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GO-Elite: a flexible solution for pathway and ontology over-representation

Alexander C. Zambon, Stan Gaj, Isaac Ho, Kristina Hanspers, Karen Vranizan, Chris T. Evelo, Bruce R. Conklin, Alexander R. Pico, Nathan Salomonis
2012 Computer applications in the biosciences : CABIOS  
We introduce GO-Elite, a flexible and powerful pathway analysis tool for a wide array of species, identifiers (IDs), pathways, ontologies and gene sets.  ...  In addition to the Gene Ontology (GO), GO-Elite allows the user to perform over-representation analysis on any structured ontology annotations, pathway database or biological IDs (e.g. gene, protein or  ...  Huang and Dr John H. Morris for their assistance in establishing the GO-Elite web service.  ... 
doi:10.1093/bioinformatics/bts366 pmid:22743224 pmcid:PMC3413395 fatcat:dayn6pkilrb4pctr77bo457g5e

AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species

Du Zhang, Qi Hu, Xinxing Liu, Kai Zou, Emmanuel Konadu Sarkodie, Xueduan Liu, Fei Gao
2020 BMC Bioinformatics  
model and non-model species from a different function classification perspective.  ...  We developed AllEnricher, a tool that calculates gene set function enrichment, with user-defined updatable libraries backing up for both model and non-model species as well as providing comprehensive functional  ...  Any restrictions to use by non-academics: non-academic use of KEGG pathway analysis generally requires a commercial license (refers to https://www. kegg.jp/kegg/legal.html).  ... 
doi:10.1186/s12859-020-3408-y pmid:32183716 fatcat:vwz7dpohdrcodb4mjcjlbk4r5m

Differential protein expression of hippocampal cells associated with heavy metals (Pb, As, and MeHg) neurotoxicity: Deepening into the molecular mechanism of neurodegenerative diseases

Venkatanaidu Karri, David Ramos, Julia Bauzá Martinez, Antonia Odena, Eliandre Oliveira, Susan L. Coort, Chris T. Evelo, Edwin C.M. Mariman, Marta Schuhmacher, Vikas Kumar
2018 Journal of Proteomics  
The functional and pathway visualization was performed by using Gene ontology and PathVisio tools.  ...  Hereby, the molecular information provided by pathway and gene functional analysis can be used to develop a more thorough understanding of each metal mechanism at the protein level for different neurological  ...  The Community and other funding organizations are not liable for any use made of the information contained therein. Appendix A.  ... 
doi:10.1016/j.jprot.2018.06.020 pmid:30017948 fatcat:svwa7cphtbgdjga7gh5lvxqxgm

Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes

Naoki Osato
2018 BMC Genomics  
It is made available under a The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/085654 doi: bioRxiv preprint first posted online Nov. 4, 2016; expression level of transcriptional  ...  16 enrichment and gene expression level of putative transcriptional target genes. 17 18 Results: Gene Ontology annotations showed four times larger numbers of functional 19 enrichments in putative transcriptional  ...  Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico 744 AR, Salomonis N: GO-Elite: a flexible solution for pathway and ontology 745 over-representation.  ... 
doi:10.1186/s12864-017-4339-5 pmid:29363429 pmcid:PMC5780744 fatcat:pbtqjkr6gzeb7jwhefwfwbhdka

Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes [article]

Naoki Osato
2016 bioRxiv   pre-print
Results: Gene Ontology annotations showed four times larger numbers of functional enrichments in putative transcriptional target genes than gene expression information alone, independent of transcriptional  ...  These analyses and characters of human putative transcriptional target genes would be useful to examine the criteria of enhancer-promoter assignments and to predict the novel mechanisms and factors such  ...  Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico 744 AR, Salomonis N: GO-Elite: a flexible solution for pathway and ontology 745 over-representation.  ... 
doi:10.1101/085654 fatcat:acgfuirhhranrexqkxbguii63q

ENOX2 NADH Oxidase: A BCR-ABL1-dependent cell surface and secreted redox protein in chronic myeloid leukemia (CML) [article]

