Visual annotation display (VLAD): a tool for finding functional themes in lists of genes

Mammalian Genome

Volumn 26, Issue 9-10, 2015, Pages 567-573

  Richardson, Joel E ^a   Bult, Carol J ^a  

^a JACKSON LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DATA ANALYSIS SOFTWARE; DETOXIFICATION; DOWN REGULATION; ENERGY METABOLISM; FATTY ACID SYNTHESIS; GENE ONTOLOGY; GENETIC ANALYSIS; NONHUMAN; ORGANOGENESIS; PHENOTYPE; STATISTICAL ANALYSIS; UPREGULATION; VISUAL ANNOTATION DISPLAY; ALGORITHM; ANIMAL; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENOMICS; HUMAN; INFORMATION RETRIEVAL; INTERNET; MOLECULAR GENETICS; MOUSE; SOFTWARE;

ALGORITHMS; ANIMALS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE ONTOLOGY; GENOMICS; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MICE; MOLECULAR SEQUENCE ANNOTATION; PHENOTYPE; SOFTWARE;

EID: 84943816306     PISSN: 09388990     EISSN: 14321777     Source Type: Journal    
DOI: 10.1007/s00335-015-9570-2     Document Type: Article

References (23)

1. 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 (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29
2. Bauer S, Gagneur J, Robinson PN (2010) GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic Acids Res 38:3523–3532
3. Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G (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 20:3710–3715
4. Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, Ami GOH, Web Presence Working G (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25:288–289
5. da Huang W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57
6. Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE, Mouse Genome Database G (2015) The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. Nucleic Acids Res 43:D726–D736
7. Ernst J, Bar-Joseph Z (2006) STEM: a tool for the analysis of short time series gene expression data. BMC Bioinform 7:191
8. Evsikov AV, Dolan ME, Genrich MP, Patek E, Bult CJ (2009) MouseCyc: a curated biochemical pathways database for the laboratory mouse. Genome Biol 10:R84
9. Gansner E, North S (1999) An open graph visualization system and its applications to software engineering. Softw Pract Exp S1:1–5
10. Gene Ontology C (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res 43:D1049–D1056
11. Glass K, Girvan M (2014) Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets. Sci Rep 4:4191
12. Kim SY, Volsky DJ (2005) PAGE: parametric analysis of gene set enrichment. BMC Bioinform 6:144
13. Luo W, Friedman MS, Shedden K, Hankenson KD, Woolf PJ (2009) GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinform 10:161
14. Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21:3448–3449
15. Noble WS (2009) How does multiple testing correction work? Nat Biotechnol 27:1135–1137
16. Prufer K, Muetzel B, Do HH, Weiss G, Khaitovich P, Rahm E, Paabo S, Lachmann M, Enard W (2007) FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinform 8:41
17. Russell MK, Longoni M, Wells J, Maalouf FI, Tracy AA, Loscertales M, Ackerman KG, Pober BR, Lage K, Bult CJ, Donahoe PK (2012) Congenital diaphragmatic hernia candidate genes derived from embryonic transcriptomes. Proc Natl Acad Sci USA 109:2978–2983
18. Smith CL, Eppig JT (2012) The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. Mamm Genome 23:653–668
19. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Consortium OBI, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnol 25:1251–1255
20. Storey JD (2002) A direct approach to false discovery rates. J Roy Stat Soc B 64:479–498
21. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102:15545–15550
22. Wang J, Duncan D, Shi Z, Zhang B (2013) WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res 41:W77–W83
23. Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, Bussey KJ, Riss J, Barrett JC, Weinstein JN (2003) GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 4:R28