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ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
2009
Nucleic Acids Research
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ToppGene Suite (http://toppgene.cchmc.org; this web site is free and open to all users and does not require a login to access) is a one-stop portal for (i) gene list functional enrichment, (ii) candidate ...
gene prioritization using either functional annotations or network analysis and (iii) identification and prioritization of novel disease candidate genes in the interactome. ...
TOPPFUN: GENE LIST FUNCTIONAL ENRICHMENT ToppFun can be used for gene list functional enrichment analysis. ...
doi:10.1093/nar/gkp427
pmid:19465376
pmcid:PMC2703978
fatcat:z6bxoqqcxvdetcdl55w3vjyzge
Prioritization of candidate genes for attention deficit hyperactivity disorder by computational analysis of multiple data sources
2012
Protein & Cell
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In this study, we surveyed the computational tools for candidate gene prioritization and selected five tools, which integrate multiple data sources for gene prioritization, to prioritize ADHD candidate ...
The prioritization analysis resulted in 16 prioritized candidate genes, which are mainly involved in several major neurotransmitter systems or in nervous system development pathways. ...
ToppGene and ToppNet are in one suite of tools for gene functional enrichment and prioritization (Chen et al., 2009b) . ...
doi:10.1007/s13238-012-2931-7
pmid:22773342
pmcid:PMC4875392
fatcat:uns4t2gfcrgaro45umkxlx7ygm
Chronic obstructive pulmonary disease candidate gene prioritization based on metabolic networks and functional information
2017
PLoS ONE
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The gene prioritization method was superior to ToppGene and ToppNet in both literature validation and functional enrichment analysis. ...
Top 100 genes might be potential markers for diagnostic and effective therapies. ...
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic acids research. 2009; 37(Web Server issue):W305-11. ...
doi:10.1371/journal.pone.0184299
pmid:28873096
pmcid:PMC5584748
fatcat:ty5tuuipvrdencapbufdrucg3y
Candidate gene prioritization for chronic obstructive pulmonary disease using expression information in protein–protein interaction networks
2021
BMC Pulmonary Medicine
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Top-ranked COPD candidate genes and their significantly enriched functions were verified to be related to COPD. ...
Results Further analysis demonstrated that the PEP method was robust in prioritizing disease candidate genes, and superior to other existing prioritization methods exploiting either topological or functional ...
Functional enrichment analysis Functional enrichment analysis was performed for the 200 candidate genes using DAVID. ...
doi:10.1186/s12890-021-01646-9
pmid:34481483
pmcid:PMC8418003
fatcat:fhw27nvzjrcifcg3qrckznoiiy
An Outranking Approach for Gene Prioritization Using Multinetworks
2021
International Journal of Computational Intelligence Systems
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Comparison to Gene Prioritization Network Tools Using Predictive Analysis We compare our integrative approach for prioritization to the gene prioritization tool ToppNet in the ToppGene suite [60] a stateof-the-art ...
GO enrichment analysis for nontop prioritized genes using our integrative approach mainly lay within GO metabolic and cellular processes. ...
doi:10.2991/ijcis.d.210608.003
fatcat:tqwvtvhg4zbojagz6lv54fzhk4
Unsupervised gene expression analyses identify IPF-severity correlated signatures, associated genes and biomarkers
2017
BMC Pulmonary Medicine
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Methods: We used data-driven unsupervised clustering analysis, combined with a knowledge-based approach to identify and characterize IPF subgroups. ...
However, the considerable heterogeneity in IPF presentation suggests that differences in gene expression profiles can help to characterize and distinguish disease severity. ...
Authors' contributions AJ and YW conceived the project, analyzed data and wrote the manuscript. JC participated in the data analysis. JY and YW implemented the Web portal. ...
doi:10.1186/s12890-017-0472-9
pmid:29058630
pmcid:PMC5649521
fatcat:odiy36xopfdpreychuuh7iwqoa
Applying Systems Biology Methodology To Identify Genetic Factors Possibly Associated with Recovery after Traumatic Brain Injury
2017
Journal of Neurotrauma
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Current genetic studies related to TBI have focused on specific candidate genes. ...
to ascertain the interactions between molecular components and to develop models for regulation and function of genes involved in TBI recovery. ...
Acknowledgments Funding for this work was supported, in part, by the Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01NS096053 and K23HD074683), National Institute of ...
doi:10.1089/neu.2016.4856
pmid:28301983
pmcid:PMC5510694
fatcat:lmmrhzv7ljdgbinp7v4cc7ldtq
Identification of candidate genes for lung adenocarcinoma using Toppgene
2010
Chinese Journal of Lung Cancer
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It is demonstrated that Toppgene is useful in identification of the candidate genes of lung adenocacinoma, which provides the proof for the discovery of the specific disease genes. ...
Finally, candidate genes of lung adenocarcinoma were screened by the tool "Toppgene". ...
