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ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems

V. Kaimal, E. E. Bardes, S. C. Tabar, A. G. Jegga, B. J. Aronow
2010 Nucleic Acids Research  
ToppCluster is a web server application that leverages a powerful enrichment analysis and underlying data environment for comparative analyses of multiple gene lists.  ...  ToppCluster's functionalities enable the identification of specialized biological functions and regulatory networks and systems biology-based dissection of biological states.  ...  The principal strength of ToppCluster lies in the ability to co-analyze multiple gene lists and to depict the results in a form that facilitates comparative and contrastive analysis.  ... 
doi:10.1093/nar/gkq418 pmid:20484371 pmcid:PMC2896202 fatcat:n7oxkgbkl5hdtfjp7imygiutqm

Systems Biology Elucidates Common Pathogenic Mechanisms between Nonalcoholic and Alcoholic-Fatty Liver Disease

Silvia Sookoian, Carlos J. Pirola, Christina Chan
2013 PLoS ONE  
To answer these questions, we used systems biology approaches, such as gene enrichment analysis, protein-protein interaction networks, and gene prioritization, based on multi-level data extracted by computational  ...  , but the putative regulatory mechanisms associated with NAFLD seem to encompass a complex network of genes and proteins, plausible of epigenetic modifications.  ...  Systems biology approaches for gene enrichment analysis and protein-protein interaction networks Based on the list of genes/proteins identified as explained earlier, we decided to explore the interactions  ... 
doi:10.1371/journal.pone.0058895 pmid:23516571 pmcid:PMC3596348 fatcat:ccotipqsdzh7zfuhtlqa42hozm

Medial prefrontal cortex: genes linked to bipolar disorder and schizophrenia have altered expression in the highly social maternal phenotype

Brian E. Eisinger, Terri M. Driessen, Changjiu Zhao, Stephen C. Gammie
2014 Frontiers in Behavioral Neuroscience  
ACKNOWLEDGMENTS The authors wish to thank Sharon Stevenson for managerial support, Wayne Davis and the University of Wisconsin-Madison Gene Expression Center for microarray technical assistance, and Kate  ...  Skogen and Jeff Alexander for animal care.  ...  listed for a particular disorder is featured in all gene-disease associa- tion databases tested in this study for that disorder.  ... 
doi:10.3389/fnbeh.2014.00110 pmid:24765068 pmcid:PMC3980118 fatcat:tsknnwa3zrhapmxqlyukxjnbsi

Addiction and reward-related genes show altered expression in the postpartum nucleus accumbens

Changjiu Zhao, Brian Earl Eisinger, Terri M. Driessen, Stephen C. Gammie
2014 Frontiers in Behavioral Neuroscience  
ToppCluster analysis found maternal NAC expression profile to be significantly enriched for genes related to the drug action of nicotine, ketamine, and dronabinol.  ...  Modular Single-set Enrichment Test (MSET) indicated that postpartum (relative to virgin) NAC gene expression profile was significantly enriched for genes related to addiction and reward in five of five  ...  ACKNOWLEDGMENTS The authors wish to thank Sharon Stevenson for managerial support, Wayne Davis and the University of Wisconsin-Madison Gene Expression Center for microarray technical assistance, and Kate  ... 
doi:10.3389/fnbeh.2014.00388 pmid:25414651 pmcid:PMC4220701 fatcat:oylv5rmehrbypaggttxyuqhtoy

MicroRNA-21 Limits In Vivo Immune Response-Mediated Activation of the IL-12/IFN- Pathway, Th1 Polarization, and the Severity of Delayed-Type Hypersensitivity

T. X. Lu, J. Hartner, E.-J. Lim, V. Fabry, M. K. Mingler, E. T. Cole, S. H. Orkin, B. J. Aronow, M. E. Rothenberg
2011 Journal of Immunology  
Hottinger for editorial assistance. Disclosures M.E.R. has an equity interest in reslizumab, a drug being developed by Cephalon, Inc. The other authors have no financial conflicts of interest.  ...  for comparative enrichment clustering and networkbased dissection of biological systems (Fig. 2C) (18) .  ...  To better understand the potential molecular basis and consequences of the dysregulated IL-12/IFN-g pathway, we performed biological network analyses using Toppcluster, a multiple gene list feature analyzer  ... 
doi:10.4049/jimmunol.1101235 pmid:21849676 pmcid:PMC3175642 fatcat:kf7vtcdn55atlektbwqwe26bfa

An Observational Study on the Molecular Profiling of Primary Melanomas Reveals a Progression Dependence on Mitochondrial Activation

