new content from pmc

figures/PMC10861149__ajpcell.00352.2023_f005.yml

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+---
+pmcid: PMC10861149
+image_filename: ajpcell.00352.2023_f005.jpg
+figure_link: /pmc/articles/PMC10861149/figure/F0005/
+number: Figure 5
+figure_title: ''
+caption: Top upregulated pathways in males (A–D) and females (E–H), based on WikiPathways
+  (WP), KEGG, and Reactome (REAC) libraries, after 24 h (A and E), 48 h (B and F),
+  72 h (C and G), and 168 h (D and H) of hindlimb unloading (HU) compared with 0 h.
+  Adjusted P value ≤0.05.
+article_title: Biological sex divergence in transcriptomic profiles during the onset
+  of hindlimb unloading-induced atrophy.
+citation: Stavroula Tsitkanou, et al. Am J Physiol Cell Physiol. 2023 Nov 1;325(5):C1276-C1293.
+
+doi: 10.1152/ajpcell.00352.2023
+journal_title: American Journal of Physiology - Cell Physiology
+journal_nlm_ta: Am J Physiol Cell Physiol
+publisher_name: American Physiological Society
+
+keywords:
+- disuse
+- fibrosis
+- hindlimb suspension
+- mitochondria
+- muscle atrophy
+
+---

figures/PMC10861149__ajpcell.00352.2023_f006.yml

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+---
+pmcid: PMC10861149
+image_filename: ajpcell.00352.2023_f006.jpg
+figure_link: /pmc/articles/PMC10861149/figure/F0006/
+number: Figure 6
+figure_title: ''
+caption: Top downregulated pathways in males (A–D) and females (E–H), based on WikiPathways
+  (WP), KEGG, and Reactome (REAC) libraries, after 24 h (A and E), 48 h (B and F),
+  72 h (C and G), and 168 h (D and H) of hindlimb unloading (HU) compared with 0 h.
+  Adjusted P value ≤0.05.
+article_title: Biological sex divergence in transcriptomic profiles during the onset
+  of hindlimb unloading-induced atrophy.
+citation: Stavroula Tsitkanou, et al. Am J Physiol Cell Physiol. 2023 Nov 1;325(5):C1276-C1293.
+
+doi: 10.1152/ajpcell.00352.2023
+journal_title: American Journal of Physiology - Cell Physiology
+journal_nlm_ta: Am J Physiol Cell Physiol
+publisher_name: American Physiological Society
+
+keywords:
+- disuse
+- fibrosis
+- hindlimb suspension
+- mitochondria
+- muscle atrophy
+
+---

figures/PMC10861149__ajpcell.00352.2023_f008.yml

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+---
+pmcid: PMC10861149
+image_filename: ajpcell.00352.2023_f008.jpg
+figure_link: /pmc/articles/PMC10861149/figure/F0008/
+number: Figure 8
+figure_title: ''
+caption: Heatmaps with the top up- and downregulated pathways (based on WikiPathways,
+  KEGG, and Reactome libraries) after 24 h (A), 48 h (B), 72 h (C), and 168 h (D)
+  of hindlimb unloading (HU) compared with 0 h in male and female mice. Adjusted P
+  value ≤0.05. The white boxes with X indicates that the pathway is not differentially
+  expressed.
+article_title: Biological sex divergence in transcriptomic profiles during the onset
+  of hindlimb unloading-induced atrophy.
+citation: Stavroula Tsitkanou, et al. Am J Physiol Cell Physiol. 2023 Nov 1;325(5):C1276-C1293.
+
+doi: 10.1152/ajpcell.00352.2023
+journal_title: American Journal of Physiology - Cell Physiology
+journal_nlm_ta: Am J Physiol Cell Physiol
+publisher_name: American Physiological Society
+
+keywords:
+- disuse
+- fibrosis
+- hindlimb suspension
+- mitochondria
+- muscle atrophy
+
+---

