CN109726352A - A kind of construction method of the gene regulatory network based on Differential Equation Model - Google Patents
A kind of construction method of the gene regulatory network based on Differential Equation Model Download PDFInfo
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- CN109726352A CN109726352A CN201811577131.0A CN201811577131A CN109726352A CN 109726352 A CN109726352 A CN 109726352A CN 201811577131 A CN201811577131 A CN 201811577131A CN 109726352 A CN109726352 A CN 109726352A
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- 108090000623 proteins and genes Proteins 0.000 title claims abstract description 47
- 230000001105 regulatory effect Effects 0.000 title claims abstract description 30
- 238000010276 construction Methods 0.000 title claims abstract description 10
- 230000014509 gene expression Effects 0.000 claims abstract description 20
- 238000000034 method Methods 0.000 claims abstract description 10
- 230000008859 change Effects 0.000 claims abstract description 6
- 230000022131 cell cycle Effects 0.000 claims abstract description 5
- 230000001276 controlling effect Effects 0.000 claims abstract description 4
- 230000003993 interaction Effects 0.000 claims abstract description 4
- 238000012916 structural analysis Methods 0.000 claims abstract description 4
- 238000012795 verification Methods 0.000 claims abstract description 3
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- 230000008569 process Effects 0.000 abstract description 2
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Abstract
The present invention provides a kind of construction method of gene regulatory network based on Differential Equation Model, it is related to biotechnology and complex network scientific domain, step: the gene expression under the conditions of cell cycle and particular state is measured in different time points, observe in various time points or in the cell cycle gene expression situation of change, find controlling gene and target gene；The time series data of gene expression is obtained, time series data uses discretization method, is separated into several expressions；Using the iterative algorithm of ODE, is made accordingly according to modeling purpose and case study it is assumed that from the interaction relationship excavated in extensive gene expression data between gene, provide the topology controlment of gene regulatory network；Set the time delay of gene regulatory network；Gene network shapeization is shown and carries out structural analysis；To target gene regulation relationship by gene regulatory network experimental verification.The present invention reduces the disadvantage that complexity is higher, computationally intensive by the initialization process of data.
Description
Technical field
The present invention relates to biotechnology and complex network scientific domain more particularly to a kind of bases based on Differential Equation Model
Because of the construction method of regulated and control network.
Background technique
Gene supports the essential structure and performance of life.The race of life is stored, blood group, breeds, grow, apoptosis etc.
The all information of process.Environment and genetics interdepend, the weight such as procreation, cell division and protein synthesis of life of deducing
Want physiology course.
Explore regulation relationship and interaction mechanism between discovery gene be research hotspot in life science and before
Along theme, and inferring gene regulatory network from gene expression data is one of its research direction.
Organism passes through the regulation of gene level, transcriptional level etc., table in ontogenetic different times, different parts
Up to part different in genome, as a result, completing cell differentiation and ontogeny.The selective expression of gene refers to thin
In born of the same parents' differentiation, gene has the phenomenon that selection is expressed under specific time and steric requirements, as a result, foring form knot.
Building gene regulatory network mainly has the methods of Boolean network, the differential equation and Bayesian network at present, these sides
Method abstracts true regulated and control network all in different levels.
Defect existing for existing differential equation building gene regulatory network: complexity is higher, computationally intensive, antinoise energy
Power is poor, and the practicability is poor.
Summary of the invention
The purpose of the present invention is to provide a kind of construction methods of gene regulatory network based on Differential Equation Model, with solution
Certainly above-mentioned technical problem.
The present invention using following technical scheme in order to solve the above technical problems, realized:
A kind of construction method of the gene regulatory network based on Differential Equation Model, which comprises the following steps:
(1) gene expression in different time points under the conditions of cell cycle and particular state is measured, and observation is each
A time point is upper or in the cell cycle gene expression situation of change, find controlling gene and target gene；
(2) time series data of gene expression is obtained, time series data uses discretization method, is separated into several tables
Up to level；
(3) iterative algorithm for utilizing ODE is made corresponding it is assumed that from big according to modeling purpose and case study
The interaction relationship between gene is excavated in scale gene expression data, provides the topology controlment of gene regulatory network；
(4) time delay of gene regulatory network is set；
(5) Gene network shapeization is shown and carries out structural analysis；To target gene regulation relationship by gene tune
Control network experiment verifying.
Preferably, the time delay of the gene regulatory network is to postpone regulated and control network algorithm based on multiple spot.
The beneficial effects of the present invention are:
A kind of construction method of the gene regulatory network based on Differential Equation Model of the present invention, at the initialization of data
Reason, reduces the disadvantage that complexity is higher, computationally intensive.Gene expression dose can be described well simultaneously to change over time
Gesture, and Reconstructing transcriptional regulatory networks, have noise resisting ability.
