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Fig. 7 | Journal of Experimental & Clinical Cancer Research

Fig. 7

From: SMAD9-MYCN positive feedback loop represents a unique dependency for MYCN-amplified neuroblastoma

Fig. 7

Transcriptome changes in response to SMAD9 knockdown. A Volcano plots showing the DEGs in BE(2)-C and IMR-32 cells after SMAD9 knockdown. The cutoff setting was |log2FC| > 0.4, P < 0.05. B Functional enrichment map depicting the functional groups of the GSEA hits for the SMAD9-high effects on BE(2)-C and IMR-32 cells based on shSMAD9 RNA-seq results. C Venn diagram showing the 784 overlapping downregulated genes between BE(2)-C and IMR-32 cells. D Top 5 gene sets functionally enriched in GO-BP terms. E The “Degree” approach using Cytoscape software (CytoHubba plugin) to show the top 10 hub genes in the overlapping 784 downregulated genes. F, G Q-RT-PCR validation of some hub genes in NB cells (F) and NB tissue samples (G) from SCH that were classified by the median expression of SMAD9. H Summary diagram describing the positive feedback loop between SMAD9 and MYCN and the MYCN-induced cancer cell cycle in MYCN-amplified NB cells. DEGs: differentially expressed genes; GO-BP: Gene Ontology, biological process; GSEA: gene set enrichment analysis; NB: neuroblastoma; Q-RT-PCR: quantitative reverse transcription polymerase chain reaction; SCH: Shanghai Children’s Hospital. *P < 0.05, **P < 0.01, and *** P < 0.001

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