new content from pmc

figures/PMC10325730__fimmu-14-1179664-g005.yml

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+---
+pmcid: PMC10325730
+image_filename: fimmu-14-1179664-g005.jpg
+figure_link: /pmc/articles/PMC10325730/figure/f5/
+number: Figure 5
+figure_title: ''
+caption: Significant modules and roles of PPI network (A) The top four key gene modules
+  identified by MCODE plug-in of Cytoscape. (B) Bubble plots of Gene ontology (GO)
+  enrichment for modules associated with the biological processes (GO-BP, blue), the
+  cellular components (GO-CC, red), and the molecular functions (GOMF, green). (C)
+  Bubble plots of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis.
+article_title: Exploring the potential common denominator pathogenesis of system lupus
+  erythematosus with COVID-19 based on comprehensive bioinformatics analysis.
+citation: Huiqiong Zeng, et al. Front Immunol. 2023;14:1179664.
+
+doi: 10.3389/fimmu.2023.1179664
+journal_title: Frontiers in Immunology
+journal_nlm_ta: Front Immunol
+publisher_name: Frontiers Media S.A.
+
+keywords:
+- bioinformatics
+- system lupus erythematosus
+- COVID-19
+- diagnostic biomarkers
+- immune cells infiltration
+
+---

figures/PMC10462626__41598_2023_40404_Fig2_HTML.yml

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+---
+pmcid: PMC10462626
+image_filename: 41598_2023_40404_Fig2_HTML.jpg
+figure_link: /pmc/articles/PMC10462626/figure/Fig2/
+number: Figure 2
+figure_title: ''
+caption: (A) PPI network of DEGs was established by STRING (http://string-db.org)
+  and visualized via Cytoscape software (version 3.9.0). The red nodes indicated upregulated
+  genes and the blue nodes indicated downregulated genes. (B) Top 20 hub genes with
+  a higher degree of connectivity. (C) KEGG pathway enrichment analysis of the top
+  20 hub genes. (D) The prognostic value (p < 0.05) of the top 20 hub genes in CRC
+  patients in the disease-free survival (DFS) curve (GEPIA). (E) The expression of
+  ORM1 between liver metastases and primary tumors, primary tumors, and normal tissues
+  of CRC in datasets GSE14297, GSE49355, and GSE81558 respectively. Data are expressed
+  as mean ± SD. ns p ≥ 0.05, ***p < 0.001, ****p < 0.0001 (unpaired t test or ANOVA).
+article_title: Orosomucoid 1 promotes colorectal cancer progression and liver metastasis
+  by affecting PI3K/AKT pathway and inducing macrophage M2 polarization.
+citation: Lei Yue, et al. Sci Rep. 2023;13:14092.
+
+doi: 10.1038/s41598-023-40404-1
+journal_title: Scientific Reports
+journal_nlm_ta: Sci Rep
+publisher_name: Nature Publishing Group UK
+
+keywords:
+- Cancer
+- Gastrointestinal cancer
+- Metastasis
+
+---

figures/PMC10462740__41598_2023_40617_Fig3_HTML.yml

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+---
+pmcid: PMC10462740
+image_filename: 41598_2023_40617_Fig3_HTML.jpg
+figure_link: /pmc/articles/PMC10462740/figure/Fig3/
+number: Figure 3
+figure_title: ''
+caption: 'LAMP1 protein–protein interaction network reveals its role in immune regulation.
+  (A) KEGG-GSEA enrichment analysis of LAMP1 correlated genes on GSE6575 (upper) and
+  GSE18123 (lower) datasets. (B) The protein–protein interacting (PPI) network of
+  LAMP1 was obtained from STRING (string-db.org) and visualized using Cytoscape software
+  (3.8.4). (C) The top 10 hub-gene was calculated using cytoHubba plugin in software
+  using Maximal Clique Centrality (MCC) algorithm. (D) PPI network connectivity for
+  LAMP1 and DEGs genes identified as up-regulated in ASD groups constructed by STRING
+  (https://string-db.org/). (E) The WikiPathway enrichment analysis according to PPIs
+  of the STRING enrichment results. (F) Human phenotype prediction of LAMP1 using
+  Harmonizome database indicating as Z-score. (G) Immune cell enrichment analysis
+  of GSE6575 using TIMER2.0 and that correlation assay between LAMP1 mRNA expression
+  associations with neutrophil enrichment content was performed. KEGG: Kyoto Encyclopedia
+  of Genes and Genomes.'
+article_title: LAMP1 as a novel molecular biomarker to predict the prognosis of the
+  children with autism spectrum disorder using bioinformatics approaches.
+citation: Sisi Deng, et al. Sci Rep. 2023;13:14040.
+
+doi: 10.1038/s41598-023-40617-4
+journal_title: Scientific Reports
+journal_nlm_ta: Sci Rep
+publisher_name: Nature Publishing Group UK
+
+keywords:
+- Biomarkers
+- Autism spectrum disorders
+
+---

figures/PMC9751040__fimmu-13-1058884-g006.yml

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+---
+pmcid: PMC9751040
+image_filename: fimmu-13-1058884-g006.jpg
+figure_link: /pmc/articles/PMC9751040/figure/f6/
+number: Figure 6
+figure_title: ''
+caption: Screening Hub genes. (A) PPI network diagram obtained after applying the
+  k-means algorithm based on machine learning to the Co-genes. The four genes in the
+  lower right-hand corner of the enlarged diagram are CASP1, NLRP3, IL1B, and IL18.
+  (B) PPI network diagram after processing with Cytoscape software. (C) The Top 11
+  hub genes are filtered using the Degree algorithm under the CytoHubba package condition.
+article_title: SARS-CoV-2 induces “cytokine storm” hyperinflammatory responses in
+  RA patients through pyroptosis.
+citation: Qingcong Zheng, et al. Front Immunol. 2022;13:1058884.
+
+doi: 10.3389/fimmu.2022.1058884
+journal_title: Frontiers in Immunology
+journal_nlm_ta: Front Immunol
+publisher_name: Frontiers Media S.A.
+
+keywords:
+- SARS-CoV-2
+- COVID-19
+- rheumatoid arthritis
+- pyroptosis
+- caspase-1
+- minocycline
+
+---

figures/fetch.log

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+https://www.ncbi.nlm.nih.gov/pmc/?term=(network-OR-PPI+cytoscape)+AND+(2023/08/01[PUBDATE]+%3A+3000/01/01[PUBDATE])&report=imagesdocsum&dispmax=100
  4 results

query_config.yml

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 terms:
 - network OR PPI
 - cytoscape
-last_run: 2023/08/01
+last_run: 2023/09/01
 date_range: ~