figures/PMC10947827__nihms-1961543-f0002.yml

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+---
+pmcid: PMC10947827
+image_filename: nihms-1961543-f0002.jpg
+figure_link: /pmc/articles/PMC10947827/figure/F2/
+number: Figure 2
+figure_title: NTX-301 induced transcriptome and methylome reprogramming in OC cells
+caption: (A) Hierarchical clustering heatmap for DEGs (FDR<0.05) measured by RNAseq
+  in OVCAR5 cells treated with NTX-301. Rows represent replicates (n=3/group). (B)
+  Volcano plot of DEGs comparing OVCAR5 cells treated with NTX-301 100nM with DMSO.
+  NTX-301-induced upregulated genes are shown in red and downregulated gene are shown
+  in blue. (C) Dot plot of Gene Set Enrichment Analysis (GSEA) of DEG shows the top
+  sixteen KEGG pathways in OVCAR5 cells treated with NTX-301 (100nM). The size of
+  the circles represents the counts of DEGs within each term, and the color of the
+  circles represents statistical significance. Gene ratio (x axis) is the relative
+  number of DEGs per term. (D) GSEA enrichment plots for the KEGG “fatty acid metabolism”
+  gene set using the gene expression profiles of OVCAR5 cells treated with NTX-301
+  (100nM) vs. DMSO (n=3). (E) WikiPathways analysis of downregulated DEGs in OVCAR5
+  OC cells treated with NTX-301 (100nM) vs. DMSO shows the top significantly enriched
+  molecular pathways. Gene expression was measured by RNA-seq (n=3 replicates per
+  group). (F, G) Hierarchical clustering heatmap for DEGs (FDR<0.05) stemness-related
+  genes (F) () and lipid metabolism (G) in OVCAR5 cells treated with NTX-301 (100nM)
+  vs. DMSO. Rows represent replicates (n=3/group). (H) Volcano plot of DMPs comparing
+  OVCAR5 cells treated with NTX-301 vs control. Hypermethylated CpG probes are shown
+  in red (positive delta Beta) and hypomethylated CpG probes are shown in blue (negative
+  delta Beta). (I) Scatter plot shows overlapping DEGs associated with promoter-associated
+  DMPs in response to treatment with NTX-301 (100nM, 3days; n = 3 replicates per group).
+  A total of 23,709 genes were both upregulated and were associated with hypomethylated
+  CpG sites (lower right quadrant), =whereas 23,302 genes were downregulated and were
+  associated with hypomethylated CpGs (lower left quadrant).
+article_title: Preclinical evaluation of NTX-301, a Novel DNA Hypomethylating Agent
+  in Ovarian Cancer.
+citation: Yinu Wang, et al. Clin Cancer Res. ;30(6):1175-1188.
+
+doi: 10.1158/1078-0432.CCR-23-2368
+journal_title: 'Clinical cancer research : an official journal of the American Association
+  for Cancer Research'
+journal_nlm_ta: Clin Cancer Res
+publisher_name: ''
+
+keywords:
+---

figures/PMC11087449__40199_2023_484_Fig5_HTML.yml

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+---
+pmcid: PMC11087449
+image_filename: 40199_2023_484_Fig5_HTML.jpg
+figure_link: /pmc/articles/PMC11087449/figure/Fig5/
+number: Fig. 5
+figure_title: ''
+caption: Proposed molecular mechanism of RP1a and other proteins under treatment with
+  the candidate compounds (created with PathVisio 3.3.0)
+article_title: Computational Screening Using a Combination of Ligand-Based Machine
+  Learning and Molecular Docking Methods for the Repurposing of Antivirals Targeting
+  the SARS-CoV-2 Main Protease.
+citation: Gusti Putu Wahyunanda Crista Yuda, et al. Daru. 2024 Jun;32(1):47-65.
+
+doi: 10.1007/s40199-023-00484-w
+journal_title: DARU Journal of Pharmaceutical Sciences
+journal_nlm_ta: Daru
+publisher_name: Springer International Publishing
+
+keywords:
+- COVID-19
+- Drug repurposing
+- Mpro
+- Ligand-based virtual screening
+- Molecular docking
+
+---

