BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

Durinck, Steffen; Moreau, Yves; Kasprzyk, Arek; Davis, Sean; Moor, Bart De; Brāzma, Alvis; Huber, Wolfgang

doi:10.1093/bioinformatics/bti525

Cited by 1,800 publications

(1,549 citation statements)

References 7 publications

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“…Some overlapping intervals could also overlap with each other, and therefore we merged them into several intervals that have no adjoining region between nonredundant intervals. The genes involved in these overlaps and their Gene Ontology (GO) annotation were retrieved using the BiomaRt package (Durinck et al, 2005).…”

Section: Methodsmentioning

confidence: 99%

Identification of pleiotropic genes and gene sets underlying growth and immunity traits: a case study on Meishan pigs

Zhang

Wang

Yang

et al. 2016

animal

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Both growth and immune capacity are important traits in animal breeding. The animal quantitative trait loci (QTL) database is a valuable resource and can be used for interpreting the genetic mechanisms that underlie growth and immune traits. However, QTL intervals often involve too many candidate genes to find the true causal genes. Therefore, the aim of this study was to provide an effective annotation pipeline that can make full use of the information of Gene Ontology terms annotation, linkage gene blocks and pathways to further identify pleiotropic genes and gene sets in the overlapping intervals of growth-related and immunity-related QTLs. In total, 55 non-redundant QTL overlapping intervals were identified, 1893 growth-related genes and 713 immunity-related genes were further classified into overlapping intervals and 405 pleiotropic genes shared by the two gene sets were determined. In addition, 19 pleiotropic gene linkage blocks and 67 pathways related to immunity and growth traits were discovered. A total of 343 growth-related genes and 144 immunity-related genes involved in pleiotropic pathways were also identified, respectively. We also sequenced and genotyped 284 individuals from Chinese Meishan pigs and European pigs and mapped the single nucleotide polymorphisms (SNPs) to the pleiotropic genes and gene sets that we identified. A total of 971 high-confidence SNPs were mapped to the pleiotropic genes and gene sets that we identified, and among them 743 SNPs were statistically significant in allele frequency between Meishan and European pigs. This study explores the relationship between growth and immunity traits from the view of QTL overlapping intervals and can be generalized to explore the relationships between other traits.

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Section: Methodsmentioning

confidence: 99%

Identification of pleiotropic genes and gene sets underlying growth and immunity traits: a case study on Meishan pigs

Zhang

Wang

Yang

et al. 2016

animal

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“…Comparison of the gene expression profiles in control cells with or without PD169316 indicated that the inhibitor by itself had a negligible impact as it resulted in the differential expression of only one gene (SERPINA1 fold change: 1.96, P ¼ 0.008). Selected differential expressed genes were annotated with GO identifiers using the biomaRt package (Durinck et al, 2005), which retrieves data from Ensembl (Birney et al, 2006). These GO terms were mapped to the generic GO slim available from the GO website (http://www.geneontology.org).…”

Section: Analysis Of Microarraysmentioning

confidence: 99%

Molecular effectors and modulators of hypericin-mediated cell death in bladder cancer cells

et al. 2007

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Photodynamic therapy (PDT) is an anticancer approach utilizing a light-absorbing molecule and visible light irradiation to generate, in the presence of O 2 , cytotoxic reactive oxygen species, which cause tumor ablation. Given that the photosensitizer hypericin is under consideration for PDT treatment of bladder cancer we used oligonucleotide microarrays in the T24 bladder cancer cell line to identify differentially expressed genes with therapeutic potential. This study reveals that the expression of several genes involved in various metabolic processes, stress-induced cell death, autophagy, proliferation, inflammation and carcinogenesis is strongly affected by PDT and pinpoints the coordinated induction of a cluster of genes involved in the unfolded protein response pathway after endoplasmic reticulum stress and in antioxidant response. Analysis of PDT-treated cells after p38 MAPK inhibition or silencing unraveled that the induction of an important subset of differentially expressed genes regulating growth and invasion, as well as adaptive mechanisms against oxidative stress, is governed by this stress-activated kinase. Moreover, p38 MAPK inhibition blocked autonomous regrowth and migration of cancer cells escaping PDT-induced cell death. This analysis identifies new molecular effectors of the cancer cell response to PDT opening attractive avenues to improve the therapeutic efficacy of hypericin-based PDT of bladder cancer.

