CN107609341A - Based on shortest path from global interactions between protein network extraction sub-network method and system - Google Patents
Based on shortest path from global interactions between protein network extraction sub-network method and system Download PDFInfo
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- CN107609341A CN107609341A CN201710703560.7A CN201710703560A CN107609341A CN 107609341 A CN107609341 A CN 107609341A CN 201710703560 A CN201710703560 A CN 201710703560A CN 107609341 A CN107609341 A CN 107609341A
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Abstract
The present invention provides a kind of method and system for extracting sub-network from global interactions between protein network based on shortest path, destination node is matched two-by-two and extracts shortest path, shortest path is split to obtain all interactions between protein pair, visual sub-network is obtained to data by interactions between protein.The inventive method is simple, fast, should be readily appreciated that and operates, and the albumen in global interactions between protein network in the absence of direct interaction can be made to find its interconnected shortest path, and form sub-network using the node involved by shortest path.
Description
Technical field
The invention belongs to field of bioinformatics, especially relates to one kind from global interactions between protein network based on most short
The method and system of path extraction sub-network.
Background technology
Global interactions between protein network describes as the important feature of bioinformatics, directly reflects living organism function.And
Usually needed in practical study for some function progress in-depth study, such as immunologic function, signal transduction pathway, this
With regard to needing the sub-network that selection is related to objective function in global interactions between protein network further to be studied, i.e., in the overall situation
Destination node interested is chosen in interactions between protein network according to research purpose, and the sub-network that these nodes are formed is carried out deep
Enter research.
Prior art means are typically directly by global interactions between protein net in the associated path between obtaining destination node
All paths related to destination node all extract composition sub-network in network, the sub-network carried such as cytoscape softwares
Abstraction function.But for the angle of biology, shorter path of information flow is more efficient, also more meets the mistake of biological evolution
Journey, i.e. biology are always towards the direction evolution most useful for its own existence.Therefore more reasonable believable destination node how is built
Sub-network, turning into needs the subject matter that solves.
The content of the invention
The problem to be solved in the present invention is to propose a kind of method, finds in global interactions between protein network and appoints between destination node
The node anticipated involved by point-to-point transmission shortest path, and form sub-network using these nodes.
In order to achieve the above object, the technical scheme taken of the present invention is：One kind is mutual from global albumen based on shortest path
The method for making to extract sub-network in network, including：Destination node is matched two-by-two and extracts shortest path, shortest path is split
All interactions between protein pair are obtained, visual sub-network is obtained to data by interactions between protein.
Further, the extracting method of the destination node is：Arbitrarily chosen from global interactions between protein network interested
Destination node, the quantity of destination node is no more than global interactions between protein nodes sum.
Further, the extracting method of the shortest path is：
(1) all destination nodes of selection are matched two-by-two, the group of all pairings is obtained according to permutation and combination method
Close；
(2) two albumen being related to during each is combined calculate most short between 2 points as beginning and end
Path；
(3) shortest path all in every kind of combination all extracts.
Further, the specific method of the shortest path fractionation is：All shortest paths extracted all split into egg
The interactions between protein pair of interaction two-by-two in vain, the repetitive proteins obtained in different shortest paths are mutually opposed deletion after fractionation, that is, obtained
Form all interactions between protein pair of interactions between protein sub-network.
Further, the method that obtains of the visualization sub-network is：By obtained interactions between protein to data input
Cytoscape softwares, obtain visual sub-network figure.
Present invention also offers a kind of system for extracting sub-network from global interactions between protein network based on shortest path, bag
Include：
Shortest path extraction module, for being matched destination node two-by-two and extracting shortest path；
Shortest path splits module, for splitting shortest path to obtain all interactions between protein pair；
Sub-network module：For data to be obtained with visual sub-network by interactions between protein.
Further, in addition to destination node chooses module, emerging for arbitrarily choosing sense from global interactions between protein network
The destination node of interest, the quantity of destination node are no more than global interactions between protein nodes sum.
Further, the shortest path extraction module includes：
Pairing unit, for being matched two-by-two to all destination nodes of selection, institute is obtained according to permutation and combination method
There is the combination of pairing；
Computing unit, two albumen for being related to during each is combined calculate at 2 points as beginning and end
Between shortest path；
Extraction unit, for shortest path all in every kind of combination all to be extracted.
Further, the shortest path splits module and included：
Split cells, for all shortest paths extracted all to be split into the interactions between protein pair of albumen interaction two-by-two；
Unit is deleted, for the repetitive proteins obtained in different shortest paths mutually to be opposed deletion after fractionation.