figures/PMC11390906__41467_2024_52214_Fig3_HTML.yml

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+---
+pmcid: PMC11390906
+image_filename: 41467_2024_52214_Fig3_HTML.jpg
+figure_link: /pmc/articles/PMC11390906/figure/Fig3/
+number: Fig. 3
+figure_title: FXII deficiency induces differential gene expression in DKD
+caption: 'a Principal component analysis (PCA) on gene sets of normoglycemic (C) and
+  hyperglycemic (DM) WT and F12-/- mice kidneys. b Heatmap of the RNA-seq data showing
+  the differentially expressed genes (DEGs) in WT-DM and F12-/--DM mice. Each column
+  represents data from an individual mouse. Color intensity represents row Z-score.
+  c Gene set enrichment analysis (GSEA) plots of the hallmark gene sets representing
+  key negatively enriched pathways when comparing F12-/--DM to WT-DM kidneys. Significance
+  is represented by the false discovery rate (FDR). d Bar graph representing the top
+  enriched pathways based on the downregulated differentially expressed genes (DEGs)
+  in F12-/--DM compared to WT-DM kidneys using KEGG (Kyoto Encyclopedia of Genes and
+  Genomes), WikiPathways, Reactome, PID (Pathway Interaction Database), and GO (Gene
+  Ontology: Biological processes) databases. The pathways were ranked by the false
+  discovery rate (FDR). Source data are provided as a “Source Data” file.'
+article_title: Factor XII signaling via uPAR-integrin β1 axis promotes tubular senescence
+  in diabetic kidney disease.
+citation: Ahmed Elwakiel, et al. Nat Commun. 2024;15:7963.
+
+doi: 10.1038/s41467-024-52214-8
+journal_title: Nature Communications
+journal_nlm_ta: Nat Commun
+publisher_name: Nature Publishing Group UK
+
+keywords:
+- Chronic kidney disease
+- Molecular biology
+- Risk factors
+- Experimental models of disease
+
+---

figures/PMC11391628__12903_2024_4775_Fig3_HTML.yml

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+---
+pmcid: PMC11391628
+image_filename: 12903_2024_4775_Fig3_HTML.jpg
+figure_link: /pmc/articles/PMC11391628/figure/Fig3/
+number: Fig. 3
+figure_title: ''
+caption: 'Bar charts of pathway enrichment analysis for shared genes between AD and
+  PT: (A) Reactome pathway, (B) BioPlanet pathway, (C) WikiPathways, (D) KEGG 2021
+  human pathway'
+article_title: Discovering common pathogenetic processes between periodontitis and
+  Alzheimer’s disease by bioinformatics and system biology approach.
+citation: Fei Ge, et al. BMC Oral Health. 2024;24:1074.
+
+doi: 10.1186/s12903-024-04775-9
+journal_title: BMC Oral Health
+journal_nlm_ta: BMC Oral Health
+publisher_name: BioMed Central
+
+keywords:
+- Periodontitis
+- Alzheimer’s disease
+- Endoplasmic reticulum stress
+- Inflammation
+- Mitochondrial dysfunction
+- Hub gene
+
+---

