Representing Kidney Development Using the Gene Ontology

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2014 Jun 19

PMID 24941002

Citations 12

Authors

Yasmin Alam-Faruque

David P Hill

Emily C Dimmer

Midori A Harris

Rebecca E Foulger

Susan Tweedie

Helen Attrill

Douglas G Howe

Stephen Randall Thomas

Duncan Davidson

Adrian S Woolf

Judith A Blake

Christopher J Mungall

Claire ODonovan

Rolf Apweiler

Rachael P Huntley

Affiliations

Soon will be listed here.

Abstract

Gene Ontology (GO) provides dynamic controlled vocabularies to aid in the description of the functional biological attributes and subcellular locations of gene products from all taxonomic groups (www.geneontology.org). Here we describe collaboration between the renal biomedical research community and the GO Consortium to improve the quality and quantity of GO terms describing renal development. In the associated annotation activity, the new and revised terms were associated with gene products involved in renal development and function. This project resulted in a total of 522 GO terms being added to the ontology and the creation of approximately 9,600 kidney-related GO term associations to 940 UniProt Knowledgebase (UniProtKB) entries, covering 66 taxonomic groups. We demonstrate the impact of these improvements on the interpretation of GO term analyses performed on genes differentially expressed in kidney glomeruli affected by diabetic nephropathy. In summary, we have produced a resource that can be utilized in the interpretation of data from small- and large-scale experiments investigating molecular mechanisms of kidney function and development and thereby help towards alleviating renal disease.

Citing Articles

Identification and Characterization of the Wilms Tumor Cancer Stem Cell.

Petrosyan A, Villani V, Aguiari P, Thornton M, Wang Y, Rajewski A Adv Sci (Weinh). 2023; 10(20):e2206787.

PMID: 37114795 PMC: 10369255. DOI: 10.1002/advs.202206787.

Investigating the Molecular Mechanism of Quercetin Protecting against Podocyte Injury to Attenuate Diabetic Nephropathy through Network Pharmacology, MicroarrayData Analysis, and Molecular Docking.

Ma X, Hao C, Yu M, Zhang Z, Huang J, Yang W Evid Based Complement Alternat Med. 2022; 2022:7291434.

PMID: 35615688 PMC: 9126727. DOI: 10.1155/2022/7291434.

Gene Ontology curation of the blood-brain barrier to improve the analysis of Alzheimer's and other neurological diseases.

Saverimuttu S, Kramarz B, Rodriguez-Lopez M, Garmiri P, Attrill H, Thurlow K Database (Oxford). 2021; 2021.

PMID: 34697638 PMC: 8546235. DOI: 10.1093/database/baab067.

Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci.

Breeze C, Batorsky A, Lee M, Szeto M, Xu X, McCartney D Genome Med. 2021; 13(1):74.

PMID: 33931109 PMC: 8088054. DOI: 10.1186/s13073-021-00877-z.

A statistical approach to identify, monitor, and manage incomplete curated data sets.

Howe D BMC Bioinformatics. 2018; 19(1):110.

PMID: 29609549 PMC: 5879614. DOI: 10.1186/s12859-018-2121-6.

References

Little M, Brennan J, Georgas K, Davies J, Davidson D, Baldock R . A high-resolution anatomical ontology of the developing murine genitourinary tract. Gene Expr Patterns. 2007; 7(6):680-99. PMC: 2117077. DOI: 10.1016/j.modgep.2007.03.002. View

Howe D, Bradford Y, Conlin T, Eagle A, Fashena D, Frazer K . ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. Nucleic Acids Res. 2012; 41(Database issue):D854-60. PMC: 3531097. DOI: 10.1093/nar/gks938. View

Carroll T, Vize P . Synergism between Pax-8 and lim-1 in embryonic kidney development. Dev Biol. 1999; 214(1):46-59. DOI: 10.1006/dbio.1999.9414. View

Siu K, Desouza L, Scorilas A, Romaschin A, Honey R, Stewart R . Differential protein expressions in renal cell carcinoma: new biomarker discovery by mass spectrometry. J Proteome Res. 2009; 8(8):3797-807. DOI: 10.1021/pr800389e. View

