publication . Other literature type . Article . 2019

modEnrichr: a suite of gene set enrichment analysis tools for model organisms

Maxim V Kuleshov; Jennifer E L Diaz; Zachary N Flamholz; Alexandra B Keenan; Alexander Lachmann; Megan L Wojciechowicz; Ross L Cagan; Avi Ma’ayan;
  • Published: 02 Jul 2019
  • Publisher: Oxford University Press (OUP)
Abstract
<jats:title>Abstract</jats:title> <jats:p>High-throughput experiments produce increasingly large datasets that are difficult to analyze and integrate. While most data integration approaches focus on aligning metadata, data integration can be achieved by abstracting experimental results into gene sets. Such gene sets can be made available for reuse through gene set enrichment analysis tools such as Enrichr. Enrichr currently only supports gene sets compiled from human and mouse, limiting accessibility for investigators that study other model organisms. modEnrichr is an expansion of Enrichr for four model organisms: fish, fly, worm and yeast. The gene set librarie...
Subjects
ACM Computing Classification System: ComputingMethodologies_PATTERNRECOGNITION
free text keywords: Web Server Issue, Genetics, Model organism, ved/biology.organism_classification_rank.species, ved/biology, Computational biology, Biology, Suite, Gene, Metadata, GeneRIF, Data integration, computer.software_genre, computer, Reuse, Organism
Funded by
NIH| Knowledge Management Center for Illuminating the Druggable Genome
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U24CA224260-02
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| Data Coordination and Integration Center for LINCS-BD2K
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U54HL127624-02
  • Funding stream: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
,
NIH| Integrated Training in Pharmacological Sciences
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 2T32GM062754-14
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NIH| A New Disease Platform Leveraging Complex Drosophila and Mammalian Models
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U54OD020353-02
  • Funding stream: OFFICE OF THE DIRECTOR, NATIONAL INSTITUTES OF HEALTH
,
NIH| Development and Implementation Plan for Community Supported FAIR Guidelines and Metrics
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3OT3OD025467-01S1
  • Funding stream: OFFICE OF THE DIRECTOR, NATIONAL INSTITUTES OF HEALTH
51 references, page 1 of 4

1.Subramanian A., Tamayo P., Mootha V.K., Mukherjee S., Ebert B.L., Gillette M.A., Paulovich A., Pomeroy S.L., Golub T.R., Lander E.S.Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Nat l. Acad. Sci. U.S.A.2005; 102:15545–15550.16199517 [OpenAIRE] [PubMed]

2.Huang D.W., Sherman B.T., Lempicki R.A.Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc.2008; 4:44–57.

3.Reich M., Liefeld T., Gould J., Lerner J., Tamayo P., Mesirov J.P.GenePattern 2.0. Nat. Genet.2006; 38:500–501.16642009 [PubMed]

4.Zhang B., Kirov S., Snoddy J.WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res.2005; 33:W741–W748.15980575 [OpenAIRE] [PubMed]

5.Carbon S., Ireland A., Mungall C.J., Shu S., Marshall B., Lewis S., Hub A., Group W.P.W.AmiGO: online access to ontology and annotation data. Bioinformatics. 2008; 25:288–289.19033274 [OpenAIRE] [PubMed]

6.Al-Shahrour F., Minguez P., Tárraga J., Montaner D., Alloza E., Vaquerizas J.M., Conde L., Blaschke C., Vera J., Dopazo J.BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res.2006; 34:W472–W476.16845052 [OpenAIRE] [PubMed]

7.Hruz T., Laule O., Szabo G., Wessendorp F., Bleuler S., Oertle L., Widmayer P., Gruissem W., Zimmermann P.Genevestigator v3: a reference expression databas e for the meta-analysis of transcriptomes. Adv.Bioinformatics. 2008; 2008:420747.19956698 [OpenAIRE] [PubMed]

8.Zheng Q., Wang X.-J.GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res.2008; 36:W358–W363.18487275 [OpenAIRE] [PubMed]

9.Mi H., Muruganujan A., Casagrande J.T., Thomas P.D.Large-scale gene function analysis with the PANTHER classification system. Nat. Protoc.2013; 8:1551–1566.23868073 [OpenAIRE] [PubMed]

10.Chen E.Y., Tan C.M., Kou Y., Duan Q., Wang Z., Meirelles G.V., Clark N.R., Ma’ayan A.Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013; 14:128.23586463 [OpenAIRE] [PubMed]

11.Kuleshov M.V., Jones M.R., Rouillard A.D., Fernandez N.F., Duan Q., Wang Z., Koplev S., Jenkins S.L., Jagodnik K.M., Lachmann A.Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res.2016; 44:W90–W97.27141961 [OpenAIRE] [PubMed]

12.Reimand J., Arak T., Adler P., Kolberg L., Reisberg S., Peterson H., Vilo J.g:Profiler-a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res.2016; 44:W83–W89.27098042 [OpenAIRE] [PubMed]

13.Xie C., Mao X., Huang J., Ding Y., Wu J., Dong S., Kong L., Gao G., Li C.-Y., Wei L.KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res.2011; 39:W316–W322.21715386 [OpenAIRE] [PubMed]

14.Kim J.H., Karnovsky A., Mahavisno V., Weymouth T., Pande M., Dolinoy D.C., Rozek L.S., Sartor M.A.LRpath analysis reveals common pathways dysregulated via DNA methylation across cancer types. BMC Genomics. 2012; 13:526.23033966 [OpenAIRE] [PubMed]

15.Sulakhe D., Xie B., Taylor A., D'Souza M., Balasubramanian S., Hashemifar S., White S., Dave U.J., Agam G., Xu J.Lynx: a knowledge base and an analytical workbench for integrative medicine. Nucleic Acids Res.2016; 44:D882–D887.26590263 [OpenAIRE] [PubMed]

51 references, page 1 of 4
Powered by OpenAIRE Open Research Graph
Any information missing or wrong?Report an Issue
publication . Other literature type . Article . 2019

modEnrichr: a suite of gene set enrichment analysis tools for model organisms

Maxim V Kuleshov; Jennifer E L Diaz; Zachary N Flamholz; Alexandra B Keenan; Alexander Lachmann; Megan L Wojciechowicz; Ross L Cagan; Avi Ma’ayan;