Jeovanis Gil, Melinda Rezeli, Elmar G. Lutz, Yonghyo Kim, Yutaka Sugihara, Johan Malm, Yevgeniy R. Semenov, Kun-Hsing Yu, Nga Nguyen, Guihong Wan, Lajos V. Kemény, Sarolta Kárpáti (+2 others)
2021 Cancers  
Most of the pathways dysregulated in this cohort were enriched in genes differentially expressed at the transcript level when similar groups are compared or metastasis to primary melanomas.  ...  Remarkably, primary melanomas in women showed higher levels of antigen processing and presentation, and activation of the immune system response.  ...  This work was done under the auspices of a Memorandum of Understanding between the European Cancer Moonshot Center in Lund and the U.S.  ... 
doi:10.3390/cancers13236066 pmid:34885173 fatcat:3rfn5dacl5fhlocq5yz4dawjhq

SOX2 regulates common and specific stem cell features in the CNS and endoderm derived organs

Daniel W. Hagey, Susanne Klum, Idha Kurtsdotter, Cecile Zaouter, Danijal Topcic, Olov Andersson, Maria Bergsland, Jonas Muhr, Hisato Kondoh
2018 PLoS Genetics  
We demonstrate that, although SOX2 binds a similar motif in the different cell types, its target regions are primarily cell-type-specific and enriched for the distinct binding motifs of appropriately expressed  ...  Stem cells are defined by their capacities to self-renew and generate progeny of multiple lineages.  ...  Holmberg for comments on the manuscript and members of the Muhr lab for fruitful discussions and advice.  ... 
doi:10.1371/journal.pgen.1007224 pmid:29432416 pmcid:PMC5825159 fatcat:7bbzk6dhqfdcpjify7q7ymildm

Disease Severity Is Associated with Differential Gene Expression at the Early and Late Phases of Infection in Nonhuman Primates Infected with Different H5N1 Highly Pathogenic Avian Influenza Viruses

Y. Muramoto, J. E. Shoemaker, M. Q. Le, Y. Itoh, D. Tamura, Y. Sakai-Tagawa, H. Imai, R. Uraki, R. Takano, E. Kawakami, M. Ito, K. Okamoto (+9 others)
2014 Journal of Virology  
to a failure to suppress virus replication and to the hyperinduction of genes related to immunity, inflammation, coagulation, and homeostasis in the late phase of infection, resulting in a more severe  ...  A comparison of global gene expression between severe and mild disease cases indicated that interferon-induced upregulation of genes related to innate immunity, apoptosis, and antigen processing/presentation  ...  This study was supported by a Grant-in-Aid for Specially Promoted Research, by the Japan Initiative for Global Research Network on Infectious Diseases from the Ministry of Education, Culture, Sports, Science  ... 
doi:10.1128/jvi.00907-14 pmid:24899188 pmcid:PMC4136255 fatcat:fsas6xrdw5ed5ovy3cyhqrpur4

An Examination of Dynamic Gene Expression Changes in the Mouse Brain During Pregnancy and the Postpartum Period

Surjyendu Ray, Ruei-Ying Tzeng, Lisa M. DiCarlo, Joseph L. Bundy, Cynthia Vied, Gary Tyson, Richard Nowakowski, Michelle N. Arbeitman
2015 G3: Genes, Genomes, Genetics  
Interestingly, a set of "early-response genes" is repressed in all brain regions during pregnancy and postpartum stages.  ...  We find that overall there are hundreds of differentially expressed genes, but each brain region and time point shows a unique molecular signature, with only 49 genes differentially expressed in all four  ...  ACKNOWLEDGMENTS We are thankful for helpful reviewer comments and suggestions and comments from laboratory members.  ... 
doi:10.1534/g3.115.020982 pmid:26596646 pmcid:PMC4704721 fatcat:jzapzi5iqnftretvfpg2flpx2y

Region-Specific PSD-95 Interactomes Contribute to Functional Diversity of Excitatory Synapses in Human Brain [article]

Adam Funk, Guillaume Labilloy, James Reigle, Rawan Alnafisah, Michael Heaven, Rosalinda Roberts, Behrouz Shamsaei, Kenneth Greis, Jarek Meller, Robert McCullumsmith
2020 bioRxiv   pre-print
We isolated postsynaptic density95 (PSD-95) complexes from four human brain regions and compared their protein interactomes using multiple bioinformatics techniques.  ...  The overarching goal of this exploratory study is to link subcellular microdomain specific protein-protein interactomes with big data analytics.  ...  ., ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems. Nucleic Acids Res, 2010. 38(Web Server issue): p.  ... 
doi:10.1101/2020.05.04.076844 fatcat:n7ce6qlf35b5hodjf3k6ckngsa

