Identification of macrophage polarisation and mitochondria-related biomarkers in diabetic retinopathy.
The activation of macrophages or microglia in patients' whole body or local eyes play significant roles in diabetic retinopathy (DR). Mitochondrial function regulates the inflammatory polarization of macrophages. Therefore, the common mechanism of mitochondrial related genes (MRGs) and macrophage polarisation related genes (MPRGs) in DR is explored in our study to illustrate the pathophysiology of DR.
Pubmed ID: 39762849 RIS Download
Research resources used in this publication
None foundAdditional research tools detected in this publication
- VennDiagram (RRID:SCR_002414)
- RCircos (RRID:SCR_003310)
- STRING (RRID:SCR_005223)
- GeneMANIA (RRID:SCR_005709)
- NCBI Epigenomics (RRID:SCR_006151)
- HPA (RRID:SCR_006710)
- KEGG (RRID:SCR_012773)
- ggplot2 (RRID:SCR_014601)
- DESeq2 (RRID:SCR_015687)
- ChIP-X Enrichment Analysis 3 (RRID:SCR_023159)
- SRAMP (RRID:SCR_024500)
Antibodies used in this publication
None foundAssociated grants
- Agency: Natural Science Foundation of Jiangxi Province,
Id: 20224BAB216049 - Agency: National Natural Science Foundation of China,
Id: 82360204 - Agency: Innovation Training Program for College Students in Nanchang University,
Id: 2024CX289
Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.
This is a list of tools and resources that we have found mentioned in this publication.
VennDiagram (tool)
RRID:SCR_002414
Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
View all literature mentionsRCircos (tool)
RRID:SCR_003310
Software package that provides a simple and flexible way to generate Circos 2D track plot images for genomic data visualization. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.
View all literature mentionsSTRING (tool)
RRID:SCR_005223
Database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations and are derived from four sources: Genomic Context, High-throughput experiments, (Conserved) Coexpression, and previous knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. The database currently covers 5''214''234 proteins from 1133 organisms. (2013)
View all literature mentionsGeneMANIA (tool)
RRID:SCR_005709
Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
View all literature mentionsNCBI Epigenomics (tool)
RRID:SCR_006151
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022.
View all literature mentionsHPA (tool)
RRID:SCR_006710
Public database with millions of high-resolution images showing the spatial distribution of proteins in different normal human tissues and cancer types, as well as different human cell lines. The data is released together with application-specific validation performed for each antibody, including immunohistochemisty, Western blot analysis and, for a large fraction, a protein array assay and immunofluorescent based confocal microscopy. The database has been developed in a gene-centric manner with the inclusion of all human genes predicted from genome efforts. Search functionalities allow for complex queries regarding protein expression profiles, protein classes and chromosome location. Antibodies included have been analyzed using a standardized protocol in a single attempt without further efforts to optimize the procedure and therefore it cannot be excluded that certain observed binding properties are due to technical rather than biological reasons and that further optimization could result in a different outcome. Submission of antibodies: The Swedish Human Proteome Atlas (HPA) program, invites submission of antibodies from both academic and commercial sources to be included in the human protein atlas. All antibodies will be validated by the HPA-program by a standard procedure and antibodies that are accepted will be use in the tissue- profiling program to generate high-resolution immunohistochemistry images representing a wide spectrum of normal tissues and cancer types.
View all literature mentionsKEGG (tool)
RRID:SCR_012773
Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.
View all literature mentionsggplot2 (tool)
RRID:SCR_014601
Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.
View all literature mentionsDESeq2 (tool)
RRID:SCR_015687
Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
View all literature mentionsChIP-X Enrichment Analysis 3 (tool)
RRID:SCR_023159
Web based transcription factor enrichment analysis. Web server ranks TFs associated with user-submitted gene sets. ChEA3 background database contains collection of gene set libraries generated from multiple sources including TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, and TF-gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate composite rank that improves prediction of correct upstream TF compared to ranks produced by individual libraries.
View all literature mentionsSRAMP (tool)
RRID:SCR_024500
Software tool as computational predictor of mammalian m(6)A site. Used for prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features.
View all literature mentions
