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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SUPERGNOVA: local genetic correlation analysis reveals heterogeneous etiologic sharing of complex traits.
Yiliang Zhang,Qiongshi Lu,Yixuan Ye,Kunling Huang,Wei Liu,Yuchang Wu,Xiaoyuan Zhong,Boyang Li,Zhaolong Yu,Brittany G. Travers,Donna M. Werling,James J. Li,Hongyu Zhao +12 more
TL;DR: SuperGNOVA as mentioned in this paper is a statistical framework to estimate local genetic correlations using summary statistics from genome-wide association studies, which outperforms existing methods through simulations and analyses of 30 complex traits.
Journal ArticleDOI
Single-cell RNA sequencing reveals time- and sex-specific responses of mouse spinal cord microglia to peripheral nerve injury and links ApoE to chronic pain
Shannon N Tansley,Sonali Uttam,Alba Urena Guzman,Moein Yaqubi,Alain Pacis,Marc Parisien,Haley Deamond,Calvin W. Wong,Oded Rabau,Nicole Brown,Lisbet Haglund,Jean Ouellet,Carlo Santaguida,Alfredo Ribeiro-da-Silva,Soroush Tahmasebi,Masha Prager-Khoutorsky,Jiannis Ragoussis,Ji Zhang,Michael W. Salter,Luda Diatchenko,Luke M. Healy,Jeffrey S. Mogil,Arkady Khoutorsky +22 more
TL;DR: In this article , a single-cell RNA-sequencing analysis of human spinal cord microglia reveals a subpopulation with a disease-related transcriptional signature, which is associated with chronic pain.
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Distinct and temporary-restricted epigenetic mechanisms regulate human αβ and γδ T cell development.
Juliette Roels,Anna Kuchmiy,Matthias De Decker,Steven Strubbe,Marieke Lavaert,Kai Ling Liang,Georges Leclercq,Bart Vandekerckhove,Filip Van Nieuwerburgh,Pieter Van Vlierberghe,Tom Taghon +10 more
TL;DR: This resource provides a framework for studying gene regulatory mechanisms that drive normal and malignant human T cell development and unravels distinct chromatin landscapes between CD4 + and CD8 + αβ-lineage cells that support their effector functions and reveal gene-specific mechanisms that define mature T cells.
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Novel non-histocompatibility antigen mismatched variants improve the ability to predict antibody-mediated rejection risk in kidney transplant
TL;DR: An integrative computational approach leveraging D/R exome sequencing and gene expression to predict clinical post-transplant outcome is developed, with considerable benefits on improving human morbidity and mortality and opens the door to precision immunosuppression and extended tx survival.
Journal ArticleDOI
Genomic footprints of dryland stress adaptation in Egyptian fat-tail sheep and their divergence from East African and western Asia cohorts.
Joram M. Mwacharo,Eui-Soo Kim,Ahmed R. Elbeltagy,Adel M. Aboul-Naga,Barbara Rischkowsky,Max F. Rothschild +5 more
TL;DR: The findings provide insights on the complexity of genome architecture regarding dryland stress adaptation in the fat-tail sheep and showcase the indigenous stocks as appropriate genotypes for adaptation planning to sustain livestock production and human livelihoods, under future climates.
References
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