new content from pmc

figures/PMC11139846__12672_2024_1047_Fig9_HTML.yml

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+---
+pmcid: PMC11139846
+image_filename: 12672_2024_1047_Fig9_HTML.jpg
+figure_link: /pmc/articles/PMC11139846/figure/Fig9/
+number: Fig. 9
+figure_title: ''
+caption: PPI network and hub genes analysis. A A total of 268 co-expression genes
+  of eight ITGBs were uploaded onto the STRING database to get the PPI network of
+  eight ITGBs. The PPI network was visualized by the Cytoscape software. The color
+  and size of each gene represent the degree of the corresponding gene. The minimum
+  degree is 1 and the maximum degree is 67. Colored edges represent the co-expression
+  values between genes. Only edges with co-expression value > 0.5 were colored with
+  continuously deepened blue. B The top 15 hub genes were identified by degree parameter
+  in the Cytoscape software. C GO analysis of the top 15 hub genes. D KEGG analysis
+  of the top 15 hub genes
+article_title: Identification of the biological functions and chemo-therapeutic responses
+  of ITGB superfamily in ovarian cancer.
+citation: Jiawen Han, et al. Discov Oncol. 2024 Dec;15:198.
+
+doi: 10.1007/s12672-024-01047-4
+journal_title: Discover Oncology
+journal_nlm_ta: Discov Oncol
+publisher_name: Springer US
+
+keywords:
+- ITGB
+- Biological function
+- Ovarian cancer
+- Chemo-therapeutic
+- Responses
+- Prognostic prediction
+
+---

figures/PMC11233489__12672_2024_1123_Fig6_HTML.yml

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+---
+pmcid: PMC11233489
+image_filename: 12672_2024_1123_Fig6_HTML.jpg
+figure_link: /pmc/articles/PMC11233489/figure/Fig6/
+number: Fig. 6
+figure_title: ''
+caption: PPI network construction and the module analysis. A The figure represents
+  a Protein–Protein Interaction (PPI) network constructed using a molecular interaction
+  list obtained from the STRING database. The size of the circles indicates the number
+  of protein interactions; the larger the circle, the darker the color. B The key
+  gene sets were obtained through the MCODE plug-in of Cytoscape software. C The MCC
+  algorithm on cytoHubba plug-in of Cytoscape software was used to obtain the Top20
+  most closely related Hub gene collections
+article_title: Investigation of prognostic values of immune infiltration and LGMN
+  expression in the microenvironment of osteosarcoma.
+citation: Hualiang Xu, et al. Discov Oncol. 2024 Dec;15:275.
+
+doi: 10.1007/s12672-024-01123-9
+journal_title: Discover Oncology
+journal_nlm_ta: Discov Oncol
+publisher_name: Springer US
+
+keywords:
+- Osteosarcoma
+- LGMN
+- Immune infiltration
+- Bioinformatics
+- Prognosis
+- Therapeutic target
+- Consensus clustering analysis
+
+---

figures/PMC11266335__12672_2024_1167_Fig4_HTML.yml

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+---
+pmcid: PMC11266335
+image_filename: 12672_2024_1167_Fig4_HTML.jpg
+figure_link: /pmc/articles/PMC11266335/figure/Fig4/
+number: Fig. 4
+figure_title: ''
+caption: Identification of HUB genes by the STRING database. A PPI network of overlapping
+  DEGs. B The most significant 15 node degree genes calculated by the cytoHubba app
+  in Cytoscape. IGF1, CDKN2A, BIRC5, and SPP1 were selected as the HUB genes. The
+  node color intensities representing different genes correlate with the degree of
+  expression values
+article_title: Autophagy-related biomarkers in hepatocellular carcinoma and their
+  relationship with immune infiltration.
+citation: Tingting Li, et al. Discov Oncol. 2024 Dec;15:299.
+
+doi: 10.1007/s12672-024-01167-x
+journal_title: Discover Oncology
+journal_nlm_ta: Discov Oncol
+publisher_name: Springer US
+
+keywords:
+- Autophagy
+- Hepatocellular carcinoma
+- Information biology
+- Immune infiltration
+- Prognosis
+
+---

