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

Journal: BMC Medical Genomics

Article Title: Comparative transcriptome analysis of Parkinson’s disease and Hutchinson-Gilford progeria syndrome reveals shared susceptible cellular network processes

doi: 10.1186/s12920-020-00761-6

Figure Lengend Snippet: Shared significantly altered gene sets between PD, HGPS, AD and PM, determined using GeneGO MetaCore TM enrichment analysis (adjusted p -value ≤0.05): a ) shared canonical pathways; b ) shared GO biological processes. *: significant overlap by Fisher’s exact test ( p -value ≤0.05)

Article Snippet: Alterations in the activity of pathways and biological processes were investigated using the software tool GeneGO MetaCore TM ( https://portal.genego.com/ ).

Techniques:

Journal: BMC Medical Genomics

Article Title: Comparative transcriptome analysis of Parkinson’s disease and Hutchinson-Gilford progeria syndrome reveals shared susceptible cellular network processes

doi: 10.1186/s12920-020-00761-6

Figure Lengend Snippet: a Overlap of significantly altered subnetworks between PD, HGPS, AD and PM, determined using GeneGO MetaCore TM network analysis. b Shared GO biological processes among the subnetworks for PD, HGPS, AD and PM. *: significant overlap by Fisher’s exact test ( p -value ≤0.05)

Article Snippet: Alterations in the activity of pathways and biological processes were investigated using the software tool GeneGO MetaCore TM ( https://portal.genego.com/ ).

Techniques:

Journal: Protein & Cell

Article Title: Extracellular signal regulated kinase 5 promotes cell migration, invasion and lung metastasis in a FAK-dependent manner

doi: 10.1007/s13238-020-00701-1

Figure Lengend Snippet: ERK5 regulates the polymerization of F-actin . (A) Ontological categories of differentially expressed proteins in ERK5-overexpression A549 cells by Metacore TM GeneGo Pathway Maps analysis. (B) Protein networks associated with the actin regulators differentially expressed in ERK5-overexpression A549 cells (higher definition image is shown in Supplementary file 2: Fig. S4). The network was generated by a shortest paths algorithm of MetaCore TM (GeneGo) software using the list of differentially expressed actin regulators identified by proteomics analysis. (C) Western blot analysis of actin nucleation and polymerization correlated proteins in ERK5-overexpression A549 cells, including ERK5, Gelsolin, N-WASP, p-PLK1and SPA1. (D) The cell shapes of A549 cells overexpressing ERK5 under light microscope. (E) ERK5 regulated the assembly of F-actin. Immunofluorescence was carried out to display F-actin (phalloidin, red), and nuclei (Hochest, blue) in ERK5-overexpression A549 cells and control A549 cells. (F) After serum starvation overnight, the cells were stimulated again with 20% fetal calf serum for 2 h. Then immunofluorescence assay was performed as that described in (E)

Article Snippet: The network was generated by a shortest paths algorithm of MetaCore TM (GeneGo) software using the list of differentially expressed actin regulators identified by proteomics analysis. (C) Western blot analysis of actin nucleation and polymerization correlated proteins in ERK5-overexpression A549 cells, including ERK5, Gelsolin, N-WASP, p-PLK1and SPA1. (D) The cell shapes of A549 cells overexpressing ERK5 under light microscope. (E) ERK5 regulated the assembly of F-actin.

Techniques: Over Expression, Generated, Software, Western Blot, Light Microscopy, Immunofluorescence, Control