ChEA3: transcription factor enrichment analysis by orthogonal omics integration.
Alexandra B Keenan,Denis Torre,Alexander Lachmann,Ariel K Leong,Megan L. Wojciechowicz,Vivian Utti,Kathleen M. Jagodnik,Eryk Kropiwnicki,Zichen Wang,Avi Ma'ayan +9 more
Reads0
Chats0
TLDR
The ChEA3 background database contains a collection of gene set libraries generated from multiple sources including TF–gene co-expression from RNA-seq studies, TF–target associations from ChIP-seq experiments, and TF-gree co-occurrence computed from crowd-submitted gene lists, which illuminate general transcription factor properties such as whether the TF behaves as an activator or a repressor.Abstract:
Identifying the transcription factors (TFs) responsible for observed changes in gene expression is an important step in understanding gene regulatory networks. ChIP-X Enrichment Analysis 3 (ChEA3) is a transcription factor enrichment analysis tool that ranks TFs associated with user-submitted gene sets. The ChEA3 background database contains a collection of gene set libraries generated from multiple sources including TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, and TF-gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate a composite rank that improves the prediction of the correct upstream TF compared to ranks produced by individual libraries. We compare ChEA3 with existing TF prediction tools and show that ChEA3 performs better. By integrating the ChEA3 libraries, we illuminate general transcription factor properties such as whether the TF behaves as an activator or a repressor. The ChEA3 web-server is available from https://amp.pharm.mssm.edu/ChEA3.read more
Citations
More filters
Journal ArticleDOI
Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV.
Alexey Stukalov,Virginie Girault,Vincent Grass,Ozge Karayel,Valter Bergant,Christian Urban,Darya A. Haas,Yiqi Huang,Lila Oubraham,Anqi Wang,M. Sabri Hamad,Antonio Piras,Fynn M. Hansen,Maria C. Tanzer,Igor Paron,Luca Zinzula,Thomas Engleitner,Maria Reinecke,Maria Reinecke,Teresa M. Lavacca,Rosina Ehmann,Roman Wölfel,Jörg Jores,Bernhard Kuster,Bernhard Kuster,Ulrike Protzer,Roland Rad,John Ziebuhr,Volker Thiel,Pietro Scaturro,Pietro Scaturro,Matthias Mann,Andreas Pichlmair +32 more
TL;DR: A concurrent multi-omics study of SARS CoV-2 and SARS-CoV was conducted in this article, where the authors profiled the interactomes of both viruses, as well as their influence on the transcriptome, proteome, ubiquitinome and phosphoproteome of a lung derived human cell line.
Posted ContentDOI
Multi-level proteomics reveals host-perturbation strategies of SARS-CoV-2 and SARS-CoV
Alexey Stukalov,Virginie Girault,Vincent Grass,Ozge Karayel,Valter Bergant,Christian Urban,Darya A. Haas,Yiqi Huang,Lila Oubraham,Anqi Wang,Sabri M. Hamad,Antonio Piras,Fynn M. Hansen,Maria C. Tanzer,Igor Paron,Luca Zinzula,Luca Zinzula,Thomas Engleitner,Maria Reinecke,Maria Reinecke,Teresa M. Lavacca,Rosina Ehmann,Roman Wölfel,Jörg Jores,Bernhard Kuster,Bernhard Kuster,Ulrike Protzer,Roland Rad,John Ziebuhr,Volker Thiel,Pietro Scaturro,Pietro Scaturro,Matthias Mann,Andreas Pichlmair +33 more
TL;DR: The TGF-β pathway, known for its involvement in tissue fibrosis, was specifically dysregulated by Sars-CoV-2 ORF8 and autophagy by SARS-CoVs ORF3, and was identified as a hotspot that can be targeted by existing drugs and it can guide rational design of virus- and host-directed therapies.
Journal ArticleDOI
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data
Christian H. Holland,Christian H. Holland,Jovan Tanevski,Jovan Tanevski,Javier Perales-Patón,Jan Gleixner,Jan Gleixner,Manu P. Kumar,Elisabetta Mereu,Brian A. Joughin,Oliver Stegle,Oliver Stegle,Douglas A. Lauffenburger,Holger Heyn,Bence Szalai,Julio Saez-Rodriguez,Julio Saez-Rodriguez +16 more
TL;DR: Bulk-based functional analysis tools that use manually curated footprint gene sets can be applied to scRNA-seq data, partially outperforming dedicated single-cell tools and finding that the performance offunctional analysis tools is more sensitive to the gene sets than to the statistic used.
Journal ArticleDOI
Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation
Hyeseung Lee,Robert J. Fenster,S. Sebastian Pineda,Whitney S. Gibbs,Shahin Mohammadi,Jose Davila-Velderrain,Jose Davila-Velderrain,Francisco J. Garcia,Martine Therrien,Martine Therrien,Hailey S. Novis,Fan Gao,Hilary Wilkinson,Thomas F. Vogt,Manolis Kellis,Manolis Kellis,Matthew J. LaVoie,Myriam Heiman,Myriam Heiman,Myriam Heiman +19 more
TL;DR: It is revealed that the activation of innate immune signaling in the most vulnerable HD neurons provides a novel framework to understand the basis of mHTT toxicity and raises new therapeutic opportunities.
Journal ArticleDOI
The neutrotime transcriptional signature defines a single continuum of neutrophils across biological compartments.
Ricardo Grieshaber-Bouyer,Felix A Radtke,Felix A Radtke,Pierre Cunin,Giuseppina Stifano,Anaïs Levescot,Brinda Vijaykumar,Nathan Nelson-Maney,Rachel B Blaustein,Paul A. Monach,Paul A. Monach,Peter A. Nigrovic,Peter A. Nigrovic +12 more
TL;DR: In this article, the authors apply single-cell RNA sequencing to neutrophils from normal and inflamed mouse tissues and identify a single developmental spectrum as the dominant organizational theme of neutrophil heterogeneity.
References
More filters
Journal ArticleDOI
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian,Pablo Tamayo,Vamsi K. Mootha,Sayan Mukherjee,Benjamin L. Ebert,Michael A. Gillette,Amanda G. Paulovich,Scott L. Pomeroy,Todd R. Golub,Eric S. Lander,Jill P. Mesirov +10 more
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Journal ArticleDOI
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon,Andrew Markiel,Owen Ozier,Nitin S. Baliga,Jonathan T. Wang,Daniel Ramage,Nada Amin,Benno Schwikowski,Trey Ideker +8 more
TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
Journal ArticleDOI
WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder,Steve Horvath +1 more
TL;DR: The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis that includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software.
Journal ArticleDOI
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang,Tao Liu,Clifford A. Meyer,Jérôme Eeckhoute,David S. Johnson,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,Richard M. Myers,Myles Brown,Wei Li,X. Shirley Liu +11 more
TL;DR: This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.
Journal ArticleDOI
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
TL;DR: The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data and provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-power gene expression and genomic hybridization experiments.