Seda Baykal Kose, Maud Voldoire, Christophe Desterke, Nathalie Sorel, Emilie Cayssials, Hyacinthe Johnson-Ansah, Agnes Guerci-Bresler, Annelise Bennaceur-Griscelli, Jean Claude Chomel, Ali G Turhan
2021 bioRxiv   pre-print
All in all, our results demonstrate for the first time the upregulation of a secreted Redox protein in a BCR-ABL1-dependent manner in CML.  ...  Western-blot analyses on UT-7 and TET-inducible Ba/F3 cell lines established the up-regulation of ENOX2 protein. BCR-ABL1 has been found to induce ENOX2 overexpression in a kinase-dependent manner.  ...  Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, et al. (2012) GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinformatics. 28: 2209-2210. 22.  ... 
doi:10.1101/2021.01.23.427819 fatcat:incentmyz5hyzjmv24s4xe7piy

Systematic transcriptomics reveals a biphasic mode of sarcomere morphogenesis in flight muscles regulated by Spalt [article]

Maria L Spletter, Christiane Barz, Assa Yeroslaviz, Xu Zhang, Sandra B Lemke, Erich Brunner, Giovanni Cardone, Konrad Basler, Bianca H Habermann, Frank Schnorrer
2017 bioRxiv   pre-print
Together, this defines a biphasic mode of sarcomere and myofibril morphogenesis - a new concept that may also apply to vertebrate muscle or heart development.  ...  Strikingly, two clusters are strongly enriched for sarcomeric components.  ...  Acknowledgements We thank Irene Ferreira for constructing the tagged kon-tiki allele and the Bloomington and VDRC stock centers for fly stocks.  ... 
doi:10.1101/229534 fatcat:6erotvez5jatne6cgkzodl2dr4

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

Luis de la Torre-Ubieta, Jason L. Stein, Hyejung Won, Carli K. Opland, Dan Liang, Daning Lu, Daniel H. Geschwind
2018 Cell  
GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinformatics 28, 2209-2210.  ...  DE protein-coding genes were input into GO-Elite (Zambon et al., 2012) (v1.2.5) using ontologies from EnsMart77Plus with a background list of all protein-coding genes (Figures S4A and S4B) .  ...  An enrichment in heritability explained was found in both fetal and adult chromatin accessibility peaks for schizophrenia and educational attainment.  ... 
doi:10.1016/j.cell.2017.12.014 pmid:29307494 pmcid:PMC5924568 fatcat:oxnoe6m7wjgufcc3mrxmvhennq

RNA-binding proteins with mixed charge domains self-assemble and aggregate in Alzheimer's Disease [article]

Isaac Bishof, Eric B Dammer, Duc M Duong, Marla Gearing, James J Lah, Allan I Levey, Nicholas T Seyfried
2018 bioRxiv   pre-print
This included structurally similar RBPs, such as LUC7L3 and RBM25, which require their respective mixed charge domains for reciprocal interactions with U1-70K and for participation in nuclear RNA granules  ...  A network-driven approach resolved functional classes of U1-70K interacting proteins that showed dependency on the U1-70K LC domain(s) for their interaction.  ...  I.B was funded by a pre-doctoral T32 NINDS training grant 3T32NS007480-16 and F31 NRSA grant F31NS09385902. We also acknowledge Dr.  ... 
doi:10.1101/243014 fatcat:owkvrbmrb5gs7dyehqfvyzayeq

A Network Approach Reveals Driver Genes Associated with Triple Negative Breast Cancer Patient Survival

Courtney D. Dill, Eric B. Dammer, Ti'ara L. Griffen, Nicholas T. Seyfried, James W. Lillard
2021 iScience  
Complementary coexpression, differential expression, genetic interaction, and survival stratification integrated by ROC optimization uncovered a panel of "linchpin survival genes" predictive of patient  ...  Finally, we tested whether integration of literature-derived genes for implicated hallmark cancer processes could improve prediction of survival.  ...  ., and Salomonis, N. (2012). GO-Elite: a flexible solution for pathway and ontology overrepresentation. Bioinformatics 28, 2209-2210. D. Dill, Eric B. Dammer, Ti'ara L. Griffen, Nicholas T.  ... 
doi:10.1016/j.isci.2021.102451 pmid:34007962 pmcid:PMC8111681 fatcat:iytrgw2lgnckthe2mgxxf4y7zy

Integrative Functional Genomic Analyses Implicate Specific Molecular Pathways and Circuits in Autism

