g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update).
TLDR
G:Profiler is now capable of analysing data from any organism, including vertebrates, plants, fungi, insects and parasites, and the 2019 update introduces an extensive technical rewrite making the services faster and more flexible.Abstract:
Biological data analysis often deals with lists of genes arising from various studies. The g:Profiler toolset is widely used for finding biological categories enriched in gene lists, conversions between gene identifiers and mappings to their orthologs. The mission of g:Profiler is to provide a reliable service based on up-to-date high quality data in a convenient manner across many evidence types, identifier spaces and organisms. g:Profiler relies on Ensembl as a primary data source and follows their quarterly release cycle while updating the other data sources simultaneously. The current update provides a better user experience due to a modern responsive web interface, standardised API and libraries. The results are delivered through an interactive and configurable web design. Results can be downloaded as publication ready visualisations or delimited text files. In the current update we have extended the support to 467 species and strains, including vertebrates, plants, fungi, insects and parasites. By supporting user uploaded custom GMT files, g:Profiler is now capable of analysing data from any organism. All past releases are maintained for reproducibility and transparency. The 2019 update introduces an extensive technical rewrite making the services faster and more flexible. g:Profiler is freely available at https://biit.cs.ut.ee/gprofiler.read more
Citations
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KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis.
Dechao Bu,Haitao Luo,Peipei Huo,Zhihao Wang,Shan Zhang,Zihao He,Yang Wu,Lianhe Zhao,Jingjia Liu,Jin-Cheng Guo,Shuangsang Fang,Wanchen Cao,Lan Yi,Yi Zhao,Lei Kong +14 more
TL;DR: A novel machine learning-based method was introduced, CGPS, which incorporates seven FCS tools and two PT tools into a single ensemble score and intelligently prioritizes the relevant biological pathways.
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WikiPathways: connecting communities.
Marvin Martens,Ammar Ammar,Anders Riutta,Andra Waagmeester,Denise Slenter,Kristina Hanspers,Ryan A. Miller,Daniela Digles,Elisson Nogueira Lopes,Friederike Ehrhart,Lauren J. Dupuis,Laurent A. Winckers,Susan L. Coort,Egon Willighagen,Chris T. Evelo,Alexander R. Pico,Martina Kutmon +16 more
TL;DR: The growth of WikiPathways over the last three years is shown, the new communities and collaborations of pathway authors and curators are highlighted, and various technologies to connect to external resources and initiatives are described.
Journal ArticleDOI
Cigarette Smoke Exposure and Inflammatory Signaling Increase the Expression of the SARS-CoV-2 Receptor ACE2 in the Respiratory Tract.
Joan C. Smith,Joan C. Smith,Erin L. Sausville,Vishruth Girish,Vishruth Girish,Monet Lou Yuan,Monet Lou Yuan,Anand Vasudevan,Kristen M. John,Kristen M. John,Jason M. Sheltzer +10 more
TL;DR: It is shown that cigarette smoke causes a dose-dependent upregulation of Angiotensin Converting Enzyme 2 (ACE2), the SARS-CoV-2 receptor, in rodent and human lungs, and this work identifies ACE2 as an interferon-stimulated gene in lung cells, suggesting that Sars-Cov-2 infections could create positive-feedback loops that increase ACE2 levels and facilitate viral dissemination.
Journal ArticleDOI
Cell-programmed nutrient partitioning in the tumour microenvironment
Bradley I. Reinfeld,Bradley I. Reinfeld,Matthew Z. Madden,Matthew Z. Madden,Melissa M. Wolf,Melissa M. Wolf,Anna Chytil,Jackie E. Bader,Andrew R. Patterson,Ayaka Sugiura,Ayaka Sugiura,Allison S. Cohen,Allison S. Cohen,Ahmed Ali,Ahmed Ali,Brian T. Do,Brian T. Do,Alexander Muir,Caroline A. Lewis,Rachel Hongo,Kirsten Young,Rachel E. Brown,Rachel E. Brown,Vera M. Todd,Vera M. Todd,Tessa Huffstater,Abin Abraham,Richard T. O’Neil,Richard T. O’Neil,Matthew H. Wilson,Matthew H. Wilson,Fuxue Xin,Fuxue Xin,M. Noor Tantawy,M. Noor Tantawy,W. David Merryman,Rachelle W. Johnson,Christopher S. Williams,Christopher S. Williams,Emily F. Mason,Frank M. Mason,Katherine E. Beckermann,Matthew G. Vander Heiden,Matthew G. Vander Heiden,H. Charles Manning,H. Charles Manning,Jeffrey C. Rathmell,Jeffrey C. Rathmell,W. Kimryn Rathmell,W. Kimryn Rathmell +49 more
TL;DR: In this article, the authors used positron emission tomography (PET) tracers to measure the access to and uptake of glucose and glutamine by specific cell subsets in the TME.
Journal ArticleDOI
SARS-CoV-2 infects and replicates in cells of the human endocrine and exocrine pancreas.
Janis A. Müller,Rüdiger Groß,Carina Conzelmann,Jana Krüger,Uta Merle,Johannes Steinhart,Tatjana Weil,Lennart Koepke,Caterina Prelli Bozzo,Clarissa Read,Giorgio Fois,Tim Eiseler,Julia Gehrmann,Joanne van Vuuren,Isabel M Wessbecher,Manfred Frick,Ivan G. Costa,Markus Breunig,Beate Grüner,Lynn Peters,Michael Schuster,Stefan Liebau,Thomas Seufferlein,Steffen Stenger,Albrecht Stenzinger,Patrick E. MacDonald,Frank Kirchhoff,Konstantin M. J. Sparrer,Paul Walther,Heiko Lickert,Thomas F. E. Barth,Martin Wagner,Jan Münch,Sandra Heller,Alexander Kleger +34 more
TL;DR: In this paper, the authors identify the human pancreas as a target of SARS-CoV-2 infection and suggest that β-cell infection could contribute to the metabolic dysregulation observed in patients with COVID-19.
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Journal ArticleDOI
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
TL;DR: 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.