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pathway and ontology databases such as go, kegg, reactome, and  (BioCarta)

 
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    Structured Review

    BioCarta pathway and ontology databases such as go, kegg, reactome, and
    Number and percentage of significant coevolved MSigDB groups in different methods
    Pathway And Ontology Databases Such As Go, Kegg, Reactome, And, supplied by BioCarta, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/reactome+pathway+database/reactome/pmc03817400-34-55-58
    Average 90 stars, based on 1 article reviews
    pathway and ontology databases such as go, kegg, reactome, and - by Bioz Stars, 2026-09
    90/100 stars

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    1) Product Images from "Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling"

    Article Title: Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling

    Journal: Molecular Systems Biology

    doi: 10.1038/msb.2013.50

    Number and percentage of significant coevolved MSigDB groups in different methods
    Figure Legend Snippet: Number and percentage of significant coevolved MSigDB groups in different methods

    Techniques Used:

    Related Articles

    other:

    Article Title: DPM2 serve as novel oncogene and prognostic marker transactivated by ESR1 in breast cancer.
    Article Snippet: F IGURE 4 Molecular basis for the role of dolichyl-phosphate mannosyltransferase subunit 2 (DPM2) in breast cancer. (A) The REACTOME and BIOCARTA pathway of DPM2 high/low expression group were analyzed by gene set enrichment analysis (GSEA). (B–D) The KEGG pathway of DPM2 high/low expression group was analyzed by GSEA. nloaded from https://onlinelibrary.w iley.com /doi/10.1002/tox.24059 by U FPR - U niversidade Federal do Parana, W iley O nline L ibrary on [14/03/2024].

    Article Title: De Novo Nano-Erythrocyte Structurally Braced by Biomimetic Au(I)-peptide Skeleton for MDM2/MDMX Predation toward Augmented Pulmonary Adenocarcinoma Immunotherapy.
    Article Snippet: DOI: 10.1002/smll.202100394 cancer-related mortality.. [1,2] Both in the US and China, more than one-quarter of all cancer deaths are ascribed to lung cancer.. [1–3] As a subset of lung cancer, lung adenocarcinoma (LUAD) is the main culprit in lung cancer-related deaths.

    Article Title: Phenelzine protects against acetaminophen induced apoptosis in HepG2 cells.
    Article Snippet: acetaminophen (aPaP) overdosing is the most common cause of drug-induced liver failure.. Despite extensive study, N-acetylcysteine is currently the only antidote utilized for treatment. the purpose of this study was to evaluate the effect and mechanisms of phenelzine, an FDa-approved antidepressant, on aPaP-induced toxicity in hepG2 cells. the human liver hepatocellular cell line hepG2 was used to investigate aPaP-induced cytotoxicity. the protective effects of phenelzine were determined by examining the cell viability, combination index calculation, caspase 3/7 activation, cytochrome c release, h2O2 levels, NO levels, Gsh activity, PeRK protein levels, and pathway enrichment analysis. elevated h2O2 production and decreased glutathione (Gsh) levels were indicators of aPaP-induced oxidative stress. the combination index of 2.04 indicated that phenelzine had an antagonistic effect on aPaP-induced toxicity.. When compared to aPaP alone, phenelzine treatment considerably reduced caspase 3/7 activation, cytochrome c release, and h2O2 generation. however, phenelzine had minimal effect on NO and Gsh levels and did not alleviate eR stress.

    Article Title: Deciphering the putative bioactive metabolites and the underlying mechanism of Juniperus horizontalis Moench (Creeping juniper) in the treatment of inflammation using network pharmacology and molecular docking.
    Article Snippet: On the contrary, the most enriched metabolic pathways related to the identified targets were classified into 19 KEGG pathways including arachidonic acid metabolism, lipid and atherosclerosis, and Alzheimer’s disease; 18 REACTOME pathways involving arachidonic acid metabolism and IL-4 and IL-13 signaling; 2 BBID pathways which are stress and CRH influence and stress_influences_immunity; and 2 BIOCARTA pathways that are deregulation of CDK5 in Alzheimer’s disease and IL-2 signaling pathway (Figure 3B).

    Article Title: Deregulated mRNA and microRNA Expression Patterns in the Prefrontal Cortex of the BTBR Mouse Model of Autism.
    Article Snippet: Pathway annotation analysis (KEGG pathway, reactome pathway, WikiPathways, and BioCarta) was carried out using DAVID 2021 (Dec. 2021 update) [41, 42].

