Journal: bioRxiv

Article Title: Dystrophin Dp71 is essential for the development and function of macrophages

doi: 10.1101/2025.04.24.650386

Figure Lengend Snippet: Proteomics analysis of BMM. (A) Rank plot displaying protein expression differences between DMD and control mice. Black dots represent significantly expressed proteins, while grey dots represent not-significantly expressed proteins. (B) Volcano plot depicting MS results, with proteins coloured in red having a Log2 DMD/Control ratio of > 1.5 and -log10(P) of >10, and proteins coloured in blue having a Log2 DMD/Control ratio of < −1.5 and -log10(P) of >10. (C) Principal component analysis using the reporter ion log 2 ratios of all analysed proteins showing mdx βgeo BMM having a distinct proteomic profile and higher heterogeneity compared to C57BL/6 BMMs. (D) MetaCore process network analysis showing that process networks related to cell adhesion, phagocytosis, cell cycle and cytoskeleton were over-represented in mdx βgeo BMM.

Article Snippet: Protein ratios were transformed to log 2 -ratios and significant changes were determined by the permutation test followed by LIMMA for bioinformatics analysis with MetaCore software (GeneGo).

Techniques: Expressing, Control

Journal: Cells

Article Title: Adiponectin Influences the Behavior of Stem Cells in Hormone-Resistant Breast Cancer

doi: 10.3390/cells14040286

Figure Lengend Snippet: MetaCore TM analysis of protein interactions. Protein–protein interaction network for DEPs in TR MCF-7 cells obtained from adiponectin-treated secondary-generation mammospheres compared to untreated cells (control, C). ( A ) MetaCore TM analysis of the network showing the Adiponectin Receptor 1 (AdipoR1)-Notch-Cyclin D1 ( p -value > 1.733 × 10 −8 ) interaction. Blue circles indicate downregulated proteins, while red circles mark upregulated proteins. ( B ) Enrichment analysis using the most significant GO annotations according to biological processes. The bar graph displays the significant biological processes of the hub proteins present in the network.

Article Snippet: For network and enrichment analysis, we used MetaCore TM (GeneGo, Clarivate Analytics, London, UK) software, a knowledge database suitable for pathway analysis of experimental data and gene lists.

Techniques: Control

Journal: Cells

Article Title: Adiponectin Influences the Behavior of Stem Cells in Hormone-Resistant Breast Cancer

doi: 10.3390/cells14040286

Figure Lengend Snippet: MetaCore TM interaction network analysis. Protein–protein interaction network for DEPs in TR MCF-7 cells obtained from adiponectin-treated secondary-generation mammospheres compared to untreated cells (control, C). ( A ) MetaCore TM analysis of the network evidencing the BID-Notch-AdipoR1 interaction ( p -value > 1.80 × 10 −8 ). Blue circles indicate downregulated proteins, while red circles mark upregulated proteins. ( B ) Enrichment analysis using the most significant GO annotations according to biological processes. The bar graph shows the significant biological processes of the hub proteins present in the network.

Article Snippet: For network and enrichment analysis, we used MetaCore TM (GeneGo, Clarivate Analytics, London, UK) software, a knowledge database suitable for pathway analysis of experimental data and gene lists.

Techniques: Control