clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

Dozmorov, 2017, Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning, Bioinformatics, 33, 3323, 10.1093/bioinformatics/btx414 Priebe, 2015, FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species, Bioinformatics, 31, 445, 10.1093/bioinformatics/btu627 Yi, 2013, PlantGSEA: a gene set enrichment analysis toolkit for plant community, Nucleic Acids Res., 41, W98, 10.1093/nar/gkt281 Nam, 2008, Gene-set approach for expression pattern analysis, Brief. Bioinform., 9, 189, 10.1093/bib/bbn001 Wadi, 2016, Impact of outdated gene annotations on pathway enrichment analysis, Nat. Methods, 13, 705, 10.1038/nmeth.3963 Melé, 2015, The human transcriptome across tissues and individuals, Science, 348, 660, 10.1126/science.aaa0355 Yu, 2012, clusterProfiler: an R Package for comparing biological themes among gene clusters, OMICS J. Integr. Biol., 16, 284, 10.1089/omi.2011.0118 Boyle, 2004, GO::TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes, Bioinformatics, 20, 3710, 10.1093/bioinformatics/bth456 Subramanian, 2005, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc. Natl. Acad. Sci. U S A, 102, 15545, 10.1073/pnas.0506580102 Yu, 2015, ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization, Bioinformatics, 31, 2382, 10.1093/bioinformatics/btv145 Yu, 2020, Gene ontology semantic similarity analysis using GOSemSim, Methods Mol. Biol. Clifton NJ, 2117, 207, 10.1007/978-1-0716-0301-7_11 Silva, 2016, TCGA Workflow: analyze cancer genomics and epigenomics data using Bioconductor packages, F1000Research., 5, 1542, 10.12688/f1000research.8923.1 Treveil, 2021, ViralLink: an integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways, PLOS Comput. Biol., 17, e1008685, 10.1371/journal.pcbi.1008685 Yousif, 2020, NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization, BMC Bioinformatics, 21, 267, 10.1186/s12859-020-03577-4 Zou, 2019, ABioTrans: a biostatistical tool for transcriptomics analysis, Front. Genet., 10, 499, 10.3389/fgene.2019.00499 2019, The gene ontology resource: 20 years and still GOing strong, Nucleic Acids Res., 47, D330, 10.1093/nar/gky1055 Yu, 2010, GOSemSim: an R package for measuring semantic similarity among GO terms and gene products, Bioinformatics, 26, 976, 10.1093/bioinformatics/btq064 Haynes, 2018, Gene annotation bias impedes biomedical research, Sci. Rep., 8, 1362, 10.1038/s41598-018-19333-x Kanehisa, 2017, KEGG: new perspectives on genomes, pathways, diseases and drugs, Nucleic Acids Res., 45, D353, 10.1093/nar/gkw1092 Zolti, 2020, The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts, Microbiome, 8, 71, 10.1186/s40168-020-00850-9 Alison, 2002, Minichromosome maintenance (MCM) proteins may be pre-cancer markers, Gut, 50, 290, 10.1136/gut.50.3.290 Miossec, 2021, Local and systemic effects of IL-17 in joint inflammation: a historical perspective from discovery to targeting, Cell. Mol. Immunol., 18, 860, 10.1038/s41423-021-00644-5 Heink, 2005, IFN-γ-induced immune adaptation of the proteasome system is an accelerated and transient response, Proc. Natl. Acad. Sci. U S A, 102, 9241, 10.1073/pnas.0501711102 Yu, 2015, DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis, Bioinformatics, 31, 608, 10.1093/bioinformatics/btu684 Yu, 2016, ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization, Mol. Biosyst., 12, 477, 10.1039/C5MB00663E Yu, 2018, Using meshes for MeSH term enrichment and semantic analyses, Bioinformatics, 34, 3766, 10.1093/bioinformatics/bty410 Martens, 2021, WikiPathways: connecting communities, Nucleic Acids Res., 49, D613, 10.1093/nar/gkaa1024 Conesa, 2005, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, 21, 3674, 10.1093/bioinformatics/bti610 Moriya, 2007, KAAS: an automatic genome annotation and pathway reconstruction server, Nucleic Acids Res., 35, W182, 10.1093/nar/gkm321 Zhang, 2019, CellMarker: a manually curated resource of cell markers in human and mouse, Nucleic Acids Res., 47, D721, 10.1093/nar/gky900 McLean, 2010, GREAT improves functional interpretation of cis-regulatory regions, Nat. Biotechnol., 28, 495, 10.1038/nbt.1630 Liu, 2019, A practical guide for DNase-seq data analysis: from data management to common applications, Brief. Bioinform, 20, 1865, 10.1093/bib/bby057 Yin, 2020, Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain, Nat. Commun., 11, 474, 10.1038/s41467-020-14368-z Oliviero, 2015, The variant Polycomb Repressor Complex 1 component PCGF1 interacts with a pluripotency sub-network that includes DPPA4, a regulator of embryogenesis, Sci. Rep., 5, 18388, 10.1038/srep18388 Cheng, 2014, KAP1 represses differentiation-inducible genes in embryonic stem cells through cooperative binding with PRC1 and derepresses pluripotency-associated genes, Mol. Cell. Biol., 34, 2075, 10.1128/MCB.01729-13 Santanach, 2017, The Polycomb group protein CBX6 is an essential regulator of embryonic stem cell identity, Nat. Commun., 8, 1235, 10.1038/s41467-017-01464-w Deng, 2019, CBX6 is negatively regulated by EZH2 and plays a potential tumor suppressor role in breast cancer, Sci. Rep., 9, 197, 10.1038/s41598-018-36560-4 Brun, 2008, Simultaneous modeling of concentration-effect and time-course patterns in gene expression data from microarrays, Cancer Genomics Proteomics, 5, 43 Korotkevich, 2021, Fast gene set enrichment analysis, bioRxiv Wimalanathan, 2021, Gene ontology Meta annotator for plants (GOMAP), bioRxiv Collado-Torres, 2017, Recount workflow: accessing over 70,000 human RNA-seq samples with Bioconductor, F1000Research., 6, 1558, 10.12688/f1000research.12223.1 Chao, 2019, RNASeqR: an R package for automated two-group RNA-Seq analysis workflow, IEEE/ACM Trans. Comput. Biol. Bioinform. Wang, 2019, Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute, Nat. Protoc., 14, 756, 10.1038/s41596-018-0113-7