new content from pmc

figures/PMC10720282__ao3c07687_0003.yml

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+---
+pmcid: PMC10720282
+image_filename: ao3c07687_0003.jpg
+figure_link: /pmc/articles/PMC10720282/figure/fig3/
+number: Figure 3
+figure_title: ''
+caption: Analysis of hub genes extracted from the common DEGs between MPXV and HIV.
+  (A) Key gene module showing 37 shared DEGs. (B) Venn diagram showing a total of
+  9 overlapping hub genes screened by seven algorithms. (C) Protein–protein interaction
+  (PPI) network of the 9 hub genes drawn by the Cytoscape plug-in CytoHubba. (D) Hub
+  genes and their co-expression genes interaction network analyzed by GeneMANIA.
+article_title: 'Monkeypox Virus Crosstalk with HIV: An Integrated Skin Transcriptome
+  and Machine Learning Study.'
+citation: Xueyao Cai, et al. ACS Omega. 2023 Dec 12;8(49):47283-47294.
+
+doi: 10.1021/acsomega.3c07687
+journal_title: ACS Omega
+journal_nlm_ta: ACS Omega
+publisher_name: American Chemical Society
+
+keywords:
+---

figures/PMC10724788__eajm-55-3-218_f003.yml

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+---
+pmcid: PMC10724788
+image_filename: eajm-55-3-218_f003.jpg
+figure_link: /pmc/articles/PMC10724788/figure/f3-eajm-55-3-218/
+number: Figure 3. A-B
+figure_title: ''
+caption: 'The illustration shows subnetworks acquired from the networks of target
+  genes of upregulated and downregulated miRNAs, respectively, using the MCC model
+  in the Cytoscape. Potential downregulated hub genes in a protein–protein interaction
+  network (PPI) (A). Possible upregulated hub genes in a network of PPI. The grade
+  of node color displays the degree of connectivity: orange color presents the intermediate
+  degree, yellow color indicates the lowest degree, and red color represents the highest
+  degree (B).'
+article_title: Exosomal Circular Ribonucleic Acid–Microribonucleic Acid Expression
+  Profile from Plasma in Alzheimer’s Disease Patients by Bioinformatics and Integrative
+  Analysis.
+citation: Nail Besli, et al. Eurasian J Med. 2023 Oct;55(3):218-227.
+
+doi: 10.5152/eurasianjmed.2023.23029
+journal_title: The Eurasian Journal of Medicine
+journal_nlm_ta: Eurasian J Med
+publisher_name: Atatürk University School of Medicine
+
+keywords:
+- Plasma
+- exosomal circRNAs–miRNAs
+- bioinformatics analysis
+- Alzheimer’s disease
+
+---

figures/PMC10725609__12967_2023_4787_Fig4_HTML.yml

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+---
+pmcid: PMC10725609
+image_filename: 12967_2023_4787_Fig4_HTML.jpg
+figure_link: /pmc/articles/PMC10725609/figure/Fig4/
+number: Fig. 4
+figure_title: ''
+caption: Protein‒protein interaction (PPI) network analysis and hub genes identification.
+  A PPI network for common DEGs that are shared by SARS-CoV-2 infection and cardiovascular
+  diseases. Red nodes represent up-regulated DEGs, and blue nodes represent down-regulated
+  DEGs. The size of the node responds to its degree in the network. The thickness
+  of the edges is related to the strength of the interaction. B A key cluster with
+  15 genes was further chosen by MCODE plugin in Cytoscape. C The 11 hub genes identified
+  according to four algorithms (MCC, MNC, degree, and EPC) of CytoHubba plugin in
+  Cytoscape (see also Table ). D The gene network and functional analysis of hub genes
+  were generated using GeneMANIA. The inner circle stands for hub genes, and the outer
+  circle refers to the corresponding reciprocal genes. Colors of nodes represent gene
+  function annotations, which refer to GO terms enriched among the genes in the network
+  displayed by GeneMANIA. Colors of edges represent interaction based on co-expression,
+  physical interactions, co-localization, shared protein domain, or predicted interaction
+article_title: 'Landscape of molecular crosstalk between SARS-CoV-2 infection and
+  cardiovascular diseases: emphasis on mitochondrial dysfunction and immune-inflammation.'
+citation: Shiyu Dai, et al. J Transl Med. 2023;21:915.
+
+doi: 10.1186/s12967-023-04787-z
+journal_title: Journal of Translational Medicine
+journal_nlm_ta: J Transl Med
+publisher_name: BioMed Central
+
+keywords:
+- SARS-CoV-2
+- COVID-19
+- Cardiovascular diseases
+- Mitochondria
+- Immune
+- Inflammation
+
+---