Comparative gene expression analysis of genital tubercle development reveals a putative appendicular Wnt7 network for the epidermal differentiation

Han Sheng Chiu, John C. Szucsik, Kylie M. Georgas, Julia L. Jones, Bree A. Rumballe, Dave Tang, Sean M. Grimmond, Alfor G. Lewis, Bruce J. Aronow, James L. Lessard, Melissa H. Little
2010 Developmental Biology  
Comparison of spatial expression patterns predicted a network of Wnt7a-associated GT-enriched epithelial genes, including Gjb2, Dsc3, Krt5, and Sostdc1.  ...  We propose that this gene network contributes to normal foreskin, scrotum, and labial development.  ...  We also thank Carol Wicking for scientific opinion on limb and facial development. ML is a Principal Research Fellow of the National Health and Medical Research Council.  ... 
doi:10.1016/j.ydbio.2010.05.495 pmid:20510229 pmcid:PMC3154616 fatcat:x7v426o3rbfjzemubmg2jlrprm

Inhibition of endocytic lipid antigen presentation by common lipophilic environmental pollutants

Manju Sharma, Xiang Zhang, Shuangmin Zhang, Liang Niu, Shuk-mei Ho, Aimin Chen, Shouxiong Huang
2017 Scientific Reports  
The process by which lipophilic pollutants target innate and adaptive immune systems to disrupt the homeostasis of inflammatory responses and trigger multiple diseases remains elusive.  ...  Using transcriptomic profiling, we discovered that the gene expression for regulating endocytic and lipid metabolic pathways was perturbed by benzo[a]pyrene.  ...  ToppCluster uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis (  ... 
doi:10.1038/s41598-017-02229-7 pmid:28522830 pmcid:PMC5437007 fatcat:m6j3s77ayvh5xaupfjzaepg3he

Natural Selection and Functional Potentials of Human Noncoding Elements Revealed by Analysis of Next Generation Sequencing Data

Pankaj Jha, Dongsheng Lu, Shuhua Xu, Ge Zhang
2015 PLoS ONE  
Notably, NCS elements are enriched for potentially functional markers such as eQTLs, TF motif, and DNase I footprints in the genome.  ...  We estimated a series of key parameters of population genetics and molecular evolution to characterize sequence variations of the noncoding genome within and between populations, and identified the natural  ...  Acknowledgments Wethank the 1000 Genomes Project Consortium for generatingdata and providing resources to public research.  ... 
doi:10.1371/journal.pone.0129023 pmid:26053627 pmcid:PMC4460046 fatcat:vcubmi44ynbx3gmv2jvtnfwnvu

MicroRNA-425-5p Expression Affects BRAF/RAS/MAPK Pathways In Colorectal Cancers

Andrea Angius, Giovanna Pira, Antonio Mario Scanu, Paolo Uva, Giovanni Sotgiu, Laura Saderi, Alessandra Manca, Caterina Serra, Elena Uleri, Claudia Piu, Maurizio Caocci, Gabriele Ibba (+7 others)
2019 International Journal of Medical Sciences  
a complex molecular network.  ...  This class of molecules represents an opportunity for the development of miRNA-based strategies to overcome the ineffectiveness of anti-EGFR therapy.  ...  Ciriaco Carru, from the Department of Biomedical Sciences of the University of Sassari, for his suggestions during the planning of the study and for the financial support, granted by Ministero dell'Istruzione  ... 
doi:10.7150/ijms.35269 pmid:31673240 pmcid:PMC6818206 fatcat:mdw7lssperaxph3cnb2wduhuk4

Developmental dynamics of the postsynaptic proteome to understand synaptic maturation and dysmaturation [article]

Takeshi Kaizuka, Takehiro Suzuki, Noriyuki Kishi, Manfred W Kilimann, Takehiko Ueyama, Masahiko Watanabe, Hideyuki Okano, Naoshi Dohmae, Toru Takumi
2022 bioRxiv   pre-print
Proteins involved in synapse regulation are enriched in the differentially expressed (288 decreased and 267 increased) proteins on mouse PSD after a 2-week-old.  ...  Our results provide a comprehensive architecture of the remodeling of PSD composition across development, which may explain the molecular basics of synapse maturation and the pathology of psychiatric disorders  ...  Acknowledgments We thank Kaori Otsuki and Shungo Adachi for the helpful discussion and all the Takumi laboratory technical staff for their assistance in preparing the experimental reagent.  ... 
doi:10.1101/2022.05.05.490828 fatcat:iwye5bsgljajlahpmtb6i4jbgy
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