TBtools - an integrative toolkit developed for interactive analyses of big biological data

Chen, Chengjie; Chen, Hao; Zhang, Yi; Thomas, Hannah; Frank, Margaret H.; He, Yehua; Xia, Rui

doi:10.1101/289660

Cited by 942 publications

(1,095 citation statements)

References 6 publications

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“…(b) Heat map presenting the expression patterns of different TFs in response to diverse treatments. The heat map was drawn with TBtools (Chen et al, ).…”

Section: Resultsmentioning

confidence: 99%

Ethylene mediates the branching of the jasmonate‐induced flavonoid biosynthesis pathway by suppressing anthocyanin biosynthesis in red Chinese pear fruits

Zhao

Tao

et al. 2019

Plant Biotechnology Journal

136

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Summary Flavonoid accumulation in most fruits is enhanced by ethylene and jasmonate. However, little is known about the hormone functions related to red pear fruit coloration or their combined effects and potential underlying mechanisms. Various treatments were used to investigate the flavonoid metabolite profile and pear transcriptome to verify the effects of ethylene and jasmonate on flavonoid biosynthesis in red pear fruits as well as the mechanism behind this. Ethylene inhibits anthocyanin biosynthesis in red Chinese pear fruits, whereas jasmonate increases anthocyanin and flavone/isoflavone biosyntheses. The branching of the jasmonate‐induced flavonoid biosynthesis pathway is determined by ethylene. Co‐expression network and Mfuzz analyses revealed 4,368 candidate transcripts. Additionally, ethylene suppresses PpMYB10 and PpMYB114 expression via TF repressors, ultimately decreasing anthocyanin biosynthesis. Jasmonate induces anthocyanin accumulation through transcriptional or post‐translational regulation of TFs‐like MYB and bHLH in the absence of ethylene. However, jasmonate induces ethylene biosynthesis and the associated signalling pathway in pear, thereby decreasing anthocyanin production, increasing the availability of the precursors for flavone/isoflavone biosynthesis and enhancing deep yellow fruit coloration. We herein present new phenotypes and fruit coloration regulatory patterns controlled by jasmonate and ethylene, and confirm that the regulation of fruit coloration is complex.

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“…(b) Heat map presenting the expression patterns of different TFs in response to diverse treatments. The heat map was drawn with TBtools (Chen et al, ).…”

Section: Resultsmentioning

confidence: 99%

Ethylene mediates the branching of the jasmonate‐induced flavonoid biosynthesis pathway by suppressing anthocyanin biosynthesis in red Chinese pear fruits

Zhao

Tao

et al. 2019

Plant Biotechnology Journal

136

View full text Add to dashboard Cite

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“…The results show that the analysis is statistically significant. The software TBtools (version 0.665) can be used to analyze the overlapping DEGs in three data sets 19 …”

Section: Methodsmentioning

confidence: 99%

Identification of potential hub genes via bioinformatics analysis combined with experimental verification in colorectal cancer

Zhou

Yang

Yue

et al. 2020

Molecular Carcinogenesis

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Colorectal cancer (CRC) is a kind of malignant cancer with high morbidity and mortality. The purpose of this study was to explore potential regulated key genes involved in CRC through bioinformatics analysis and experimental verification. The gene expression profile data were downloaded from the Gene Expression Omnibus, and the differential expression genes were detected in cancerous and paracancerous samples of CRC patients, respectively. Then functional enrichment analysis, such as the Kyoto Encyclopedia of Genes and Genomes pathway analysis as well as the protein‐protein interaction network were constructed, and the highly related genes were clustered by Molecular COmplex DEtection algorithm to find out the core interaction in different genes' crosstalk. The genes affecting CRC prognosis were screened by the Human Protein Atlas database. In addition, the expression level of core genes was detected by GEPIA database, and the core genes' changes in large‐scale cancer genome data set were directly analyzed by cBioPortal database. The expression of the predicted hub genes DSN1, AHCY, and ERCC6L was verified by reverse‐transcription quantitative polymerase chain reaction in CRC cells. The gene function of DSN1 was analyzed by wound healing and colony formation assays. The results showed that silencing of DSN1 could significantly reduce the migration and proliferation of CRC cells. Further, BUB1B, the potential interacting protein of DSN1, was also predicted via bioinformatics analysis. Above all, this study shows that bioinformatics analysis combined with experimental method verification provide more potential vital genes for the prevention and therapy of CRC.

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“…Conservation of miR528 precursors was presented using Circos according to the method from (Chorostecki et al, 2017). Syntenic relationships among species were analyzed using MCScanX and visualized by TBTOOLS (Chen et al, 2018a). The un-rooted tree of laccases was reconstructed with RAXML with default settings (Stamatakis, 2014).…”

Section: Comparative Genomic Analysismentioning

confidence: 99%

MicroRNA528, a hub regulator modulating ROS homeostasis via targeting of a diverse set of genes encoding copper‐containing proteins in monocots

et al. 2019

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Summary Plant microRNAs (miRNAs) regulate vital cellular processes, including responses to extreme temperatures with which reactive oxygen species (ROS) are often closely associated. In the present study, it was found that aberrant temperatures caused extensive changes in abundance to numerous miRNAs in banana fruit, especially the copper (Cu)‐associated miRNAs. Among them, miR528 was significantly downregulated under cold stress and it was found to target genes encoding polyphenol oxidase (PPO), different from those identified in rice and maize. Expression of PPO genes was upregulated by > 100‐fold in cold conditions, leading to ROS surge and subsequent peel browning of banana fruit. Extensive comparative genomic analyses revealed that the monocot‐specific miR528 can potentially target a large collection of genes encoding Cu‐containing proteins. Most of them are actively involved in cellular ROS metabolism, including not only ROS generating oxidases, but also ROS scavenging enzymes. It also was demonstrated that miR528 has evolved a distinct preference of target genes in different monocots, with its target site varying in position among/within gene families, implying a highly dynamic process of target gene diversification. Its broad capacity to target genes encoding Cu‐containing protein implicates miR528 as a key regulator for modulating the cellular ROS homeostasis in monocots.

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TBtools - an integrative toolkit developed for interactive analyses of big biological data

Cited by 942 publications

References 6 publications

Ethylene mediates the branching of the jasmonate‐induced flavonoid biosynthesis pathway by suppressing anthocyanin biosynthesis in red Chinese pear fruits

Ethylene mediates the branching of the jasmonate‐induced flavonoid biosynthesis pathway by suppressing anthocyanin biosynthesis in red Chinese pear fruits

Identification of potential hub genes via bioinformatics analysis combined with experimental verification in colorectal cancer

MicroRNA528, a hub regulator modulating ROS homeostasis via targeting of a diverse set of genes encoding copper‐containing proteins in monocots

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