Further, the sub-network module includes：
Cytoscape software units, for, to data input cytoscape softwares, obtaining can by obtained interactions between protein
Depending on the sub-network figure of change.
The method and system proposed by the present invention for extracting sub-network from global interactions between protein network based on shortest path, with
Prior art is compared, and is had the beneficial effect that：
(1) by means of the invention it is possible to make the albumen in global interactions between protein network in the absence of direct interaction find it
Interconnected shortest path, and form sub-network using the node involved by shortest path；
(2) the inventive method is simple, fast, should be readily appreciated that and operates.
(3) method of this method by extracting shortest path, obtain closer to real information transmittance process in organism
Interactions between protein path, then fractionation and visualization by shortest path, obtain the sub-network being more consistent with objective function, with
Prior art is compared, and this method more conforms to biological evolution theory, and obtained sub-network is more rationally credible, with more biology
Meaning.
Brief description of the drawings
Fig. 1 is the schematic flow sheet of the present invention；
The shortest path that Fig. 2 is the present invention chooses schematic diagram；
Fig. 3 is that sub-network figure is immunized in the wnt signal paths of the embodiment of the present invention.
Embodiment
With reference to specific embodiment, the present invention will be further described.
Need to choose destination node from global interactions between protein network in bioinformatics research, but between these destination nodes
Directly interaction phenomenon two-by-two may be not present, can be found between destination node using the method for the present invention most short between any two points
Node involved by path, and form sub-network using these nodes.The method of the present invention is as shown in figure 1, be divided into target section
Point is chosen, extracts shortest path, path is split and sub-network visualizes four steps.
(1) destination node is chosen：According to the research purpose of user, it is emerging sense can arbitrarily to be chosen from global albumen network
The destination node of interest, the quantity of destination node are no more than global network interior joint sum.
(2) shortest path is extracted：All destination nodes of selection are matched two-by-two, obtained according to permutation and combination method
The combination of all pairings.Two albumen being related to during each is combined are calculated between 2 points as beginning and end
Shortest path.As shown in Fig. 2 do not have direct interaction between destination node A albumen and Z albumen, but by following
What four approach connected together：A-B-C-D-Z；A-E-F-Z；A-G-H-Z；A-W-Q-M-N-Z.And shortest path rule is to carry
Take out A to Z between institute through node at least that paths.It is A-E-F-Z and A-G-H-Z in fig. 2.Involved by point-to-point transmission
Shortest path may more than one, we need to extract them.All albumen can be obtained in this way
Shortest path between two albumen of centering.
(3) path is split：All shortest paths extracted in step (2) are all split into the shape of albumen interaction two-by-two
Formula, as the A-E-F-Z paths in Fig. 2 may be split into A-E, tri- interactions between protein pair of E-F, F-Z.By different shortest paths after fractionation
In obtained repetitive proteins mutually oppose deletion, that is, obtain forming all interactions between protein pair of interactions between protein sub-network.
(4) sub-network visualizes：By the interactions between protein obtained in step (3) to data input cytoscape softwares, you can
Obtain visual sub-network figure.
Lower mask body is applied to the extraction conduct that sub-network is immunized in Environment of Litopenaeus vannamei Low wnt signal paths with the inventive method
Embodiment illustrates：
Experiment uses in the early-stage Study of laboratory the Environment of Litopenaeus vannamei Low immune protein interaction network that builds as global network,
The network altogether comprising point 2446, choose condition and be included in global interaction network by 32815, side, target protein, and
Approach annotation is the albumen of wnt signal paths in KEGG databases.Then, exempted from using this patent methods described from Environment of Litopenaeus vannamei Low
The shortest path between the albumen with immunologic function in wnt signal paths, structure are extracted in epidemic disease albumen overall situation interaction network
Sub-network is immunized into wnt signal paths.Specific method is as follows：
(1) destination node is chosen：Choose and be included in Environment of Litopenaeus vannamei Low immune protein overall situation interaction network, and
Approach annotates the albumen for wnt signal paths as destination node in KEGG databases, and 6 destination nodes are obtained, are respectively
P09615, P18289, Q9V3Q6, Q7JWS8, P49768, P18537, but be not arbitrarily between the two between these destination nodes
All there is direct interaction relationship；
(2) all destination nodes of selection are matched two-by-two, the group of all pairings is obtained according to permutation and combination method
Close, totally 15 pairs.Wherein there was only two pairs of direct interaction relationships of presence, direct interaction relationship is not present in other.