figures/PMC11398484__nihpp-2024.09.05.609098v1-f0003.yml

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+---
+pmcid: PMC11398484
+image_filename: nihpp-2024.09.05.609098v1-f0003.jpg
+figure_link: /pmc/articles/PMC11398484/figure/F3/
+number: Figure 3
+figure_title: Co-regulation analysis maps cooperative protein associations to known
+  protein complexes and pathways
+caption: '(A) Scatterplots comparing abundances across selected protein pairs across
+  samples. (B) Distribution of rPearson based on observed (top) and permuted (bottom)
+  data. Observed distribution was obtained by calculating rPearson across all possible
+  protein-protein pairs. Permuted distributions were generated by randomly sampling
+  50,000 protein pairs after randomly shuffling their respective timepoints 10 times
+  each prior to calculating rPearson. Colors indicate strongly correlated (>=0.95;
+  blue) or anticorrelated (<=−0.95; red) edges. (C) Distribution of protein edge counts
+  across the trimmed correlation network. On average, each protein in the network
+  participated in 174 edges. (D) Ratio of enrichment for the annotated edges in the
+  correlation network (“observed network”) compared to the expected edge annotation
+  frequencies across Gene Ontology biological process (GOBP), cellular component (GOCC),
+  molecular function (GOMF), localization, pathways, protein-protein interactions
+  (BioPlex) or protein complexes. Specifically, we calculated the enrichment for annotated
+  edges as the fraction of annotated edges per category in the observed correlation
+  network divided by the fraction of annotated edges among all possible edges involving
+  the 5,227 proteins in the correlation network. The expected frequency of annotated
+  edges was calculated by generating all possible pairs from 5,227 human proteins
+  (Uniprot, 07/2024) and computing the number of pairs explained by each functional
+  category. (E) Network analysis identifies known associations between proteins for
+  BMP1 and RPL7A. (F-G) Network structure of the (F) 26S proteasome and (G) Citric
+  Acid cycle pathway. Magenta nodes indicate known complex members annotated either
+  from CORUM or EMBL ComplexPortal for protein complexes, or from BioCarta, KEGG,
+  Protein Interaction Database (PID), Reactome, and WikiPathways (WP) for biochemical
+  pathways. Blue edges indicate positive correlations between nodes while red edges
+  indicate anticorrelations. (H-I) Cooperative proteins are highly correlated with
+  members of established protein complexes including: (H) NuA4 chromatin remodeling
+  complex and (I) Chaperonin-containing T (TRiC/CCT) complex. Magenta nodes indicate
+  subunits of a given complex, while orange nodes indicate cooperative proteins i.e.
+  proteins with correlated profiles to proteins constituting a particular protein
+  complex. Cooperative node sizes indicate the negative log10 of the BH-adjusted p-value
+  after computing significance from Fisher’s exact tests to determine cooperative
+  association of a protein to a particular module. Blue edges indicate correlated
+  edges while orange edges link cooperative proteins to members of a particular module.
+  (J) Bioplex interaction network of the TRiC/CCT complex. Orange nodes are cooperative
+  proteins with correlated profiles to proteins found in the TRiC/CCT complex. Gray
+  edges indicate BioPlex evidence. (K) Histogram of protein complexes (x-axis) and
+  their respective numbers of cooperative proteins (y-axis). (L) Heuristic to identify
+  shared cooperative proteins between complexes. (M) Heatmap depicting a subset of
+  shared cooperative proteins across manually curated EMBL ComplexPortal protein complexes
+  namely exosomes, SWI/SNFs, ATAC remodelers, nucleosome remodelers (NuRDs), and histone
+  acetyltransferase (HAT) and deacetylase (HDAC) complexes. Heatmap colored by Jaccard
+  similarity coefficients calculated from overlapping sets of cooperative proteins
+  between protein complex pairs and clustered using euclidean distances with average
+  linkage.'
+article_title: The proteomic landscape and temporal dynamics of mammalian gastruloid
+  development.
+citation: Riddhiman K. Garge, et al. bioRxiv. 2024 Sep 7:2024.09.05.609098.
+
+doi: 10.1101/2024.09.05.609098
+journal_title: bioRxiv
+journal_nlm_ta: bioRxiv
+publisher_name: Cold Spring Harbor Laboratory
+
+keywords:
+---

