Enrichr-KG: bridging enrichment analysis across multiple libraries

被引:81
作者
Evangelista, John Erol [1 ]
Xie, Zhuorui [1 ]
Marino, Giacomo B. [1 ]
Nguyen, Nhi [1 ]
Clarke, Daniel J. B. [1 ]
Ma'ayan, Avi [1 ]
机构
[1] Icahn Sch Med Mt Sinai, Mt Sinai Ctr Bioinformat, Dept Pharmacol Sci, New York, NY 10029 USA
关键词
CELLULAR SENESCENCE; GRAPH-THEORY; TRANSCRIPTOME ANALYSIS; NETWORK BIOLOGY; WEB SERVER; DISEASE; EXPRESSION; DATABASE; CELLS; INHIBITION;
D O I
10.1093/nar/gkad393
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Gene and protein set enrichment analysis is a critical step in the analysis of data collected from omics experiments. Enrichr is a popular gene set enrichment analysis web-server search engine that contains hundreds of thousands of annotated gene sets. While Enrichr has been useful in providing enrichment analysis with many gene set libraries from different categories, integrating enrichment results across libraries and domains of knowledge can further hypothesis generation. To this end, Enrichr-KG is a knowledge graph database and a web-server application that combines selected gene set libraries from Enrichr for integrative enrichment analysis and visualization. The enrichment results are presented as subgraphs made of nodes and links that connect genes to their enriched terms. In addition, users of Enrichr-KG can add gene-gene links, as well as predicted genes to the subgraphs. This graphical representation of cross-library results with enriched and predicted genes can illuminate hidden associa-tions between genes and annotated enriched terms from across datasets and resources. Enrichr-KG cur-rently serves 26 gene set libraries from different categories that include transcription, pathways, on-tologies, diseases/drugs, and cell types. To demon-strate the utility of Enrichr-KG we provide several case studies. Enrichr-KG is freely available at: https: //maayanlab.cloud/enrichr-kg.
引用
收藏
页码:W168 / W179
页数:12
相关论文
共 105 条
[1]   FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs [J].
Abugessaisa, Imad ;
Ramilowski, Jordan A. ;
Lizio, Marina ;
Severin, Jesicca ;
Hasegawa, Akira ;
Harshbarger, Jayson ;
Kondo, Atsushi ;
Noguchi, Shuhei ;
Yip, Chi Wai ;
Ooi, Jasmine Li Ching ;
Tagami, Michihira ;
Hori, Fumi ;
Agrawal, Saumya ;
Hon, Chung Chau ;
Cardon, Melissa ;
Ikeda, Shuya ;
Ono, Hiromasa ;
Bono, Hidemasa ;
Kato, Masaki ;
Hashimoto, Kosuke ;
Bonetti, Alessandro ;
Kobayashi, Norio ;
Shin, Jay ;
de Hoon, Michiel ;
Hayashizakil, Yoshihide ;
Carninci, Piero ;
Kawaji, Hideya ;
Kasukawa, Takeya .
NUCLEIC ACIDS RESEARCH, 2021, 49 (D1) :D892-D898
[2]  
[Anonymous], 2019, NATURE, V574, P187
[3]   Gene Ontology: tool for the unification of biology [J].
Ashburner, M ;
Ball, CA ;
Blake, JA ;
Botstein, D ;
Butler, H ;
Cherry, JM ;
Davis, AP ;
Dolinski, K ;
Dwight, SS ;
Eppig, JT ;
Harris, MA ;
Hill, DP ;
Issel-Tarver, L ;
Kasarskis, A ;
Lewis, S ;
Matese, JC ;
Richardson, JE ;
Ringwald, M ;
Rubin, GM ;
Sherlock, G .
NATURE GENETICS, 2000, 25 (01) :25-29
[4]   Single-Cell Transcriptome Analysis Reveals RGS1 as a New Marker and Promoting Factor for T-Cell Exhaustion in Multiple Cancers [J].
Bai, Yunmeng ;
Hu, Meiling ;
Chen, Zixi ;
Wei, Jinfen ;
Du, Hongli .
FRONTIERS IN IMMUNOLOGY, 2021, 12
[5]  
Bairoch Amos, 2018, J Biomol Tech, V29, P25, DOI 10.7171/jbt.18-2902-002
[6]   Network biology:: Understanding the cell's functional organization [J].
Barabási, AL ;
Oltvai, ZN .
NATURE REVIEWS GENETICS, 2004, 5 (02) :101-U15
[7]  
Barker JNWN, 1999, BRIT J DERMATOL, V141, P274
[8]   Insulin-like effect of pinitol [J].
Bates, SH ;
Jones, RB ;
Bailey, CJ .
BRITISH JOURNAL OF PHARMACOLOGY, 2000, 130 (08) :1944-1948
[9]   Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases [J].
Berger, Seth I. ;
Posner, Jeremy M. ;
Ma'ayan, Avi .
BMC BIOINFORMATICS, 2007, 8 (1)
[10]   Enhanced Expression of Janus Kinase-Signal Transducer and Activator of Transcription Pathway Members in Human Diabetic Nephropathy [J].
Berthier, Celine C. ;
Zhang, Hongyru ;
Schin, MaryLee ;
Henger, Anna ;
Nelson, Robert G. ;
Yee, Berne ;
Boucherot, Anissa ;
Neusser, Matthias A. ;
Cohen, Clemens D. ;
Carter-Su, Christin ;
Argetsinger, Lawrence S. ;
Rastaldi, Maria P. ;
Brosius, Frank C. ;
Kretzler, Matthias .
DIABETES, 2009, 58 (02) :469-477