    Protein-Protein interactions:

    Article Title: Random gene sets in predicting survival of patients with hepatocellular carcinoma.
    Article Snippet: Despite multiple publications, molecular signatures predicting the course of hepatocellular carcinoma (HCC) have not yet been integrated into clinical routine decision-making.. Given the diversity of published signatures, optimal number, best combinations, and benefit of functional associations of genes in prognostic signatures remain to be defined.. We investigated a vast number of randomly chosen gene sets (varying between 1 and 10,000 genes) to encompass the full range of prognostic gene sets on 242 transcriptomic profiles of patients with HCC.

    Functional Assay:

    Article Title: RTN2, a new member of circadian clock genes identified by database mining and bioinformatics prediction, is highly expressed in ovarian cancer.
    Article Snippet: in total, 217,249 PPi pairs were retrieved from reactome (v.2014; http://www.reactome.org) (16), based on BioGrid, the database of interacting Proteins (17), Human Protein reference database (18), i2d (19), intacT (20) and MinT (21), in addition to gene co‐expression data generated by high‐throughput tech‐ niques such as yeast two‐hybrid, mass spectrometry pull‐down and dna microarray assays (22). a PPi network was generated with cytoscape (v.3.2.1; http://www.cytoscape.org) (23). .. Pathway enrichment analysis for the functional interaction network. reactome FiViz was utilized in cytoscape for pathway analysis (24). cell Map (http://www.pathwaycom‐ mons.org/pc/dbSnapshot.do?snapshot_id=8), reactome (16), Kyoto encyclopedia of Genes and Genomes (25), Panther Pathways (26), nci‐Pathway interaction database (nci‐Pid) (27) and Biocarta (http://www.biocarta. com/genes/index.asp) were used as pathway annotation sources, with an Fdr of 0.05 as the cut‐off criterion. ..

    Cell Culture:

    Article Title: Identification of reversible and druggable pathways to improve beta-cell function and survival in Type 2 diabetes
    Article Snippet: .. INS1E cells were cultured in high glucose (HG, 20 mM) for 72 h or HG for an initial 24 h followed by drug addition (exendin-4, metformin and sodium salicylate) for the remaining 48 h. RNAseq (Illumina TruSeq), gene set enrichment analysis (GSEA) and pathway analysis (using Broad Institute, Reactome, KEGG and Biocarta platforms) were used to identify changes in molecular pathways. ..

    RNA sequencing:

    Article Title: Identification of reversible and druggable pathways to improve beta-cell function and survival in Type 2 diabetes
    Article Snippet: .. INS1E cells were cultured in high glucose (HG, 20 mM) for 72 h or HG for an initial 24 h followed by drug addition (exendin-4, metformin and sodium salicylate) for the remaining 48 h. RNAseq (Illumina TruSeq), gene set enrichment analysis (GSEA) and pathway analysis (using Broad Institute, Reactome, KEGG and Biocarta platforms) were used to identify changes in molecular pathways. ..



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    Image Search Results


    Number and percentage of significant coevolved MSigDB groups in different methods

    Journal: Molecular Systems Biology

    Article Title: Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling

    doi: 10.1038/msb.2013.50

    Figure Lengend Snippet: Number and percentage of significant coevolved MSigDB groups in different methods

    Article Snippet: These gene sets include genes that are significantly changed in expression in tumors ( ; ; ), gene coexpressed under similar conditions, genes that bear similar transcriptional or miRNA regulatory sequences ( ; ), or genes annotated to function in similar processes based on the pathway and ontology databases such as GO , KEGG , REACTOME , and BIOCARTA.

    Techniques:

    Data sources used by WhichGenes to automatically construct gene sets

    Journal: Nucleic Acids Research

    Article Title: WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis

    doi: 10.1093/nar/gkp263

    Figure Lengend Snippet: Data sources used by WhichGenes to automatically construct gene sets

    Article Snippet: WhichGenes currently supports queries about Homo sapiens and Mus musculus organisms by retrieving up-to-date gene lists directly coming from multiple databases, currently including Ensembl, MSigDB, KEGG/Biocarta/Reactome pathway databases, GeneCards, CancerGenes, Decipher, Diseases CTD, TargetScan, miRBase, Chemical CTD, AmiGO and IntAct.

    Techniques: Construct