Neelroop N. Parikshak, Rui Luo, Alice Zhang, Hyejung Won, Jennifer K. Lowe, Vijayendran Chandran, Steve Horvath, Daniel H. Geschwind
2013 Cell  
Furthermore, we show that the patterns of ASD and ID risk genes are distinct, providing a biological framework for further investigating the pathophysiology of ASD.  ...  At a circuit level, ASD genes are enriched in superficial cortical layers and glutamatergic projection neurons.  ...  ., Conklin, cognition: unexpected roles for chromatin. Nat. Rev. Genet. 14, 347–359. B.R., Pico, A.R., and Salomonis, N. (2012). GO-Elite: a flexible solution for Ropers, H.H. (2008).  ... 
doi:10.1016/j.cell.2013.10.031 pmid:24267887 pmcid:PMC3934107 fatcat:itxsorwonncp7ofukptfstc5di

Complexity and graded regulation of neuronal cell type-specific alternative splicing revealed by single-cell RNA sequencing [article]

Huijuan Feng, Daniel F Moakley, Shuonan Chen, Melissa G McKenzie, Vilas Menon, Chaolin Zhang
2021 bioRxiv   pre-print
The enormous neuronal cellular diversity in the mammalian brain, which is highly prototypical and organized in a hierarchical manner, is dictated by cell type-specific gene regulatory programs at the molecular  ...  Here we systematically investigated AS regulation across over 100 transcriptomically defined neuronal types of the adult mouse cortex using deep single cell RNA-sequencing (scRNA-seq) data.  ...  ., GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinformatics 28, 2209-2210 (2012). of digital gene expression data. Bioinformatics 26, 139-140 (2010). 61. S.  ... 
doi:10.1101/2021.01.27.428525 fatcat:cviz32jel5fp3dgk6clbvkbke4

BRG1/BRM-associated factor complex subunit diversity promotes temporally distinct gene expression programs in cardiogenesis [article]

Swetansu Hota, Jeffrey Johnson, Erik Verschueren, Yiwen Zhu, Xin Sun, Len Pennacchio, Janet Rossant, Nevan Krogan, Benoit Bruneau
2017 bioRxiv   pre-print
The catalytic subunit Brg1 has a specific role in CPs to initiate cardiac gene expression programs and repress non-cardiac fates, a role shared by Baf60c and Baf170.  ...  In CMs, BAF60c and BAF170 are found in BRG1 and BRM-associated complexes, and are essential for maintaining the cardiac program, largely by repressing non-cardiac gene expression.  ...  Acknowledgements We thank Katherine Pollard for advice and guidance on computational aspects of this project. We thank A. Williams and S. Thomas (Gladstone Bioinformatics Core) for data analysis, L.  ... 
doi:10.1101/166983 fatcat:7nvsowlk6jhutk5uiwumy6diiu

Transcriptomic networks implicate neuronal energetic abnormalities in three mouse models harboring autism and schizophrenia-associated mutations [article]

Aaron Gordon, Annika Gronborg-Forsingdal, Ib Vestergaard Klewe, Jacob Nielsen, Michael Didriksen, Thomas Werge, Daniel H Geschwind
2019 bioRxiv   pre-print
A growing body of genetic and genomic studies suggest that such shared molecular pathways exist across disorders with different clinical presentations, such as schizophrenia and autism spectrum disorder  ...  Genetic risk for psychiatric illness is complex, so identification of shared molecular pathways where distinct forms of genetic risk might coincide is of substantial interest.  ...  GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinformatics 2012; 28(16): 2209-2210.  ... 
doi:10.1101/625368 fatcat:mgu45ro5ira3pficrth4my5ooq

Position, the command of expressive space : the function of ritual and legitimacy instanced in late twentieth century Australia theatre [article]

Garry Fry, University, The Australian National, University, The Australian National
2018
The 'popular group' in the playground, the fashionable party-going elite of the teenage environment at her school encourage Lennie, her friend, to join them.  ...  His orientation is an ontology of communication and appears to focus on the social representations adopted in relation to argumentation.  ...  A stated aim of the Association of Community Theatres for the Festival expressed its central concern for broad representation in Australian theatre: to celebrate the emergence of indigenous Australian  ... 
doi:10.25911/5d63be34f2daf fatcat:t7vaomvyivetbh2xzgrffd4kq4
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