Specific embodiment
In order to be easy to understand the technical means, the creative features, the aims and the efficiencies achieved by the present invention, tie below
Specific embodiment is closed, the present invention is further explained, and however, the following embodiments are merely preferred embodiments of the present invention, and not all.
Based on the implementation example in the implementation mode, those skilled in the art's obtained other realities without making creative work
Example is applied, protection scope of the present invention is belonged to.Experimental method in following embodiments is unless otherwise specified conventional method,
The materials, reagents and the like used in the following examples is commercially available unless otherwise specified.
Embodiment 1
A kind of construction method of the gene regulatory network based on Differential Equation Model, comprising the following steps:
(1) gene expression in different time points under the conditions of cell cycle and particular state is measured, and observation is each
A time point is upper or in the cell cycle gene expression situation of change, find controlling gene and target gene；
(2) time series data of gene expression is obtained, time series data uses discretization method, is separated into several tables
Up to level；
(3) time delay of gene regulatory network is set；
(4) algorithm for utilizing Differential Equation Model, determines function according to the relationship between function and its change rate；According to building
Mould purpose and case study are made simple it is assumed that the differential equation is established according to inherent law or with analogy method, to derive base
Because of regulated and control network；
(5) regulated and control network graphical representation and structural analysis is carried out；Experimental verification is carried out to target gene regulation relationship.
The basic principles, main features and advantages of the present invention have been shown and described above.The technology of the industry
For personnel it should be appreciated that the present invention is not limited to the above embodiments, described in the above embodiment and specification is only the present invention
Preference, be not intended to limit the invention, without departing from the spirit and scope of the present invention, the present invention also has various
Changes and improvements, these changes and improvements all fall within the protetion scope of the claimed invention.The claimed scope of the invention is by institute
Attached claims and its equivalent thereof.
Claims (2)
1. a kind of construction method of the gene regulatory network based on Differential Equation Model, which comprises the following steps:
(1) gene expression in different time points under the conditions of cell cycle and particular state is measured, when observing each
Between put the situation of change of gene expression in the upper or cell cycle, find controlling gene and target gene；
(2) time series data of gene expression is obtained, time series data uses discretization method, is separated into several expression water
It is flat；
(3) iterative algorithm for utilizing ODE is made corresponding it is assumed that from extensive according to modeling purpose and case study
The interaction relationship between gene is excavated in gene expression data, provides the topology controlment of gene regulatory network；
(4) time delay of gene regulatory network is set；
(5) Gene network shapeization is shown and carries out structural analysis；To target gene regulation relationship by gene regulatory network
Network experimental verification.
2. the construction method of the gene regulatory network according to claim 1 based on Differential Equation Model, it is characterised in that:
The time delay of the gene regulatory network is to postpone regulated and control network algorithm based on multiple spot.
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Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN111613268A (en) * | 2020-05-27 | 2020-09-01 | 中山大学 | Method for determining gene expression regulation mechanism based on single cell transcriptome data |
| CN113486952A (en) * | 2021-07-06 | 2021-10-08 | 大连海事大学 | Multi-factor model optimization method of gene regulation and control network |
Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN1717585A (en) * | 2002-11-25 | 2006-01-04 | Gni美国公司 | Inferring gene regulatory networks from time-ordered gene expression data using differential equations |
| CN102013039A (en) * | 2010-12-01 | 2011-04-13 | 杭州师范大学 | Gene regulatory network constructing method based on dynamic Bayesian network |
| CN106599607A (en) * | 2016-12-13 | 2017-04-26 | 北京林业大学 | Method for constructing photosynthetic pathway gene regulation network |
-
2018
- 2018-12-12 CN CN201811577131.0A patent/CN109726352A/en active Pending
Patent Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN1717585A (en) * | 2002-11-25 | 2006-01-04 | Gni美国公司 | Inferring gene regulatory networks from time-ordered gene expression data using differential equations |
| CN102013039A (en) * | 2010-12-01 | 2011-04-13 | 杭州师范大学 | Gene regulatory network constructing method based on dynamic Bayesian network |
| CN106599607A (en) * | 2016-12-13 | 2017-04-26 | 北京林业大学 | Method for constructing photosynthetic pathway gene regulation network |
Cited By (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN111613268A (en) * | 2020-05-27 | 2020-09-01 | 中山大学 | Method for determining gene expression regulation mechanism based on single cell transcriptome data |
| CN111613268B (en) * | 2020-05-27 | 2023-02-24 | 中山大学 | Method for determining gene expression regulation mechanism based on single cell transcriptome data |
| CN113486952A (en) * | 2021-07-06 | 2021-10-08 | 大连海事大学 | Multi-factor model optimization method of gene regulation and control network |
| CN113486952B (en) * | 2021-07-06 | 2023-09-05 | 大连海事大学 | Multi-factor model optimization method of gene regulation network |
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Application publication date: 20190507 |