Mungall C, Torniai C, Gkoutos G, Lewis S, Haendel M . Uberon, an integrative multi-species anatomy ontology. Genome Biol. 2012; 13(1):R5. PMC: 3334586. DOI: 10.1186/gb-2012-13-1-r5. View

Raciti D, Reggiani L, Geffers L, Jiang Q, Bacchion F, Subrizi A . Organization of the pronephric kidney revealed by large-scale gene expression mapping. Genome Biol. 2008; 9(5):R84. PMC: 2441470. DOI: 10.1186/gb-2008-9-5-r84. View

Balakrishnan R, Harris M, Huntley R, Van Auken K, Cherry J . A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford). 2013; 2013:bat054. PMC: 3706743. DOI: 10.1093/database/bat054. View

Tang S, Leung J, Chan L, Tsang A, Lai K . Activation of tubular epithelial cells in diabetic nephropathy and the role of the peroxisome proliferator-activated receptor-gamma agonist. J Am Soc Nephrol. 2006; 17(6):1633-43. DOI: 10.1681/ASN.2005101113. View

Dihazi H, Asif A, Agarwal N, Doncheva Y, Muller G . Proteomic analysis of cellular response to osmotic stress in thick ascending limb of Henle's loop (TALH) cells. Mol Cell Proteomics. 2005; 4(10):1445-58. DOI: 10.1074/mcp.M400184-MCP200. View

10.

Janech M, Raymond J, Arthur J . Proteomics in renal research. Am J Physiol Renal Physiol. 2006; 292(2):F501-12. DOI: 10.1152/ajprenal.00298.2006. View

11.

Zambon A, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo C . GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinformatics. 2012; 28(16):2209-10. PMC: 3413395. DOI: 10.1093/bioinformatics/bts366. View

12.

. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2013; 42(Database issue):D7-17. PMC: 3965057. DOI: 10.1093/nar/gkt1146. View

13.

Hills C, Squires P . The role of TGF-β and epithelial-to mesenchymal transition in diabetic nephropathy. Cytokine Growth Factor Rev. 2011; 22(3):131-9. DOI: 10.1016/j.cytogfr.2011.06.002. View

14.

Narlis M, Grote D, Gaitan Y, Boualia S, Bouchard M . Pax2 and pax8 regulate branching morphogenesis and nephron differentiation in the developing kidney. J Am Soc Nephrol. 2007; 18(4):1121-9. DOI: 10.1681/ASN.2006070739. View

15.

Mungall C, Bada M, Berardini T, Deegan J, Ireland A, Harris M . Cross-product extensions of the Gene Ontology. J Biomed Inform. 2010; 44(1):80-6. PMC: 2910209. DOI: 10.1016/j.jbi.2010.02.002. View

16.

Baelde H, Eikmans M, Doran P, Lappin D, de Heer E, Bruijn J . Gene expression profiling in glomeruli from human kidneys with diabetic nephropathy. Am J Kidney Dis. 2004; 43(4):636-50. DOI: 10.1053/j.ajkd.2003.12.028. View

17.

Khodiyar V, Hill D, Howe D, Berardini T, Tweedie S, Talmud P . The representation of heart development in the gene ontology. Dev Biol. 2011; 354(1):9-17. PMC: 3302178. DOI: 10.1016/j.ydbio.2011.03.011. View

18.

Alam-Faruque Y, Dimmer E, Huntley R, ODonovan C, Scambler P, Apweiler R . The Renal Gene Ontology Annotation Initiative. Organogenesis. 2010; 6(2):71-5. PMC: 2901810. DOI: 10.4161/org.6.2.11294. View

19.

Lan Y, Ovitt C, Cho E, Maltby K, Wang Q, Jiang R . Odd-skipped related 2 (Osr2) encodes a key intrinsic regulator of secondary palate growth and morphogenesis. Development. 2004; 131(13):3207-16. DOI: 10.1242/dev.01175. View

20.

Doniger S, Salomonis N, Dahlquist K, Vranizan K, Lawlor S, Conklin B . MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol. 2003; 4(1):R7. PMC: 151291. DOI: 10.1186/gb-2003-4-1-r7. View