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucl Acids Res, 2009, 37 (web server issue) : W305-W311. hsa04080)相关。 ...
doi:10.3779/j.issn.1009-3419.2010.04.02
pmid:20677550
pmcid:PMC6000438
fatcat:wuwtot57ybbapprlhvskehl6zq
Prioritizing Disease Candidate Proteins in Cardiomyopathy-Specific Protein-Protein Interaction Networks Based on "Guilt by Association" Analysis
2013
PLoS ONE
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Based on "guilt by association" analysis, we prioritized candidate proteins involving in human cardiomyopathies. ...
We then developed a method in prioritizing disease candidate proteins to rank candidate proteins in the network based on "guilt by association" analysis. ...
DADA was built up as a suite to prioritize disease candidate genes accounting for the degree distribution of known disease and candidate genes, using a PPI network [33] . ...
doi:10.1371/journal.pone.0071191
pmid:23940716
pmcid:PMC3733802
fatcat:ixb5h3loc5gxtkiwlv5gocdcoi
Genome-wide association study to identify genomic regions and positional candidate genes associated with male fertility in beef cattle
2020
Scientific Reports
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Functional candidate gene prioritization analysis revealed 14 prioritized candidate genes for SC of which MAP3K1 and VIP were previously found to play roles in male fertility. ...
Significant enrichment results were identified for fertility and body conformation QTLs within the candidate windows. ...
*Prioritized candidate gene identified by GUILDify and ToppGene analysis. Sperm motility genome wide association study and QTL enrichment. ...
doi:10.1038/s41598-020-75758-3
pmid:33208801
pmcid:PMC7676258
fatcat:wsp6itwuvfaytprttetewxkyse
Functional relevance for central cornea thickness-associated genetic variants by using integrative analyses
2018
BioData Mining
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Functional annotations were conducted by CADD, GWAVA, and Eigen. Enrichment analyses for CCT-associated genes were performed using ToppGene suite. ...
Methods: Integrative analyses including functional annotations, enrichment analysis, and protein-protein interaction analyses were performed on all reported CCT GWAS lead SNPs, together with their proxy ...
Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Received: 24 February 2018 Accepted: 29 July 2018 ...
doi:10.1186/s13040-018-0179-3
pmid:30127857
pmcid:PMC6094462
fatcat:uyu72kgalzfe3eibj4xodznl4u
Transcriptional profile of SH-SY5Y human neuroblastoma cells transfected by Toxoplasma rhoptry protein 16
2016
Molecular Medicine Reports
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The ToppGene Suite was used to select candidate genes from the differentially expressed genes. ...
A total of 15 candidate genes from the DEGs were screened using the ToppGene Suite. No significant differences in expression were observed between the RT-qPCR data and the microarray data. ...
ToppGene Suite is an advanced bioinformatics tool for examining and prioritizing candidate genes through comprehensive assessment of factors, including GO annotation, phenotype, signaling pathway and protein ...
doi:10.3892/mmr.2016.5758
pmid:27666388
pmcid:PMC5101894
fatcat:75vwx4va4zgenjjujmcwl3whaq
Genome-wide association study of antipsychotic-induced sinus bradycardia in Chinese schizophrenia patients
2021
PLoS ONE
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The result of gene prioritization analysis showed CTNNA3 was strongly correlated with sinus bradycardia, hinting it was a susceptibility gene of this ADR. ...
Using gene-set functional analysis, we tested that if top 500 SNPs mapped genes were relevant to sinus bradycardia. ...
Acknowledgments We thank Haifeng Li from Institutes for Shanghai Pudong Decoding Life for assistance and valuable discussion with the data analysis. ...
doi:10.1371/journal.pone.0249997
pmid:33914752
fatcat:2y6axo3idvenpglqzcr7delbmi
ToppMiR: ranking microRNAs and their mRNA targets based on biological functions and context
2014
Nucleic Acids Research
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associated annotations are used to train a machine learning-based analysis engine. ...
This scoring matrix is then used to jointly rank both the test/candidate miRs and mRNAs. Results of these analyses are provided as downloadable tables or network file formats usable in Cytoscape. ...
Gene set functional enrichment ToppMiR adopts the approaches of gene set functional enrichment analysis from ToppGene Suite which applies Hypergeometric distribution with Bonferroni or False Discovery ...
doi:10.1093/nar/gku409
pmid:24829448
pmcid:PMC4086116
fatcat:xfiekqshmne4roqwleqep3bc6y
Database for Gene Variants and Metabolic Networks Implicated in Familial Gastroschisis
2019
Data
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This is the first database for gene variants and metabolic networks implicated in familial gastroschisis. ...
bioinformatic-aided analysis can help to address new insights into human biology and molecular mechanisms involved in gastroschisis. ...
Acknowledgments: The authors are grateful to the participating family for their valuable cooperation. ...
doi:10.3390/data4030097
fatcat:h6ueruofufgurlylhzum3sh2ji
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