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“…The significance cutoff used was 0.05, after a multiple hypothesis testing correction using the package qvalue (Storey and Tibshirani 2003;Dabney 2012). The bioconductor package goseq (Young et al 2010) was used to determine pathway overrepresentation in overlaps with Seong's data (Seong et al 2011), with the necessary input of "all gene names" coming from the list of genes given by the bioconductor package BiomaRt (Durinck et al 2005;Durinck et al 2009). All pathways marked as significant in this analysis had a non-FDR corrected p value of less than 0.007.…”

Section: Comparison Of Gene Expression Datamentioning

confidence: 99%

Drosophila MelanogasterShow a Threshold Effect in Response to Radiation

et al. 2014

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ᮀ We investigate the biological effects of radiation using adult Drosophila melanogaster as a model organism, focusing on gene expression and lifespan analysis to determine the effect of different radiation doses. Our results support a threshold effect in response to radiation: no effect on lifespan and no permanent effect on gene expression is seen at incident radiation levels below 100 J/kg. We also find that it is more appropriate to compare radiation effects in flies using the absorbed energy rather than incident radiation levels. Although it is reasonable to assume that radiation damage to DNA and other cellular machinery is linear as a function of radiation dosage (as has been used in development of radiation protection standards), actual damage is mitigated by cellular repair mechanisms. These repair mechanisms probably increase initially, then reach a maximum so that, depending on parameters, various non-linear curves are possible. It may even be that there is a protective effect due to increased damage response to small amounts of radiation or other types of biological stress. Key terms: low dose radiation, gene expression, Drosophila melanogaster, threshold effect INTRODUCTIONThe goal of this paper is to investigate the biological effects of radiation using Drosophila melanogaster as a model organism, focusing on gene expression and lifespan analysis to determine the effect of different radiation doses, especially near the threshold. Previous research has been done on the effects of radiation on Drosophila lifespan, including research Address correspondence to Leon N. Cooper. Box 1843, Brown University, Providence, RI 02912-1843; Phone: (401) 863-2172; Email: Leon_Cooper@brown.edu on flies in different developmental stages (Vaiserman et al. 1999; Vaiserman et al. 2003; Vaiserman et al. 2004a; Vaiserman et al. 2004b;Moskalev et al. 2011;Seong et al. 2011;Koana et al. 2012) and in adults (Gowen and Stadler 1952;Strehler 1962;Sacher 1963;Lamb 1964;Noethel 1965;Baxter and Blair 1967a;Lamb and Smith 1969;Giess and Planel 1973;Planel and Giess 1973). Each of these papers supports the idea of a threshold -a model where radiation dose does not affect mortality negatively below a certain dose. RESULTS Demography ExperimentA demography experiment was done, as detailed in the methods section. Adult flies were irradiated at age 24-48 hours post-eclosion with incident radiation levels 1 ranging from 0 to 400 J/kg. The results of the demography experiment are shown in Figure 2 and Table 1, as well as supplemental Figure S1. We did not detect any significant difference among the lifespans of flies exposed to radiation less than or equal to 50 J/kg (based on log rank test results, shown in supplemental Tables S2 For comparison to (Baxter and Blair 1967a) data whose incident irradiation values are reported in Roentgen (R), we take these values as the proportional ionization analogue of ICRU recommended air kerma (ICRU 2011) and convert them to J/kg (or Gy) using 1R = 0.01 J/kg (Gy) (e.g. Wyckoff (1983) 1 R = 0...

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BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

Cited by 1,800 publications

References 7 publications

Identification of pleiotropic genes and gene sets underlying growth and immunity traits: a case study on Meishan pigs

Identification of pleiotropic genes and gene sets underlying growth and immunity traits: a case study on Meishan pigs

Molecular effectors and modulators of hypericin-mediated cell death in bladder cancer cells

Drosophila MelanogasterShow a Threshold Effect in Response to Radiation

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