Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

Petryszak, Robert; Keays, Maria; Tang, Y. Amy; Fonseca, Nuno A.; Barrera, Elisabet; Burdett, Tony; Füllgrabe, Anja; Fuentes, Alfonso Muñoz-Pomer; Jupp, Simon; Koskinen, Satu; Mannion, Oliver; Huerta, Laura; Mégy, Karyn; Snow, Catherine; Williams, Eleanor; Barzine, Mitra; Hastings, Emma; Weisser, Hendrik; Wright, James C.; Jaiswal, Pankaj; Huber, Wolfgang; Choudhary, Jyoti S.; Parkinson, Helen; Brāzma, Alvis

doi:10.1093/nar/gkv1045

Cited by 512 publications

(474 citation statements)

References 29 publications

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“…Specifically, we evaluated FAD2 mRNA levels by qRT-PCR using RNA isolated from the dissected scutellar and radicle tissues. Bioinformatic analysis of maize genome data (Sen et al, 2010;Petryszak et al, 2016) identified six putative FAD2 genes based upon sequence homology to the Arabidopsis FAD2 gene (At3g12120); these were annotated as GRMZM2G169240, GRMZM2G169261, GRMZM2G174766, GRMZM2G056252, GRMZM2G161792, and GRMZM2G064701. Initial assays (Supplemental Table S5) identified that only GRMZM2G056252 and GRMZM2G064701 are expressed at measurable levels in germinating embryonic tissue during the initial 36 h after imbibition; the expression of the other four FAD2-like genes was detectable by RT-PCR, but their levels were too low to obtain robust quantitative expression data.…”

Section: Differential Distributions Of Lipid Classes Accentuated In Tmentioning

confidence: 99%

Spatial Mapping and Profiling of Metabolite Distributions during Germination

et al. 2017

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Germination is a highly complex process by which seeds begin to develop and establish themselves as viable organisms. In this study, we utilize a combination of gas chromatography-mass spectrometry, liquid chromatography-fluorescence, and mass spectrometry imaging approaches to profile and visualize the metabolic distributions of germinating seeds from two different inbreds of maize (Zea mays) seeds, B73 and Mo17. Gas chromatography and liquid chromatography analyses demonstrate that the two inbreds are highly differentiated in their metabolite profiles throughout the course of germination, especially with regard to amino acids, sugar alcohols, and small organic acids. Crude dissection of the seed followed by gas chromatography-mass spectrometry analysis of polar metabolites also revealed that many compounds were highly sequestered among the various seed tissue types. To further localize compounds, matrix-assisted laser desorption/ionization mass spectrometry imaging was utilized to visualize compounds in fine detail in their native environments over the course of germination. Most notably, the fatty acyl chain-dependent differential localization of phospholipids and triacylglycerols was observed within the embryo and radicle, showing correlation with the heterogeneous distribution of fatty acids. Other interesting observations include unusual localization of ceramides on the endosperm/scutellum boundary and subcellular localization of ferulate in the aleurone.Plants use seeds as the propagule to ensure reproduction to the next generation, and over the past 10,000 years, human civilizations have established agricultural practices to ensure a seed-based food supply (Larson et al., 2014). Therefore, deciphering the processes that enable seeds to perform their biological functions is of importance in understanding how plants are propagated and also is of practical importance to improve agriculture. Seeds are designed to survive long periods of dormancy in a relatively dry state, and the process of germination is initiated by the imbibition of water. During this germination process, many metabolic changes occur, most of which are associated with the catabolism of seed storage products (proteins, polysaccharides, and lipids) into metabolically usable, simpler chemical forms that are either used as precursors to assemble the growing seedling or are oxidized via energy-producing biochemical pathways to thermodynamically support growth (Bewley, 1997(Bewley, , 2001.The specific metabolic processes that support seed germination are somewhat dependent on the taxonomic clade of the plant, which determines seed tissue/ organ organization and the nature of the seed storage compounds. Specifically, the seeds of the Poaceae family of monocots are characterized by a starch-and protein-filled endosperm, and their catabolism by digestive enzymes produced in the outermost layer of the endosperm (i.e. the aleurone) provides the carbonbased and nitrogenous precursors for the growth of the embryo, which is composed of the embryonic ax...

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Section: Differential Distributions Of Lipid Classes Accentuated In Tmentioning

confidence: 99%

Spatial Mapping and Profiling of Metabolite Distributions during Germination

et al. 2017

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“…Processing of over 55 million tandem mass spectra from different publicly available datasets using OpenMS led them to discover over 40 new protein-coding gene annotations in the GENCODE human reference genome [45] . In addition to the identification of novel genes, the information gained in a proteogenomic analysis pertaining to known proteins can also be utilized, for example, to elucidate tissue-specific protein expression levels [46] .…”

Section: Swath Data Analysismentioning

confidence: 99%

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

et al. 2016

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“…(Zhao et al, 2014) Ferritin up-regulation occurred after SPION and Au-NP treatment, and similar effects were observed after C. elegans exposure to arsenic, cadmium and ethosuximide. (Chen et al, 2013, Chen et al, 2015, Petryszak et al, 2016 Hence, the effects of SPIONs in iron homeostasis might be part of a more general response to toxicants and not necessarily linked to oxidative dissolution of the SPION core into free iron.…”

Section: Evaluation Of Specific Molecular Markersmentioning

confidence: 99%

Toxicogenomics of iron oxide nanoparticles in the nematodeC. elegans

Gonzalez-Moragas

Benseny‐Cases

et al. 2017

Nanotoxicology

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Toxicogenomics of iron oxide nanoparticles in the nematode C. elegansWe present a mechanistic study of the effect of iron oxide nanoparticles (SPIONs) in C. elegans combining a genome-wide analysis with the investigation of specific molecular markers frequently linked to nanotoxicity. The effects of two different coatings were explored: citrate, an anionic stabilizer, and bovine serum albumin, as a pre-formed protein corona. The transcriptomic study identified differentially expressed genes following an exposure to SPIONs. The expression of genes involved in oxidative stress, metal detoxification response, endocytosis, intestinal integrity and iron homeostasis was quantitatively evaluated. The role of oxidative stress was confirmed by gene expression analysis and by synchrotron Fourier Transform infrared microscopy based on the higher tissue oxidation of NP-treated animals. The observed transcriptional modulation of key signaling pathways such as MAPK and Wnt suggests that SPIONs might be endocytosed by clathrin-mediated processes, a putative mechanism of nanotoxicity which deserves further mechanistic investigations.

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Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

Cited by 512 publications

References 29 publications

Spatial Mapping and Profiling of Metabolite Distributions during Germination

Spatial Mapping and Profiling of Metabolite Distributions during Germination

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

Toxicogenomics of iron oxide nanoparticles in the nematodeC. elegans

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