figures/PMC11399446__41467_2024_52306_Fig3_HTML.yml

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+---
+pmcid: PMC11399446
+image_filename: 41467_2024_52306_Fig3_HTML.jpg
+figure_link: /pmc/articles/PMC11399446/figure/Fig3/
+number: Fig. 3
+figure_title: snRNA-seq analysis showing the clustering signature and composition
+caption: a Uniform Manifold Approximation and Projection (UMAP) plot shows the 78,979
+  nuclei, mapping to 18 clusters. b Dot plot showing cluster identities aligned to
+  canonical cell types in the adult mouse kidney based on a variety of cell type-specific
+  marker genes. PT proximal tubules, LH(DL) Loop of Henle (Descending loop), LH(AL)
+  Loop of Henle (Ascending loop), DCT distal convoluted tubule, CNT connecting tubule,
+  CD-PC collecting duct principal cell, IC intercalated cell, Mø macrophage, PEC parietal
+  epithelial cell, Prolif.PT Proliferating proximal tubules, Mes mesangial, Endo endothelial,
+  Pod podocyte. Dot plot of all significantly (c) upregulated and (d) downregulated
+  genes in the podocyte cluster between KLF6PODTA vs NPHS2-rtTA mice under diabetic
+  conditions. Expression level of these genes is shown by the heat map and the percentage
+  of cells expressing the gene in the cluster is shown by the size. The default statistical
+  test (Wilcoxon Rank Sum test, adjusted p-value based on Bonferroni correction) in
+  Seurat package was used. Significantly expressed genes are determined by adjusted
+  p < 0.05. Reactome, WikiPathways and KEGG enrichment analysis of these (e) upregulated
+  and (f) downregulated genes in the podocyte cluster between KLF6PODTA vs NPHS2-rtTA
+  mice under diabetic conditions. The default statistical test (fisher’s exact test)
+  in Enrichr was used.
+article_title: Podocyte-specific KLF6 primes proximal tubule CaMK1D signaling to attenuate
+  diabetic kidney disease.
+citation: Nehaben A. Gujarati, et al. Nat Commun. 2024;15:8038.
+
+doi: 10.1038/s41467-024-52306-5
+journal_title: Nature Communications
+journal_nlm_ta: Nat Commun
+publisher_name: Nature Publishing Group UK
+
+keywords:
+- Diabetic nephropathy
+- Chronic kidney disease
+- Podocytes
+
+---

figures/PMC11403004__gr8.yml

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+---
+pmcid: PMC11403004
+image_filename: gr8.jpg
+figure_link: /pmc/articles/PMC11403004/figure/fig8/
+number: Figure 8
+figure_title: ''
+caption: Identification of core immune genes of head and neck squamous cell carcinoma.
+  (A, B) The optimal soft threshold was determined by WGCNA. (C) Dendrogram of all
+  differentially expressed genes based on dissimilarity measure (1-TOM) clustering.
+  (D) The four modules obtained by WGCNA. (E) Comparison of immune subtype scores
+  in different modules. (F) Multifactor Cox analysis of different module scores. (G)
+  Prognostic curves of MEblue. (H) The network diagram showing the relationship between
+  the enrichment pathways. (I) The bar chart showing the top 20 enriched functions
+  and pathways of genes, including Kyoto Encyclopedia of Genes and Genomes, Gene Ontology,
+  WikiPathways, and Reactome database enrichment analysis results.
+article_title: Identification of ferroptosis-associated tumor antigens as the potential
+  targets to prevent head and neck squamous cell carcinoma.
+citation: Qiming Zhai, et al. Genes Dis. 2024 Nov;11(6):101212.
+
+doi: 10.1016/j.gendis.2024.101212
+journal_title: Genes & Diseases
+journal_nlm_ta: Genes Dis
+publisher_name: Chongqing Medical University
+
+keywords:
+- Ferroptosis
+- Ferroptosis subtypes
+- Head and neck squamous cell carcinoma
+- Immunotherapy
+- Tumor antigens
+
+---