figures/PMC11335254__18_2024_5375_Fig2_HTML.yml

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+---
+pmcid: PMC11335254
+image_filename: 18_2024_5375_Fig2_HTML.jpg
+figure_link: /pmc/articles/PMC11335254/figure/Fig2/
+number: Fig. 2
+figure_title: ''
+caption: Eight differential genes were selected as potential pathogenic genes for
+  COPD. A 23 overlapping genes were identified at the intersection of the negatively
+  correlated gene set, and seven overlapping genes were found in the positively correlated
+  gene set. B Display of the enrichment results for Molecular Function (MF), Biological
+  Process (BP), Reactome, and KEGG pathways of 30 overlapping genes, with p-values
+  represented as log10 values. C Schematic representation of the PPI network of RRA
+  genes according to the 30 overlapping genes. Top 15 hub genes screened by Cytobubba
+  plugin with Cytoscape according to the PPI network. D Gene selection by the LASSO
+  regression according to the occurrence of COPD in GSE47460. E Eight overlapping
+  genes were identified after intersecting the results from five machine learning
+  methods (SVM-RFE, LASSO Model, Ridge Regression, Elastic Net, and Random Forest
+  Model). F The coefficient values of the 8 genes from the LASSO Model, Ridge Regression,
+  Elastic Net, and Random Forest Model results. G The expression of 8 overlapping
+  genes in GSE47460 (left) and GSE125521 (right). Data are expressed as mean ± SD.
+  P values shown in charts determined by a two-tailed Mann–Whitney test (G)
+article_title: The influence of CLEC5A on early macrophage-mediated inflammation in
+  COPD progression.
+citation: Qingyang Li, et al. Cell Mol Life Sci. 2024 Dec;81(1):330.
+
+doi: 10.1007/s00018-024-05375-0
+journal_title: 'Cellular and Molecular Life Sciences: CMLS'
+journal_nlm_ta: Cell Mol Life Sci
+publisher_name: Springer International Publishing
+
+keywords:
+- Chronic obstructive pulmonary disease
+- CLEC5A
+- Macrophages
+- ScRNA-seq
+- Mendelian randomization
+
+---

figures/PMC11364741__12672_2024_1233_Fig11_HTML.yml

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+---
+pmcid: PMC11364741
+image_filename: 12672_2024_1233_Fig11_HTML.jpg
+figure_link: /pmc/articles/PMC11364741/figure/Fig11/
+number: Fig. 11
+figure_title: ''
+caption: We applied PPI to filter core genes and conducted single-gene survival analysis.
+  We collected protein-protein interaction data from the STRING website (https://string-db.org/)
+  and visualized the topological structure of the PPI network using Cytoscape software
+  (A). We selected the top 10 core genes using the Degree method, with redder color
+  indicating richer interactions with other proteins (B). Additionally, we plotted
+  Kaplan-Meier survival curves for the core genes KIT (C), BLK (D), AP3B1 (E), GAB2
+  (F), CD84 (G), GGA2 (H), GATA2 (I), FUCA1 (J), AP1S3 (K), and PLEKHM1 (L)
+article_title: Construction and analysis of a lysosome-dependent cell death score-based
+  prediction model for non-small cell lung cancer.
+citation: Jiangping Fu, et al. Discov Oncol. 2024 Dec;15:388.
+
+doi: 10.1007/s12672-024-01233-4
+journal_title: Discover Oncology
+journal_nlm_ta: Discov Oncol
+publisher_name: Springer US
+
+keywords:
+- Non-small cell lung cancer
+- Lysosome-dependent cell death
+- Single-cell
+
+---

figures/PMC11377177__CNS-30-e14914-g001.yml

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+---
+pmcid: PMC11377177
+image_filename: CNS-30-e14914-g001.jpg
+figure_link: /pmc/articles/PMC11377177/figure/cns14914-fig-0002/
+number: FIGURE 2
+figure_title: ''
+caption: Bioinformatics analysis of Alzheimer's disease candidate genes regulated
+  by Gingko leaf extract and its key signaling pathways. (A) Schematic representation
+  of the bioinformatics analysis workflow, illustrating the analytical steps involved
+  in the potential regulation of AD key signaling pathways by Gingko leaf extract.
+  (B–D) GO analysis results of AD candidate genes possibly regulated by Gingko leaf
+  extract, showing the top 10 results for biological processes (BP), cellular components
+  (CC), and molecular functions (MF), with adjusted p‐values. (E) KEGG pathway analysis
+  results of 35 AD candidate genes potentially regulated by Gingko leaf extract, represented
+  by a GOKEGG‐EMAP diagram, with the size of the dots indicating the number of selected
+  genes and the color intensity representing the significance of the enrichment analysis
+  (p‐value). (F) KEGG enriched pathways for gene heatmap analysis (G) protein–protein
+  interaction (PPI) network diagram of the 35 AD candidate genes potentially regulated
+  by Gingko leaf extract, constructed using STRING database data and visualized using
+  Cytoscape software. The font size and background color of the genes in the network
+  diagram represent the degree value. (H) Ranking of degree values in the protein–protein
+  interaction network, highlighting the proteins that may play a crucial role in AD.
+article_title: Investigating the effects of Ginkgo biloba leaf extract on cognitive
+  function in Alzheimer's disease.
+citation: Cheng Zhu, et al. CNS Neurosci Ther. 2024 Sep;30(9):e14914.
+
+doi: 10.1111/cns.14914
+journal_title: CNS Neuroscience & Therapeutics
+journal_nlm_ta: CNS Neurosci Ther
+publisher_name: John Wiley and Sons Inc.
+
+keywords:
+- Alzheimer's disease
+- Ginkgo biloba leaf extract
+- kaempferol
+- luteolin
+- PI3K/AKT/NF‐κB signaling pathway
+- quercetin
+
+---

