Increased expression of LCN2 formed a positive feedback loop with activation of the ERK pathway in human kidney cells during kidney stone formation

Zhang, Hui; Zhu, Jiang; Du, Qian; Zhao, Bo; Qiyuan, Kang; Shaohua, Bian; Yuan, Wenbing; Liu, Wei; Luo, Cheng; Shuangning, Liu; Li, Zhengyi; Li, Yingyi

doi:10.1038/s41598-020-75670-w

Cited by 4 publications

(4 citation statements)

References 18 publications

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“…One possible mechanism of “the increase of one gene’s expression level further increases its expression level” is a positive feedback loop between two genes (Hui et al. 2020 ). Here and promote each other, so that the increase of increases , which in return further increases .…”

Section: Setup and Main Resultsmentioning

confidence: 99%

Inference on autoregulation in gene expression with variance-to-mean ratio

Wang

2023

J. Math. Biol.

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Some genes can promote or repress their own expressions, which is called autoregulation. Although gene regulation is a central topic in biology, autoregulation is much less studied. In general, it is extremely difficult to determine the existence of autoregulation with direct biochemical approaches. Nevertheless, some papers have observed that certain types of autoregulations are linked to noise levels in gene expression. We generalize these results by two propositions on discrete-state continuous-time Markov chains. These two propositions form a simple but robust method to infer the existence of autoregulation from gene expression data. This method only needs to compare the mean and variance of the gene expression level. Compared to other methods for inferring autoregulation, our method only requires non-interventional one-time data, and does not need to estimate parameters. Besides, our method has few restrictions on the model. We apply this method to four groups of experimental data and find some genes that might have autoregulation. Some inferred autoregulations have been verified by experiments or other theoretical works.

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Section: Setup and Main Resultsmentioning

confidence: 99%

Inference on autoregulation in gene expression with variance-to-mean ratio

Wang

2023

J. Math. Biol.

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“…One possible mechanism of "the increase of one gene's expression level further increases its expression level" is a positive feedback loop between two genes [31]. Here V 1 and V 2 promote each other, so that the increase of V 1 increases V 2 , which in return further increases V 1 .…”

Section: Setup and Main Resultsmentioning

confidence: 99%

Fano factors in determining certain types of gene autoregulation

Wang¹,

He²

2023

Preprint

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The expression of one gene might be regulated by its corresponding protein, which is called autoregulation. Although gene regulation is a central topic in biology, autoregulation is much less studied. In general, it is extremely difficult to determine the existence of autoregulation with direct biochemical approaches. Nevertheless, some papers have observed that certain types of autoregulations are linked to noise levels in gene expression. We generalize these results by two propositions on discrete-state continuous-time Markov chains. These two propositions form a simple but robust method to infer the existence of autoregulation in certain scenarios from gene expression data. This method only depends on the Fano factor, namely the ratio of variance and mean of the gene expression level. Compared to other methods for inferring autoregulation, our method only requires non-interventional one-time data, and does not need to estimate parameters. Besides, our method has few restrictions on the model. We apply this method to four groups of experimental data and find some genes that might have autoregulation. Some inferred autoregulations have been verified by experiments or other theoretical works.

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“…For genes with position-specific expressions during development, it is common that the increase of one gene can further increase or decrease its level [8]. Nevertheless, this might due to a positive feedback loop between two genes [9], not necessarily autoregulation. We propose a rigorous definition for autoregulation.…”

Section: Introductionmentioning

confidence: 99%

Inference on autoregulation in gene expression

Wang¹,

He²

2022

Preprint

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Some genes can promote or repress their own expressions, which is called autoregulation. In general, it is extremely difficult to determine the existence of autoregulation with direct biochemical approaches. Nevertheless, autoregulations reveal themselves in gene expression profiles. We prove some mathematical propositions. Based on these propositions, we develop some simple but robust mathematical methods that infer the existence of autoregulation from gene expression data. We also apply our methods to experimental data to determine some genes that might have autoregulation.

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Increased expression of LCN2 formed a positive feedback loop with activation of the ERK pathway in human kidney cells during kidney stone formation

Cited by 4 publications

References 18 publications

Inference on autoregulation in gene expression with variance-to-mean ratio

Inference on autoregulation in gene expression with variance-to-mean ratio

Fano factors in determining certain types of gene autoregulation

Inference on autoregulation in gene expression

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