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ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

J. Chen, E. E. Bardes, B. J. Aronow, A. G. Jegga
2009 Nucleic Acids Research  
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

Suhua Chang, Weina Zhang, Lei Gao, Jing Wang
2012 Protein & Cell  
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

Xinyan Wang, Wan Li, Yihua Zhang, Yuyan Feng, Xilei Zhao, Yuehan He, Jun Zhang, Lina Chen, Aran Singanayagam
2017 PLoS ONE  
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

Wan Li, Yihua Zhang, Yahui Wang, Zherou Rong, Chenyu Liu, Hui Miao, Hongwei Chen, Yuehan He, Weiming He, Lina Chen
2021 BMC Pulmonary Medicine  
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

Jesús Jaime Solano Noriega, Juan Carlos Leyva López, Fiona Browne, Jun Liu
2021 International Journal of Computational Intelligence Systems  
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

Yunguan Wang, Jaswanth Yella, Jing Chen, Francis X. McCormack, Satish K. Madala, Anil G. Jegga
2017 BMC Pulmonary Medicine  
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

Brad G. Kurowski, Amery Treble-Barna, Alexis J. Pitzer, Shari L. Wade, Lisa J. Martin, Ranjit S. Chima, Anil Jegga
2017 Journal of Neurotrauma  
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

Guiping Wang, Yun Ye, Wenling Zheng, Wenli Ma
2010 Chinese Journal of Lung Cancer  
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

Wan Li, Lina Chen, Weiming He, Weiguo Li, Xiaoli Qu, Binhua Liang, Qianping Gao, Chenchen Feng, Xu Jia, Yana Lv, Siya Zhang, Xia Li (+1 others)
2013 PLoS ONE  
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

H. Sweett, P. A. S. Fonseca, A. Suárez-Vega, A. Livernois, F. Miglior, A. Cánovas
2020 Scientific Reports  
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

Jing Zhang, Dan Wu, Yiqin Dai, Jianjiang Xu
2018 BioData Mining  
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

Weiwei Fan, Shuang Chang, Xiumei Shan, Dejun Gao, Steven Qian Zhang, Jin Zhang, Nan Jiang, Duan Ma, Zuohua Mao
2016 Molecular Medicine Reports  
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

Saizheng Weng, Bo Wang, Mo Li, Shan Chao, Ruiqian Lin, Rongyan Zheng, Yinliang Yu, Shaonan Guo, Xianhao Lin, Yun Li
2021 PLoS ONE  
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

Chao Wu, Eric E. Bardes, Anil G. Jegga, Bruce J. Aronow
2014 Nucleic Acids Research  
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

Víctor M. Salinas-Torres, Hugo L. Gallardo-Blanco, Rafael A. Salinas-Torres, Laura E. Martínez de Villarreal
2019 Data  
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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