Two albumen being related to during each is combined calculate the shortest path between 2 points, are obtained as beginning and end
59 shortest paths；
(3) shortest path obtained in step (2) is split as to the albumen pair of interaction two-by-two, 132 albumen are obtained
Mutually oppose, wherein there are 56 repetitive proteins mutually to oppose, remove after repeating, 76 interactions between protein pair are obtained；
(4) interactions between protein that step (3) obtains is obtained into visual wnt letters to data input cytoscape softwares
Number path is immunized sub-network, and the network includes node 41,76, side, as shown in Figure 3.
The foregoing is only the present invention specific embodiment, the protection domain being not intended to limit the present invention, it is all
Within the spirit and principles in the present invention, any modification, equivalent substitution and improvements done etc., the protection of the present invention should be included in
Within the scope of.
Claims (10)
- A kind of 1. method for extracting sub-network from global interactions between protein network based on shortest path, it is characterised in that including：Will Destination node is matched and extracts shortest path two-by-two, and shortest path is split to obtain all interactions between protein pair, passes through interactions between protein Data are obtained with visual sub-network.
- 2. according to the method for claim 1, it is characterised in that the extracting method of the destination node is：From global albumen Destination node interested is arbitrarily chosen in interaction network, the quantity of destination node is no more than global interactions between protein nodes Sum.
- 3. according to the method for claim 1, it is characterised in that the extracting method of the shortest path is：(1) all destination nodes of selection are matched two-by-two, the combination of all pairings is obtained according to permutation and combination method；(2) two albumen being related to during each is combined calculate the shortest path between 2 points as beginning and end；(3) shortest path all in every kind of combination all extracts.
- 4. according to the method for claim 1, it is characterised in that the specific method that the shortest path is split is：Extract All shortest paths all split into the interactions between protein pair of albumen interaction two-by-two, the weight that will be obtained after fractionation in different shortest paths Recoverin is mutually opposed deletion, that is, obtains forming all interactions between protein pair of interactions between protein sub-network.
- 5. according to the method for claim 1, it is characterised in that it is described visualization sub-network the method that obtains be：It will obtain Interactions between protein to data input cytoscape softwares, obtain visual sub-network figure.
- A kind of 6. system for extracting sub-network from global interactions between protein network based on shortest path, it is characterised in that including：Shortest path extraction module, for being matched destination node two-by-two and extracting shortest path；Shortest path splits module, for splitting shortest path to obtain all interactions between protein pair；Sub-network module：For data to be obtained with visual sub-network by interactions between protein.
- 7. system according to claim 6, it is characterised in that also module is chosen including destination node, for from global egg Destination node interested is arbitrarily chosen in white interaction network, the quantity of destination node, which is no more than in global interactions between protein network, to be saved Point sum.
- 8. system according to claim 6, it is characterised in that the shortest path extraction module includes：Pairing unit, for being matched two-by-two to all destination nodes of selection, all match somebody with somebody is obtained according to permutation and combination method To combination；Computing unit, two albumen for being related to during each is combined are calculated between 2 points as beginning and end Shortest path；Extraction unit, for shortest path all in every kind of combination all to be extracted.
- 9. system according to claim 6, it is characterised in that the shortest path, which splits module, to be included：Split cells, for all shortest paths extracted all to be split into the interactions between protein pair of albumen interaction two-by-two；Unit is deleted, for the repetitive proteins obtained in different shortest paths mutually to be opposed deletion after fractionation.
- 10. system according to claim 6, it is characterised in that the sub-network module includes：Cytoscape software units, for obtained interactions between protein to data input cytoscape softwares, to be visualized Sub-network figure.
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| CN102339362A (en) * | 2011-11-08 | 2012-02-01 | 苏州大学 | Method for extracting protein interaction relationship |
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| CN106874708A (en) * | 2017-01-23 | 2017-06-20 | 陕西师范大学 | The method that key protein matter is recognized using the artificial bee colony optimized algorithm of the mechanism of looking for food |
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| US20040059522A1 (en) * | 2002-09-23 | 2004-03-25 | Kyungsook Han | Method for partitioned layout of protein interaction networks |
| CN101246520A (en) * | 2008-03-18 | 2008-08-20 | 中南大学 | Protein complex recognizing method based on range estimation |
| CN102339362A (en) * | 2011-11-08 | 2012-02-01 | 苏州大学 | Method for extracting protein interaction relationship |
| CN103093119A (en) * | 2013-01-24 | 2013-05-08 | 南京大学 | Method for recognizing significant biologic pathway through utilization of network structural information |
| CN106874708A (en) * | 2017-01-23 | 2017-06-20 | 陕西师范大学 | The method that key protein matter is recognized using the artificial bee colony optimized algorithm of the mechanism of looking for food |
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