Analysis of the chemical toxicity effects using the enrichment of Gene Ontology terms and KEGG pathways

Lei, Chen; Zhang, Yuhang; Zou, Quan; Chu, Chengcai; Ji, Zhiliang

doi:10.1016/j.bbagen.2016.05.015

Cited by 16 publications

(8 citation statements)

References 70 publications

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“…Some important KEGG signaling pathways were found, which were inferred to be significant in determining chemical toxicity. The discovery can promote our understanding of different mechanisms of chemical toxicity and help us to develop the potential of new chemical toxicity prediction . So KEGG pathway annotation of differentially expressed proteins can help us understand the metabolic or signaling processes that these differentially expressed proteins may participate. , …”

Section: Resultsmentioning

confidence: 99%

“…The discovery can promote our understanding of different mechanisms of chemical toxicity and help us to develop the potential of new chemical toxicity prediction. 29 So KEGG pathway annotation of differentially expressed proteins can help us understand the metabolic or signaling processes that these differentially expressed proteins may participate. 30,31 As shown in Figure 6A, KEGG results of up-regulation of differentially expressed proteins showed that the most differentially expressed proteins were found in metabolic pathway, biosynthesis of secondary metabolites, biosynthesis of antibiotics, biosynthesis of amino acids, and ribosome pathway.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

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Mechanism of Action of Novel Pyrazole Carboxamide Containing a Diarylamine Scaffold against Rhizoctonia solani

Zhao

Yang

Deng

et al. 2020

J. Agric. Food Chem.

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In the last few decades, Rhizoctonia solani causing rice sheath blight has resulted in a lot of economic losses in the world. Therefore, many novel pyrazole carboxamide fungicides have been intensively researched and employed to fight against it. In this regard, in recent years, our group reported a novel pyrazole carboxamide containing a diarylamine scaffold with good antifungal activity against rice sheath blight in the pot test and field trial. Following this project, the antifungal mechanism of action of the pyrazole carboxamide has been elucidated in this work. The antifungal result showed that compound SCU2028, N-[2-[(3chlorophenyl)amino]-phenyl]-3-(difluoromethyl)-1-methyl-1H-pyrazole-4-carboxamide, was equivalent to the commercial fungicide thifluzamide and its EC 50 value was 0.022 mg/L against R. solani. Also, the observation results by scanning electron microscopy and transmission electron microscopy showed that it could destroy the fungus' cell walls or membranes and result in the leakage of contents and increase of the number of mitochondria and abnormal morphology. Meanwhile, the result on the mitochondrial membrane potential (MMP) showed that it could decrease R. solani's MMP. Furthermore, the results by label-free quantitative proteomic analysis showed that 1153 proteins were found after R. solani was treated with compound SCU2028, including 212 proteins in the control group and 257 proteins in the treatment group. A total of 142 differential proteins were obtained, of which 92 proteins were upregulated and 50 proteins were downregulated. The differentially expressed proteins affected a series of physiological and biochemical pathways in the mitochondria, endoplasmic reticulum, ribosome, and other related GO and KEGG pathways. In particular, the inhibition of the respiratory chain caused by the TCA cycle and oxidative phosphorylation KEGG pathway indicated that complex II (succinate dehydrogenase) and complex IV (cytochrome oxidase) might be compound SCU2028's main action targets. In addition, multiple experiments of qRT-PCR, enzyme activity detection, and molecular docking confirmed complex II and complex IV as targets. It could be seen that these findings provided a theoretical support for further research and development of the pyrazole carboxamide fungicides.