figures/PMC11377401__12672_2024_1257_Fig6_HTML.yml

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+---
+pmcid: PMC11377401
+image_filename: 12672_2024_1257_Fig6_HTML.jpg
+figure_link: /pmc/articles/PMC11377401/figure/Fig6/
+number: Fig. 6
+figure_title: ''
+caption: Results of analysis between immune infiltration and KLF5 expression. A, B
+  Relation between the 24 immune cells’ relative abundances and KLF5 expression level.
+  C–F Tcm cells were considerably positively associated with KLF5 expression as well
+  as infiltration level in various KLF5 expression groups and Th1 cells were inversely
+  correlated with KLF5 expression and infiltration level in various KLF5 expression
+  groups. G Cytoscape was used to build the DEG PPI network. H The KLF5 Network and
+  prospective coexpression genes in KLF5-related DEGs
+article_title: 'The role of KLF5 in gut microbiota and lung adenocarcinoma: unveiling
+  programmed cell death pathways and prognostic biomarkers.'
+citation: Qingliang Fang, et al. Discov Oncol. 2024 Dec;15:408.
+
+doi: 10.1007/s12672-024-01257-w
+journal_title: Discover Oncology
+journal_nlm_ta: Discov Oncol
+publisher_name: Springer US
+
+keywords:
+- Gut microbiota
+- Biomarkers
+- Intestinal mucosal-related cancer
+- Lung adenocarcinoma
+- KLF5
+
+---

figures/PMC11383191__iovs-65-11-13-f009.yml

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+---
+pmcid: PMC11383191
+image_filename: iovs-65-11-13-f009.jpg
+figure_link: /pmc/articles/PMC11383191/figure/fig10/
+number: Figure 9
+figure_title: ''
+caption: 'PPI networks. (A) Integrated protein‒protein interaction network of significantly
+  enriched pathways in hCMFs. (B–E) Subnetworks of the four pathways related to the
+  genes exhibiting the most significant enrichment: EMT (B), mTORC1 signaling (C),
+  TGFβ signaling (D), and angiogenesis (E), derived from GSEA using gene counts. Influential
+  nodes, as determined by the MCC algorithm using CytoHubba in Cytoscape, are emphasized
+  to indicate their central role in the network (red to yellow color scale, with red
+  indicating the most influential nodes).'
+article_title: RNA-Seq Analysis Unraveling Novel Genes and Pathways Influencing Corneal
+  Wound Healing.
+citation: Rajnish Kumar, et al. Invest Ophthalmol Vis Sci. 2024 Sep;65(11):13.
+
+doi: 10.1167/iovs.65.11.13
+journal_title: Investigative Ophthalmology & Visual Science
+journal_nlm_ta: Invest Ophthalmol Vis Sci
+publisher_name: The Association for Research in Vision and Ophthalmology
+
+keywords:
+- cornea
+- fibrosis
+- RNA-seq
+- sequencing
+- wound healing
+
+---

