Cell communication analysis method and system

A technology of cell communication and analysis method, applied in biostatistics, bioinformatics, informatics, etc., to achieve a wide range of applications, easy in-depth interpretation, and easy correlation effects

Active Publication Date: 2021-03-09
GUANGZHOU GENE DENOVO BIOTECH
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

To sum up, the analysis technology of cell communication is very important and widely used, but there is no comprehensive and in-depth study of the molecular mechanism of intercellular communication, and the data results are displayed in various graphical forms. Therefore, the present invention provides a cell communication analysis method, which can be applied to further cell communication analysis of single-cell transcriptome sequencing data. The analysis process is efficient, the analysis content is comprehensive, and the analysis results are visualized.

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  • Cell communication analysis method and system
  • Cell communication analysis method and system

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Embodiment 1

[0038] Such as figure 1 As shown, the present invention discloses a cell communication analysis method, including cell communication prediction and ligand-target gene regulatory prediction, the specific method is as follows:

[0039] Cell communication forecast

[0040] 1.1 Response to expression abundance analysis

[0041] Enter a single cell gene expression matrix, using the ligand-receptor information contained in the CellPhoneDB software, based on a cell expressing receptor and another cell expression ligand to analyze each pair of cell ligand-receptor pairs Express abundance.

[0042] This embodiment analyzes only the receptors and ligands that are larger than the cell expression of the threshold percentage percentage in a particular cluster (by default 10%). Only the top 25 pair of p-value is shown in the top 10 to the previous 10 to the expression abundance information ( figure 2 ). Preferably, the information specifically displayed by the graphic can be adjusted accordin...

Embodiment 2

[0062] Such as Figure 7 As shown, the present invention also provides a cell communication analysis system including a cell communication prediction module and a ligand-target gene regulatory prediction module;

[0063] The cell communication prediction module includes:

[0064] Responsible to the expression abundance analysis unit for inputting a single cell gene expression matrix, using the ligand-receptor information contained in the CellPhoneDB software, based on a cell expressing receptor and another cell expression ligand Each pair of ligands - receptor pairs have abundance.

[0065] The surrogate pair number analysis unit is used to obtain the number of surcharges expressed in each of the cells based on the analysis of the abundance of each pair of cells - receptor on each pair of cells, whereby the cells can be obtained. The communication relationship is preliminary assessment.

[0066] Significantly enrichment of the surcharge to the number of analytical units for compar...

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Abstract

The invention discloses a cell communication analysis method and system. The method comprises cell communication prediction and ligand-target gene regulation prediction. Cell communication predictioncomprises analysis of expression abundance of a ligand-receptor pair, analysis of the number of ligand-receptor pairs, analysis of the number of significantly enriched ligand-receptor pairs and construction of a cell interaction network diagram. The ligand-target gene regulation and control prediction comprises ligand activity analysis and ligand-target gene regulation and control potential analysis; the cell communication analysis method mainly comprises the following steps: describing an incidence relation among cells, constructing a cell communication network by utilizing CellphoneDB software based on a single-cell gene expression quantity matrix, and analyzing ligand activity and the regulation potential of a ligand on a target gene by utilizing NicheNet software based on a ligand-target gene expression relation. Various graphical results are displayed, so that the incidence relation between cells is convenient to research; a new basic scientific research idea can be provided for revealing a certain cell behavior and deeply analyzing a cell communication result.

Description

Technical field [0001] The present invention relates to the field of biological information analysis, and more particularly to a cell communication analysis method and system. Background technique [0002] Complex extracellular reactions begin with the binding of the ligand and its receptor and activation of a particular cellular signaling path, therefore, understanding and plotting the interaction of these ligands and receptors is to understand cellular behavior and the basis for adjacent cellular reactions. Many foundations of research mechanism research. However, the interaction mechanism within the organizational cell is very complicated, involving a variety of cells, as well as potential for thousands of ligand-receptor relationships, screening with traditional molecular biology methods, relying on researchers' experience, it is difficult to directly Lock the key cell interaction relationship. If the person is not accurate, the function verifies that there is a false positiv...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B40/00G16B50/00
CPCG16B40/00G16B50/00
Inventor 周煌凯高川陈飞钦艾鹏张秋雪
Owner GUANGZHOU GENE DENOVO BIOTECH
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