figures/PMC10725692__DDDT-17-3723-g0002.yml

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+---
+pmcid: PMC10725692
+image_filename: DDDT-17-3723-g0002.jpg
+figure_link: /pmc/articles/PMC10725692/figure/f0001/
+number: Figure 1
+figure_title: ''
+caption: Potential targets of Jin Gu Lian capsule for the treatment of rheumatoid
+  arthritis. (A) Venn diagram of compound targets and disease targets. (B) The protein–protein
+  interaction (PPI) network was constructed and visualized by Cytoscape 3.8.0. Hub
+  genes resided in the inner layer of the network. The size and color of the nodes
+  were based on degree. The degree value from large to small followed a continuous
+  mapping from red to yellow.
+article_title: Integrated Network Pharmacology and Experimental Approach to Investigate
+  the Protective Effect of Jin Gu Lian Capsule on Rheumatoid Arthritis by Inhibiting
+  Inflammation via IL-17/NF-κB Pathway.
+citation: Tengfei Chen, et al. Drug Des Devel Ther. 2023;17:3723-3748.
+
+doi: 10.2147/DDDT.S423022
+journal_title: Drug Design, Development and Therapy
+journal_nlm_ta: Drug Des Devel Ther
+publisher_name: Dove
+
+keywords:
+- rheumatoid arthritis
+- Jin Gu Lian capsules
+- network pharmacology
+- experimental validation
+- immune-mediated inflammation
+
+---

figures/PMC10725710__SYB2-17-316-g005.yml

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+---
+pmcid: PMC10725710
+image_filename: SYB2-17-316-g005.jpg
+figure_link: /pmc/articles/PMC10725710/figure/syb212078-fig-0003/
+number: FIGURE 3
+figure_title: ''
+caption: PPI network of BMs related DEGs visualised by Cytoscape. (a) Identification
+  of a significant module based on the degree of importance examined for DEGs. PPI
+  network was composed of 28 nodes and 157 edges. Blues represent upregulated genes.
+  Yellows represent downregulated genes. (b) The top 10 genes with the highest degree
+  values were identified. Red represents higher degree value. Yellow represents lower
+  degree value.
+article_title: Identification of basement membrane markers in diabetic kidney disease
+  and immune infiltration by using bioinformatics analysis and experimental verification.
+citation: Rui Shi, et al. IET Syst Biol. 2023 Dec;17(6):316-326.
+
+doi: 10.1049/syb2.12078
+journal_title: IET Systems Biology
+journal_nlm_ta: IET Syst Biol
+publisher_name: John Wiley and Sons Inc.
+
+keywords:
+- bioinformatics
+- diseases
+- genetics
+- medical disorders
+
+---

figures/PMC10726892__CAM4-12-21256-g003.yml

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+---
+pmcid: PMC10726892
+image_filename: CAM4-12-21256-g003.jpg
+figure_link: /pmc/articles/PMC10726892/figure/cam46704-fig-0004/
+number: FIGURE 4
+figure_title: ''
+caption: Deferentially expressed proteins (DEPs) and biological pathways upregulated
+  in patients showing pathologic complete response (pCR) to neoadjuvant chemotherapy.
+  (A) Protein–protein interaction (PPI) network of DEPs constructed using the STRING
+  database. Connected nodes were visualized in Cytoscape, and node sizes were associated
+  to the log fold change of the DEPs. Pink nodes were DEPs upregulated in the pCR
+  group, and blue nodes denoted DEPs downregulated in the pCR group. (B) Enrichment
+  analysis of the DEPs. The –log10 (p) values were visualized and color‐coded by the
+  category of biological functions; light blue for mitochondrial energy metabolism,
+  green for vesicle budding and vascular transportation, orange for leukocyte apoptotic
+  process, purple for glucose metabolism, brick for protein localization to membranes,
+  steel blue for messenger ribonucleic acid processing, and pink for cytoskeleton‐dependent
+  trafficking. (C) Single‐sample GSEA scores of immune response and immune suppressive
+  markers were shown by bloxplots. Patients showing PCR were indicated by gray boxes,
+  whereas nonresponders were indicated by light blue boxes.
+article_title: Imaging‐proteomic analysis for prediction of neoadjuvant chemotherapy
+  responses in patients with breast cancer.
+citation: Jingxian Duan, et al. Cancer Med. 2023 Dec;12(23):21256-21269.
+
+doi: 10.1002/cam4.6704
+journal_title: Cancer Medicine
+journal_nlm_ta: Cancer Med
+publisher_name: John Wiley and Sons Inc.
+
+keywords:
+- breast cancer
+- deep learning
+- neoadjuvant chemotherapy
+- pathologic complete response
+- Radiogenomics
+
+---

