ArrayExpress--a public repository for microarray gene expression data at the EBI

Parkinson, Helen; Sarkans, Ugis; Shojatalab, Mohammadreza; Abeygunawardena, Niran; Contrino, Sergio; Coulson, Richard M. R.; Farne, Anna; Lara, Gonzalo Garcia; Holloway, Ele; Kapushesky, Misha; Lilja, Per; Mukherjee, Gaurab; Oezcimen, Ahmet; Rayner, Tim; Rocca-Serra, Philippe; Sharma, Ashish; Sansone, Susanna-Assunta; Brāzma, Alvis

doi:10.1093/nar/gki056

Cited by 573 publications

(168 citation statements)

References 15 publications

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“…Band intensities were evaluated by densitometry. For microarray analysis, the synthesis of 33 P-CTP-labeled cDNA and the hybridization, washing, and stripping of Genefilters (Research Genetics, Huntsville, AL) were performed as described previously (Rep et al, Parkinson et al, 2005) under the accession number E-MEXP-1136. Statistical analysis of overrepresentation of functional groups was performed by using FUNSPEC (Robinson et al, 2002).…”

Section: Northern Blot and Microarray Analysismentioning

confidence: 99%

Isc1p Plays a Key Role in Hydrogen Peroxide Resistance and Chronological Lifespan through Modulation of Iron Levels and Apoptosis

Almeida

Marques

Mojžita

et al. 2008

MBoC

109

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The inositolphosphosphingolipid phospholipase C (Isc1p) of Saccharomyces cerevisiae belongs to the family of neutral sphingomyelinases that generates the bioactive sphingolipid ceramide. In this work the role of Isc1p in oxidative stress resistance and chronological lifespan was investigated. Loss of Isc1p resulted in a higher sensitivity to hydrogen peroxide that was associated with an increase in oxidative stress markers, namely intracellular oxidation, protein carbonylation, and lipid peroxidation. Microarray analysis showed that Isc1p deficiency up-regulated the iron regulon leading to increased levels of iron, which is known to catalyze the production of the highly reactive hydroxyl radicals via the Fenton reaction. In agreement, iron chelation suppressed hydrogen peroxide sensitivity of isc1⌬ mutants. Cells lacking Isc1p also displayed a shortened chronological lifespan associated with oxidative stress markers and aging of parental cells was correlated with a decrease in Isc1p activity. The analysis of DNA fragmentation and caspase-like activity showed that Isc1p deficiency increased apoptotic cell death associated with oxidative stress and aging. Furthermore, deletion of Yca1p metacaspase suppressed the oxidative stress sensitivity and premature aging phenotypes of isc1⌬ mutants. These results indicate that Isc1p plays an important role in the regulation of cellular redox homeostasis, through modulation of iron levels, and of apoptosis.

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Section: Northern Blot and Microarray Analysismentioning

confidence: 99%

Isc1p Plays a Key Role in Hydrogen Peroxide Resistance and Chronological Lifespan through Modulation of Iron Levels and Apoptosis

Almeida

Marques

Mojžita

et al. 2008

MBoC

109

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show abstract

“…The microarray experiment databases GEO (Barrett et al 2005) at NCBI and ArrayExpress (Parkinson et al 2005) at European Bioinformatics Institute (EBI) contain tomato gene expression data from six sets of experiments obtained by using different platforms such as "Cornell-CGEP Tomato 13K TOM1" and "Potato 10k cDNA array".…”

Section: Gene Expression Datamentioning

confidence: 99%

Genomic Databases for Tomato

Yano

Aoki

Shibata

2007

Plant Biotechnology

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“…Human HRH1 gene (NM_003118) was used as query sequences for the BLAST programs. The expression profiles for normal human tissues were obtained from GeneAnnot (26) and ArrayExpress (27). Northern analysis of NCBI's uniGene dataset was also extracted (21).…”

Section: Identificationmentioning

confidence: 99%

Integrative genomic analyses of the histamine H1 receptor and its role in cancer prediction

Wang

Wei

Shi

et al. 2014

International Journal of Molecular Medicine

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Abstract. The human histamine receptor H1 (HRH1) gene is located on chromosome 3p25 and encodes for a 487 amino acid G protein-coupled receptor (GPCR) with a long third intracellular loop (IL3). The HRH1 predominantly couples to Gα q/11 proteins, leading to the activation of phospholipase C (PLC) and subsequent release of the second messengers inositol trisphosphate (IP 3 ) and diacylglycerol (DAG) followed by the activation of PKC and the release of [Ca 2+ ] i . In the present study, we identified HRH1 genes from 14 vertebrate genomes and found that HRH1 exists in all types of vertebrates including fish, amphibians, birds and mammals. We identified 88 SNPs including 4 available alleles disrupting an existing exonic splicing enhancer and 84 SNPs causing missense mutation, which may impact the effect of histamine on the HRH1 protein. We found that the human HRH1 gene was expressed in many tissues or organs, and predominant expression of HRH1 was shown in the bone marrow, whole blood, lymph node, thymus, brain, cerebellum, retina, spinal cord, heart, smooth muscle, skeletal muscle, small intestine, colon, adipocytes, kidney, liver, lung, pancreas, thyroid salivary gland, skin, ovary, uterus, placenta, prostate and testis. When searched in the PrognoScan database, human HRH1 was also found to be expressed in bladder cancer, blood cancer, brain cancer, breast cancer, colorectal cancer, eye cancer, head and neck cancer, lung cancer, ovarian cancer, skin cancer and soft tissue cancer tissues. The relationship between the expression of HRH1 and prognosis was found to vary in different types of cancers, even in the same cancer from different databases. This implies that the function of HRH1 in these tumors may be multidimensional. GR, STAT5A and c-Myb regulatory transcription factor binding sites were identified in the HRH1 gene upstream (promoter) region, which may be involved in the effect of HRH1 in tumors.

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ArrayExpress--a public repository for microarray gene expression data at the EBI

Cited by 573 publications

References 15 publications

Isc1p Plays a Key Role in Hydrogen Peroxide Resistance and Chronological Lifespan through Modulation of Iron Levels and Apoptosis

Isc1p Plays a Key Role in Hydrogen Peroxide Resistance and Chronological Lifespan through Modulation of Iron Levels and Apoptosis

Genomic Databases for Tomato

Integrative genomic analyses of the histamine H1 receptor and its role in cancer prediction

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