Exploring FlyBase Data Using QuickSearch

Marygold, Steven J; Antonazzo, Giulia; Attrill, Helen; Costa, Marta; Crosby, Madeline A.; Santos, Gilberto dos; Goodman, Joshua L.; Gramates, L. Sian; Matthews, Beverley; Rey, Alix J.; Thurmond, Jim

doi:10.1002/cpbi.19

Cited by 7 publications

(7 citation statements)

References 25 publications

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“…The D. melanogaster genome contains 29 genes coding for putative prolinehydroxylases (Flybase annotation; Marygold et al 2016) and of these 19 are exclusively expressed in the adult MAG (FlyAtlas2; Leader et al 2018). These enzymes might have different substrate specificities defined by the positional context of the amino acid in the peptide.…”

Section: Discussionmentioning

confidence: 99%

The structure of the Drosophila melanogaster sex peptide: Identification of hydroxylated isoleucine and a strain variation in the pattern of amino acid hydroxylation

Sturm

Dowle

Audsley

et al. 2020

Insect Biochemistry and Molecular Biology

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Section: Discussionmentioning

confidence: 99%

The structure of the Drosophila melanogaster sex peptide: Identification of hydroxylated isoleucine and a strain variation in the pattern of amino acid hydroxylation

Sturm

Dowle

Audsley

et al. 2020

Insect Biochemistry and Molecular Biology

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“…In D. melanogaster , the spineless gene is the homolog of the LmAhR gene, which is highly expressed in the brain cell body rind and gnathal ganglion during adult stages . In Tribolium castaneum embryos, the TcAhR gene is primarily expressed in the head appendages .…”

Section: Discussionmentioning

confidence: 99%

Aryl hydrocarbon receptor regulates the expression of LmGSTd7 and is associated with chlorpyrifos susceptibility in Locusta migratoria

Zhang

Dong

Liu

et al. 2019

Pest Management Science

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BACKGROUND: The aryl hydrocarbon receptor (AhR) belongs to the bHLH-PAS (basic Helix-Loop-Helix -Period/ARNT/Single minded) family of transcription factors. AhR is a ligand-activated transcription factor, which participates in the sensing and transmitting stimuli of endogenous and exogenous chemicals, and subsequently activates the transcription of genes related to various physiological and detoxification functions. RESULT: In this study, a single full-length LmAhR sequence was cloned and characterized. RNA interference (RNAi) and insecticide bioassays showed that LmAhR plays a vital role in chlorpyrifos susceptibility. To better identify aryl hydrocarbon receptor from locusta migratoria (LmAhR)-regulated genes involved in chlorpyrifos susceptibility, a comparative transcriptome analysis was performed using double-stranded (ds)GFP-and dsLmAhR-injected Locusta migratoria. Differential gene expression analysis identified 145 down-regulated and 67 up-regulated genes (P ≤ 0.05 and fold change ≥2) in dsLmAhR-knockdown insects. We selected 27 down-regulated genes and verified their expression levels using reverse transcription quantitative PCR. Finally, one glutathione S-transferase (GST) gene (LmGSTd7) was selected as a candidate detoxification gene and was further validated via RNAi and chlorpyrifos bioassays. CONCLUSION: Our data suggest that AhR is associated with chlorpyrifos susceptibility via the regulation of LmGSTd7 expression in L. migratoria. (Ma) † These authors contributed equally to this work.

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“…Term Reports themselves can be queried/accessed by either of two FlyBase search tools: QuickSearch or Vocabularies. QuickSearch is located in the center of the FlyBase homepage and allows rapid querying of almost all data in FlyBase via a tabbed interface [7]. In each QuickSearch tab, a link to specific documentation is provided via the question mark icon.…”

Section: Methodsmentioning

confidence: 99%

Using FlyBase to Find Functionally Related Drosophila Genes

Rey

Attrill

Marygold

2018

Methods in Molecular Biology

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For more than 25 years, FlyBase (flybase.org) has served as an online database of biological information on the genus Drosophila, concentrating on the model organism D. melanogaster. Traditionally, FlyBase data have been organized and presented at a gene-by-gene level, which remains a useful perspective when the object of interest is a specific gene or gene product. However, in the modern era of a fully sequenced genome and an increasingly characterized proteome, it is often desirable to compile and analyze lists of genes related by a common function. This may be achieved in FlyBase by searching for genes annotated with relevant Gene Ontology (GO) terms and/or protein domain data. In addition, FlyBase provides preassembled lists of functionally related D. melanogaster genes within “Gene Group” reports. These are compiled manually from the published literature or expert databases and greatly facilitate access to, and analysis of, established gene sets. This chapter describes protocols to produce lists of functionally related genes in FlyBase using GO annotations, protein domain data and the Gene Groups resource, and provides guidance and advice for their further analysis and processing.

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Exploring FlyBase Data Using QuickSearch

Cited by 7 publications

References 25 publications

The structure of the Drosophila melanogaster sex peptide: Identification of hydroxylated isoleucine and a strain variation in the pattern of amino acid hydroxylation

The structure of the Drosophila melanogaster sex peptide: Identification of hydroxylated isoleucine and a strain variation in the pattern of amino acid hydroxylation

Aryl hydrocarbon receptor regulates the expression of LmGSTd7 and is associated with chlorpyrifos susceptibility in Locusta migratoria

Using FlyBase to Find Functionally Related Drosophila Genes

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