figures/PMC11383270__medi-103-e35529-g006.yml

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+---
+pmcid: PMC11383270
+image_filename: medi-103-e35529-g006.jpg
+figure_link: /pmc/articles/PMC11383270/figure/F5/
+number: Figure 5
+figure_title: ''
+caption: PPI network, which was completed in the Cytoscape and CytoHubba. It consists
+  of 80 nodes, and 2732 edges. The nodes represent the common targets between the
+  URTI-related targets and the predicted Trollius chinensis targets. The edges represent
+  the interaction between the targets. Size of the node and shades of color are proportional
+  to the degree of interaction. The darker the color, the larger the figure, the higher
+  and more significant the score. PPI = protein-protein interaction, URTI = upper
+  respiratory tract infection.
+article_title: Network pharmacology-based study on the mechanism of action of Trollius
+  chinensis capsule in the treatment of upper respiratory tract infection.
+citation: Jun Wu, et al. Medicine (Baltimore). 2024 Sep 6;103(36):e35529.
+
+doi: 10.1097/MD.0000000000035529
+journal_title: Medicine
+journal_nlm_ta: Medicine (Baltimore)
+publisher_name: Lippincott Williams & Wilkins
+
+keywords:
+- molecular docking
+- network pharmacology
+- Trollius chinensis
+- upper respiratory tract infection
+
+---

figures/PMC11428309__12920_2024_2011_Fig5_HTML.yml

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+---
+pmcid: PMC11428309
+image_filename: 12920_2024_2011_Fig5_HTML.jpg
+figure_link: /pmc/articles/PMC11428309/figure/Fig5/
+number: Fig. 5
+figure_title: ''
+caption: 'A: PPI network of DEGs. B: A cluster was obtained by MCODE in Cytoscape'
+article_title: Bioinformatics analysis of ferroptosis in frozen shoulder.
+citation: Hongcui Zhang, et al. BMC Med Genomics. 2024;17:234.
+
+doi: 10.1186/s12920-024-02011-5
+journal_title: BMC Medical Genomics
+journal_nlm_ta: BMC Med Genomics
+publisher_name: BioMed Central
+
+keywords:
+- Frozen shoulders
+- Ferroptosis
+- Bioinformatics
+
+---

figures/PMC11431537__foods-13-02984-g007.yml

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+---
+pmcid: PMC11431537
+image_filename: foods-13-02984-g007.jpg
+figure_link: /pmc/articles/PMC11431537/figure/foods-13-02984-f007/
+number: Figure 7
+figure_title: ''
+caption: PPI network of identified DEGs affected by SA. The DEGs were imported to
+  the STRING database to form an association network by automatic comparison (A).
+  The PPI network was further analyzed using Cytoscape software, and a diagram of
+  the interactive network is presented (B). A node represents a protein. The node
+  size and color were determined by the degree of DEG interaction. The combined score
+  represents the interaction between nodes. The edge size and color were determined
+  by the combined score. The core gene is marked with the blue dashed circle.
+article_title: Role and Mechanism of Sialic Acid in Alleviating Acute Lung Injury
+  through In Vivo and In Vitro Models.
+citation: Dan Li, et al. Foods. 2024 Sep;13(18):2984.
+
+doi: 10.3390/foods13182984
+journal_title: Foods
+journal_nlm_ta: Foods
+publisher_name: MDPI
+
+keywords:
+- sialic acid
+- acute lung injury
+- transcriptome
+- anti-inflammatory activity
+- anti-oxidant effect
+
+---

figures/PMC11432224__ijms-25-09978-g004.yml

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+---
+pmcid: PMC11432224
+image_filename: ijms-25-09978-g004.jpg
+figure_link: /pmc/articles/PMC11432224/figure/ijms-25-09978-f004/
+number: Figure 4
+figure_title: ''
+caption: PPI network construction and hub genes extraction of DEPs. (A) The PPI network
+  of the DEPs is shown. Network nodes represent proteins; edges represent protein–protein
+  associations. Network analysis was set at high confidence (STRING score = 0.4) and
+  high FDR stringency (0.01). Red indicates significantly increased; green indicates
+  significantly decreased; width represents the degree of the interactions. (B) The
+  top 10 hub genes were extracted with cytoHubba plug-in of Cytoscape software, and
+  the eight algorithms are shown. Network nodes represent proteins; edges represent
+  protein–protein associations. Color represents the score. MCC, Matthews Correlation
+  Coefficient; DMNC, Neighborhood Component Centrality; MNC, Maximum Neighbor Connectivity;
+  EPC, Edge Percolated Component.
+article_title: ITRAQ Based Proteomics Reveals the Potential Mechanism of Placental
+  Injury Induced by Prenatal Stress.
+citation: Yujie Li, et al. Int J Mol Sci. 2024 Sep;25(18):9978.
+
+doi: 10.3390/ijms25189978
+journal_title: International Journal of Molecular Sciences
+journal_nlm_ta: Int J Mol Sci
+publisher_name: MDPI
+
+keywords:
+- prenatal stress
+- placental damage
+- proteomics analyses
+- PI3K/AKT/mTOR pathway
+
+---