protein structural domain enrichment analysis  (InterPro Inc)

Journal: Journal of Ovarian Research

Article Title: 4D quantitative proteomics of ovarian granulosa cells reveals the involvement of oxidative phosphorylation in non-elderly women with diminished ovarian reserve

doi: 10.1186/s13048-025-01688-1

Figure Lengend Snippet: Domain annotation and subcellular localization of DEPs. A Protein structural domain enrichment analysis of DEPs using the InterPro database. Among all enrichment results, the pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (IPR023753, adjusted p -value = 2.10 × 10⁻. 5 ) exhibited the most significant enrichment. B Subcellular localization prediction of DEP. The majority of DEPs localized to the mitochondria (28.62%), followed by nucleus (22.30%) and cytoplasm (16.36%), implicating mitochondrial dysfunction in the disease phenotype. C GSEA of subcellular localized DEPs demonstrated that mitochondrial proteins exhibited the most statistically significant enrichment (NES = −1.85, adjusted p -value < 0.001)

Article Snippet: A Protein structural domain enrichment analysis of DEPs using the InterPro database.

Techniques: Binding Assay

Journal: Journal of Ovarian Research

Article Title: 4D quantitative proteomics of ovarian granulosa cells reveals the involvement of oxidative phosphorylation in non-elderly women with diminished ovarian reserve

doi: 10.1186/s13048-025-01688-1

Figure Lengend Snippet: PPI network analysis of DEPs. A The network was constructed using the STRING database (confidence score ≥ 0.7) and visualized in Cytoscape. B GO enrichment analysis of the top two protein clusters based on MCODE algorithm. Significantly enriched biological processes included “mitochondrial matrix” (GO:0005759), followed by “oxidoreductase activity” (GO:0016491), and “amide biosynthetic process” (GO:0043604)

Article Snippet: A Protein structural domain enrichment analysis of DEPs using the InterPro database.

Techniques: Construct, Activity Assay

Journal: Communications Biology

Article Title: The Hsf1-sHsp cascade has pan-antiviral activity in mosquito cells

doi: 10.1038/s42003-024-07435-4

Figure Lengend Snippet: A Hierarchical clustering of differentially expressed (DE) genes at 4, 8, and 48 hpi of mock or CHIKV infection (MOI = 5) in Aedes aegypti Aag2 cells, as quantified from RNA-seq data ( n = 3 biological replicates). DEgenes ( p < 0.05) at each time point are color labeled on the left; KEGG pathway and InterPro enrichment is shown on the right. Z scores were calculated based on log-transformed Fragments per Kilobase per Million mapped reads (FPKM). B Gene structure and protein domain analysis of heat shock proteins upregulated at 8 hpi of CHIKV infection. A neighbor-joining tree was constructed based on amino acid sequences (left). The log 2 fold changes in gene expression were quantified by RNA-seq (middle). The gene structure and InterPro protein domains are shown along the gene body (right). C Hi-C interaction track with topologically associated domains (TADs) shown as horizontal blue bars ( p < 0.05). D Genome browser tracks showing RNA-seq data of mock and CHIKV infected Aag2 cells and chromatin profiling data from uninfected Aag2 cells (ATAC-seq, histone marks and RNA pol II ChIP-seq) within the indicated TAD. Eight upregulated sHsp genes at 8 hpi are highlighted in orange, other genes in gray. Predicted Hsf1 motifs are shown as green arrowheads at the bottom. E Expression of the indicated genes in mock (-) or CHIKV (MOI = 5) infected Aag2 cells upon RNAi-mediated silencing of Hsf1 at 8 hpi. Luciferase dsRNA served as a non-targeting control (ctr). RT-qPCR was performed in biological quintuplicates and shown as dots, with horizontal lines and the bars indicating mean ± SD. Symbols denote statistical significance in unpaired t -tests (ns, not significant, * p < 0.05; ** p < 0.01; *** p < 0.001).

Article Snippet: STRING was used for KEGG pathway and InterPro protein domain enrichment analysis .

Techniques: Infection, RNA Sequencing, Labeling, Transformation Assay, Construct, Gene Expression, Hi-C, ChIP-sequencing, Expressing, Luciferase, Control, Quantitative RT-PCR