, miR-200a, miR-7c and miR-132) and TFs (MYB, MYC, STAT3, ARNT, PAX5, CUX1, E2F1 and CEBPA). These identified potential genes and miRNA/TFs candidates may play direct/indirect roles in the molecular pathogenesis of BCC.

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Basal cell carcinoma


Gene expression omnibus


Principal component analysis


DisGeNET v5.0


Network of Cancer Genes 5.0


Gene Ontology


Kyoto Encyclopedia of Genes and Genomes


Inhibitor of growth protein 3


Protein patched homolog 1.




Transformation-related protein 63


Matrix metalloproteinase-11


Hypoxia-inducible factor 1-alpha


Adenomatous polyposis coli


Vascular endothelial growth factor A


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This study was funded by CW from National Natural Science Foundation of China (81860484).

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Correspondence to Chuan Wan.

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Wan, C., Li, Y. Integrative analysis of mRNA-miRNA-TFs reveals the key regulatory connections involved in basal cell carcinoma. Arch Dermatol Res 312, 133–143 (2020).

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  • Basal cell carcinoma
  • microRNA expression
  • mRNA expression
  • Tumorigenesis
  • Transcription factors
  • Gene expression omnibus