figures/PMC10731348__tcr-12-11-3129-f8.yml

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+---
+pmcid: PMC10731348
+image_filename: tcr-12-11-3129-f8.jpg
+figure_link: /pmc/articles/PMC10731348/figure/f8/
+number: Figure 8
+figure_title: ''
+caption: Screening of key genes. Cytoscape software was used to visualize the entire
+  PPI, draw the PPI network using node and logFC, and introduce BC to draw the protein
+  interactions. The MCODE plugin in Cytoscape was used to build the functional modules.
+  The results showed that three modules had a specific score >6 (A-C). The core genes
+  of the three modules were ADAMTSL1, GRIN2A, and ITGAX, and the genes filtered by
+  the CytoHubba plugin in Cytoscape were intersected with the genes of the three core
+  modules to obtain the top 10 key genes (D). PPI, protein-protein interaction; BC,
+  betweenness centrality; MCODE, Molecular Complex Detection; FC, fold change.
+article_title: Glucocorticoid receptor regulates the epithelial-mesenchymal transition
+  process through GR/ZEB1/E-cad and is involved in breast cancer endocrine drug resistance—a
+  bioinformatics analysis.
+citation: Yuhan Tang, et al. Transl Cancer Res. 2023 Nov 30;12(11):3129-3146.
+
+doi: 10.21037/tcr-23-1628
+journal_title: Translational Cancer Research
+journal_nlm_ta: Transl Cancer Res
+publisher_name: AME Publishing Company
+
+keywords:
+- Glucocorticoid receptor (GR)
+- ZEB1
+- breast cancer
+- epithelial-mesenchymal transition (EMT)
+
+---

figures/PMC10733940__ene-2023-0086-0006-533397_F04.yml

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+---
+pmcid: PMC10733940
+image_filename: ene-2023-0086-0006-533397_F04.jpg
+figure_link: /pmc/articles/PMC10733940/figure/F4/
+number: Fig. 4
+figure_title: ''
+caption: Protein-protein interaction (PPI) construction and hub gene identification
+  through CytoHubba plug-in in Cytoscape software. a PPI network of the common DEGs
+  between AD and MS. b Intersection plot of top 10 hub genes among the five algorithms.
+article_title: 'Exploring Shared Genetic Signatures of Alzheimer’s Disease and Multiple
+  Sclerosis: A Bioinformatic Analysis Study.'
+citation: Dasen Yuan, et al. Eur Neurol. 2023 Dec;86(6):363-376.
+
+doi: 10.1159/000533397
+journal_title: European Neurology
+journal_nlm_ta: Eur Neurol
+publisher_name: S. Karger AG
+
+keywords:
+- Alzheimer’s disease
+- Bioinformatics
+- Differentially expressed genes
+- Hub gene
+- Multiple sclerosis
+
+---

figures/PMC10735105__medi-102-e36615-g001.yml

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+---
+pmcid: PMC10735105
+image_filename: medi-102-e36615-g001.jpg
+figure_link: /pmc/articles/PMC10735105/figure/F1/
+number: Figure 1
+figure_title: ''
+caption: Venn diagram, PPI network, and the most significant module of DEGs. (A) DEGs
+  were selected with a fold change > 2 and P value < .001 among the mRNA expression
+  profiling sets GSE143939, GSE196006, and GSE200427. The three datasets showed an
+  overlap of 241 genes. (B) The most significant module. (C) The PPI network of DEGs
+  was constructed using Cytoscape. Upregulated genes are marked in light red; downregulated
+  genes are kept in light blue. DEGs = differentially expressed genes, PPI = protein-protein
+  interaction.
+article_title: Identification of potential key genes for colorectal cancer based on
+  bioinformatics analysis.
+citation: Chongyang Li, et al. Medicine (Baltimore). 2023 Dec 22;102(51):e36615.
+
+doi: 10.1097/MD.0000000000036615
+journal_title: Medicine
+journal_nlm_ta: Medicine (Baltimore)
+publisher_name: Lippincott Williams & Wilkins
+
+keywords:
+- bioinformatics analysis
+- biomarkers
+- CDK1
+- CEP55
+- colorectal cancer
+- MKI67
+- TOP2A
+
+---

figures/fetch.log

@@ -1,2 +1,2 @@
-https://www.ncbi.nlm.nih.gov/pmc/?term=(network-OR-PPI+cytoscape)+AND+(2023/12/01[PUBDATE]+%3A+3000/01/01[PUBDATE])&report=imagesdocsum&dispmax=100
- 100 results
+https://www.ncbi.nlm.nih.gov/pmc/?term=(network-OR-PPI+cytoscape)+AND+(2024/01/01[PUBDATE]+%3A+3000/01/01[PUBDATE])&report=imagesdocsum&dispmax=100
+ 10 results

query_config.yml

@@ -1,5 +1,5 @@
 terms:
 - network OR PPI
 - cytoscape
-last_run: 2024/01/01
+last_run: 2024/02/01
 date_range: ~