A Gene Network Inference Method Based on Modular Recognition

A gene network and reasoning method technology, which is applied in the field of gene network reasoning based on modular recognition, can solve problems such as inability to cut into research gene modules, and achieve the effect of increasing biological interpretability, speed and accuracy

Active Publication Date: 2022-07-12
ZHEJIANG UNIV
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Problems solved by technology

However, the prerequisite for the application of most classical gene module identification algorithms is the nee...

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  • A Gene Network Inference Method Based on Modular Recognition
  • A Gene Network Inference Method Based on Modular Recognition
  • A Gene Network Inference Method Based on Modular Recognition

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Embodiment Construction

[0060] The specific embodiments of the present invention are described below to facilitate any person skilled in the art to understand the present invention, but the protection scope of the present invention is not limited to the scope of the specific embodiments. The technical solution of the invention and its inventive concept are equivalently replaced or changed, and should be covered within the protection scope of the present invention.

[0061] The technical solutions of the present invention will be further described in detail below through embodiments and in conjunction with the accompanying drawings.

[0062] The hardware environment in which this embodiment runs: a laptop computer, CPU: 2.6GHz, RAM: 8.0GB; software environment: Python 3.6, R 3.3.3; operating platform: Win10.

[0063] This example tests the effect of the proposed method on time-series datasets and single-cell datasets. The datasets include: the gonadal sex determination (GSD) dataset in the BEELINE pro...

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Abstract

The invention discloses a gene network reasoning method based on modular identification. The method takes the expression information of n genes as the training set, and each gene has m samples; uses the ICA-FDR algorithm to identify the gene modules and divides the n genes into different gene modules; the regulation relationship within the gene module The algorithm based on gradient boosting tree is used for inference, and the regulatory relationship between gene modules is inferred by the algorithm based on sparse regression, and the correlation score of each gene pair is obtained; for each gene module and inter-module reasoning The obtained correlation scores were respectively normalized and merged, and sorted in descending order to obtain the final gene regulatory network. The invention provides a seamless fusion framework for gene module identification and gene network reasoning, improves the accuracy of gene module identification, and increases the interpretability of gene regulation network functions.

Description

technical field [0001] The invention belongs to the field of gene regulation network reasoning in bioinformatics, in particular to a gene network reasoning method based on modular recognition. Background technique [0002] How to accurately elucidate the regulatory relationship between regulatory factors and target genes at the transcriptional level is one of the core challenges of computational biology and bioinformatics in recent years. A more accurate identification of the regulatory relationship between transcriptional regulators and target genes is crucial for exploring the laws of cell growth and division, cell differentiation and development. In addition, the gene regulatory network provides a powerful help for modern medical research, which can simulate and predict disease-causing genes from the perspective of the lowest level of life activities - gene control, which will help medical staff to accurately implement targeted therapy for patients, and have Contribute t...

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Application Information

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IPC IPC(8): G16B5/00G16B40/00
CPCG16B5/00G16B40/00Y02A90/10
Inventor 张蔚李心语张建明李光
Owner ZHEJIANG UNIV
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