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Lung cancer brain metastases refer to intracranial space-occupying lesions formed by the metastasis of tumor cells from the lung to the brain parenchyma or dissemination in the meninges. The datasets GSE200563 and GSE126548 for lung cancer brain metastasis were obtained from gene expression omnibus database with the platform files GPL21697 and GPL16791. Differentially expressed genes analysis was conducted, followed by weighted gene co-expression network analysis, construction and analysis of protein-protein interaction networks, functional enrichment analysis, gene set enrichment analysis, comparative toxicogenomics database analysis. Five hundred differentially expressed genes were identified. According to gene ontology, they were mainly enriched in terms of fucosyltransferase activity, protein-DNA complex, cAMP signaling pathway, and transcriptional misregulation in cancer. Ten core genes (JUN, IL1A, VEGFA, MMP1, EDN1, SOCS3, NOD2, NCOR2, VDR, and HDAC2) were obtained. Comparative toxicogenomics database analysis revealed associations between core genes (JUN, IL1A, VEGFA, MMP1, EDN1, SOCS3, NOD2, NCOR2, VDR, and HDAC2) and tumor cell transformation, non-small cell carcinoma, lung neoplasms, tumor invasiveness, tumor metastasis, and inflammation. JUN and MMP1 are abnormally highly expressed in lung cancer brain metastasis tissues, which may be their molecular targets.
Pubmed ID: 40760541
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Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.
View all literature mentionsSoftware R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art.
View all literature mentionsDatabase 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 mentionsSoftware package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.
View all literature mentionsIntegrated 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 mentionsCollection of techniques to remove inter-study bias when combining gene expression data originating from different studies.
View all literature mentionsSoftware that clusters a given network based on topology to find densely connected regions. It can be used to find protein complexes and parts of pathways in protein-protein interaction networks or protein families in protein similarity networks.
View all literature mentionsWeb service to analyze gene or protein lists. Provides automated meta analysis tools to understand pathways within a group of orthogonal target-discovery studies.
View all literature mentionsSoftware R package for statistical analysis and visualization of functional profiles for genes and gene clusters.
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