Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Maxim V. Kuleshov,Matthew R. Jones,Andrew D. Rouillard,Nicolas F. Fernandez,Qiaonan Duan,Zichen Wang,Simon Koplev,Sherry L. Jenkins,Kathleen M. Jagodnik,Alexander Lachmann,Michael G. McDermott,Caroline D. Monteiro,Gregory W. Gundersen,Avi Ma'ayan +13 more
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TLDR
A significant update to one of the tools in this domain called Enrichr, a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries is presented.Abstract:
Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.read more
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Ubiquitin-Specific Protease USP6 Regulates the Stability of the c-Jun Protein.
Lisheng Li,Hong Yang,Yan He,Ting Li,Jinan Feng,Wanze Chen,Lu Ao,Xuying Shi,Yingying Lin,Haoyun Liu,Enrun Zheng,Qiaofa Lin,Jingjing Bu,Yanhua Zeng,Min Zheng,Yan Xu,Zhijun Liao,Jiacheng Lin,Dexin Lin +18 more
TL;DR: USP6 is an enzyme that deubiquitinates c-Jun and regulates its downstream cellular functions and many aberrant genes that are upregulated in USP6 translocated nodular fasciitis are great potential targets regulated by c- Jun.
Journal ArticleDOI
Genome-wide DNA methylation analysis of heavy cannabis exposure in a New Zealand longitudinal cohort.
Amy J. Osborne,John F. Pearson,Alexandra J. Noble,Neil J. Gemmell,L. John Horwood,Joseph M. Boden,Miles C. Benton,Donia Macartney-Coxson,Martin A. Kennedy +8 more
TL;DR: The effects of cannabis use on the mature human blood methylome differ from, and are less pronounced than, the effects of tobacco use, and that larger sample sizes are required to investigate this further.
ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis （SCI影响因子IF=5.5）
TL;DR: This work proposes a powerful computational method, Edge Set Enrichment Analysis (ESEA), for the identification of dysregulated pathways, and develops a freely available R-based tool of ESEA, which can support pathway analysis of the seven public databases.
Journal ArticleDOI
DNA Methylation Trajectories During Pregnancy
Olena Gruzieva,Olena Gruzieva,Simon Kebede Merid,Su Chen,Nandini Mukherjee,Anna Hedman,Catarina Almqvist,Catarina Almqvist,Ellika Andolf,Yu Jiang,Juha Kere,Juha Kere,Juha Kere,Annika Scheynius,Annika Scheynius,Annika Scheynius,Cilla Söderhäll,Vilhelmina Ullemar,Wilfried Karmaus,Erik Melén,Erik Melén,Syed Hasan Arshad,Göran Pershagen,Göran Pershagen +23 more
TL;DR: Biological pathway analysis demonstrated that FDR-significant CpGs belong to genes overrepresented in metabolism-related pathways, such as adipose tissue development, regulation of insulin receptor signaling, and mammary gland fat development, which contribute to a better understanding of the biological mechanisms underlying important physiological alterations and adaptations for pregnancy and lactation.
Journal ArticleDOI
Human induced pluripotent stem cell-derived vocal fold mucosa mimics development and responses to smoke exposure
TL;DR: E engineered VF mucosae from hiPSC, transfected via TALEN constructs for green fluorescent protein, that mimic development of VF epithelial cells in utero are developed and inflammation on exposure to cigarette smoke abstract is demonstrated.
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