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Section: Resultsmentioning

confidence: 99%

Section: ■ Results and Discussionmentioning

confidence: 99%

Mechanism of Action of Novel Pyrazole Carboxamide Containing a Diarylamine Scaffold against Rhizoctonia solani

Zhao

Yang

Deng

et al. 2020

J. Agric. Food Chem.

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“…With the advance of high-throughput sequencing technologies, GO annotations have been good predictors of the functions and trends of genes [42]. KEGG is a reference knowledge database that describes the functional pathways that contribute to disease processes, and it is extensively used in enrichment analyses [43,44]. Reactome analysis is utilized to visualize mRNA expression data and can be combined with other databases [45].…”

Section: Discussionmentioning

confidence: 99%

Expression Profile Analysis of Differentially Expressed Circular RNAs in Steroid-Induced Osteonecrosis of the Femoral Head

Zhu

et al. 2019

Disease Markers

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Background. A growing number of studies have suggested that circular RNAs (circRNAs) serve as potential diagnostic biomarkers in many diseases. However, the role of circRNAs in steroid-induced osteonecrosis of the femoral head (SONFH) has not been reported. Methods. Secondary sequencing was performed to profile circRNA expression in peripheral blood samples from three SONFH patients and three healthy individuals. We confirmed our preliminary findings by qRT-PCR. Bioinformatics analysis was conducted to predict their functions. Results. The result showed 345 dysregulated circRNAs. qRT-PCR of eight selected circRNAs preliminarily confirmed the results, which were consistent with RNA sequencing. Bioinformatics analyses were performed to predict the functions of circRNAs to target the genes of miRNAs and the networks of circRNA-miRNA-mRNA interactions. Conclusions. This study provides a new and fundamental circRNA profile of SONFH and a theoretical basis for further studies on the functions of circRNAs in SONFH.

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“…According to Chen, previously described differentially expressed genes methods were used for Gene Ontology and KEGG enrichment analysis [29]. Unigenes were annotated by using Nr (non-redundant protein) annotation results.…”

Section: Methodsmentioning

confidence: 99%

Comparative transcriptomic analysis and endocuticular protein gene expression of alate adults, workers and soldiers of the termite Reticulitermes aculabialis

Rasheed

Meng

et al. 2019

BMC Genomics

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Background The insect cuticle is mainly composed of exocuticle and endocuticle layers that consist of a large number of structural proteins. The thickness and synthesis of the exocuticle depend on different castes that perform various functions in alates, workers and soldiers. However, it is not clear whether the soft endocuticle is involved in the division of labour in termite colonies. To reveal the structural characteristics of the endocuticle in different castes, we investigated the thickness of endocuticle layers in alates, workers and soldiers of the termite Reticulitermes aculabialis, and then we sequenced their transcriptome and detected the endocuticle protein genes. The differential expression levels of the endocuticular protein genes were confirmed in the three castes. Results We found that there was a great difference in the thickness of the endocuticle among the alates, soldiers and workers. The thickest endocuticle layers were found in the heads of the workers 7.88 ± 1.67 μm. The endocuticle layer in the head of the workers was approximately three-fold and nine-fold thicker than that in the heads of soldiers and alates, respectively. The thinnest endocuticle layers occurred in the head, thorax and abdomen of alates, which were 0.86 ± 0.15, 0.76 ± 0.24 and 0.52 ± 0.17 μm thick, respectively, and had no significant differences. A total of 43,531,650 clean sequencing reads was obtained, and 89,475 unigenes were assembled. Of the 70 identified cuticular protein genes, 10 endocuticular genes that belong to the RR-1 family were selected. qRT-PCR analysis of the five endocuticular genes (SgAbd-2, SgAbd-9, Abd-5, SgAbd-2-like and Abd-4-like) revealed that the endocuticle genes were more highly expressed in workers than in soldiers and alates. Conclusion These results suggest that SgAbd and Abd are the key components of the endocuticle. We infer that the thicker endocuticle in workers is helpful for them to perform their functions against environmental stress.

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Analysis of the chemical toxicity effects using the enrichment of Gene Ontology terms and KEGG pathways

Cited by 16 publications

References 70 publications

Mechanism of Action of Novel Pyrazole Carboxamide Containing a Diarylamine Scaffold against Rhizoctonia solani

Mechanism of Action of Novel Pyrazole Carboxamide Containing a Diarylamine Scaffold against Rhizoctonia solani

Expression Profile Analysis of Differentially Expressed Circular RNAs in Steroid-Induced Osteonecrosis of the Femoral Head

Comparative transcriptomic analysis and endocuticular protein gene expression of alate adults, workers and soldiers of the termite Reticulitermes aculabialis

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