KR100957386B1 - Method and system for extracting and displaying interaction networks between proteins and signal pathways by mapping protein-protein interaction and signal pathway information - Google Patents

Abstract

The present invention relates to a method and system for deriving and mapping the relationship between proteins and signaling pathways through the mapping of protein interaction information and protein signaling pathway information. The present invention provides a Protein-Protein Interaction (PPI) module that provides a schematic function of proteins interacting with the protein of interest; A Pathfinder module that provides a function of finding a signaling pathway including a protein that interacts with a single protein; A Path-Linker module that provides a function of representing an interaction distance between a plurality of proteins and a final protein present on a signaling pathway of interest; A Path-Marker module that provides a function of displaying a location and a frequency of final proteins interacting with a plurality of proteins on a signal transduction map; A path that finds a signal transduction path that is related to a plurality of proteins according to an interaction distance, statistically processes the signal transduction path according to the starting protein and the number of paths, and the priority of the final protein share in the signal transduction path. List (Path-Lister) module; And organisms, interaction types, interaction detection methods, number of information (number of DBs provided, and more) that can provide users with more accurate and reliable information. Filter module to apply filtering functions such as the number of related articles and the number of interaction detection methods).

Protein, interaction, signaling pathway, protein information database, protein interaction database, signaling pathway information database

Description

Method and system for extracting and displaying interaction networks between proteins and signal pathways by mapping protein-protein interaction and signal pathway information}

The present invention relates to a method and system for deriving and plotting a relationship between a protein and a signaling pathway through interaction between proteins and protein signaling pathway information. More particularly, the present invention relates to a starting protein name information and a signal related to a starting protein. A signaling pathway between the starting protein and the final protein, using the interaction distance information between the final protein and the starting protein present on the signal pathway, the name of the final protein and the signaling pathway information. A method and system for deriving interaction relationships.

Because proteins are the products of transcription and translation from DNA, replication is very difficult or practically impossible. Therefore, since a sample of a protein must be obtained directly from a living organism producing a protein, there are various ethical and technical limitations in obtaining a human protein sample. In this limited experimental environment, accurate information and a more intensive and organized database are needed for the sample that meets the purpose of the experiment.

Databases for existing protein groups contain only protein signaling pathways and genetic information, contain only protein interaction relationship information, or store only protein signaling pathway maps, allowing numerous proteins to systematically present interaction relationship information to users. There is no way to provide it.

That is, in the related art, the interaction or signaling pathways between proteins are independently displayed, so that systematic information on how proteins interacting with each other and how they are related to each other is shown. There is a problem that can not provide a systematic research direction for protein research to protein researchers.

In addition, since it is difficult to obtain individual information of the identified protein by performing proteome analysis, it is very difficult to process the identified proteome at once to obtain information of a common signaling pathway or proteins that interact in common.

In order to solve the above problems, the present invention derives not only the interaction relationship between proteins but also the related signaling pathways, thereby providing a basis for the direction of biological function research on proteins. Its purpose is to provide a method and system for deriving interaction relationships.

In addition, in order to solve the above problems, the present invention proceeds to the proteome analysis, etc. to provide the user or to prioritize common signaling pathway information or commonly interacting protein information for the identified protein It is an object of the present invention to provide a method and system for deriving interaction relationships between proteins.

In addition, in order to solve the above problems, the present invention provides information in the process of searching the interaction information and signaling information of the starting protein and the final protein to provide more accurate and reliable information to the user It is an object of the present invention to provide a method and system for filtering and searching. Where filtration, including species, interaction type, interaction detection method, number of information (number of DBs provided, number of related articles, number of interaction detection methods), etc. Provide the function.

In order to achieve the above object, the present invention comprises the steps of obtaining the name information of the starting protein from the user; Obtaining interaction distance information between a final protein interacting with the starting protein and the starting protein from the user; Obtaining name information of a final protein interacting with the starting protein from the user; Obtaining interaction relationship information of the starting protein and the final protein from a first database storing interaction relationship information between proteins; Obtaining desired signaling pathway information from the user, from among signaling pathway information related to the starting protein and the final protein, from a second database storing a signaling pathway; And the signaling path map displaying the signaling path information using the name information of the starting protein, the interaction distance information, the name information of the final protein, the interaction relationship information, and the signaling path information. The method provides a method for deriving a relationship between a protein and a signaling pathway, the method comprising: displaying a path between the starting protein and the final protein within an interaction distance.

In addition, to achieve the above object, the present invention comprises the steps of obtaining a plurality of starting protein name information from the user; Obtaining desired signaling path information from the user; Obtaining interaction distance information between a final protein located on the signaling pathway and the plurality of starting proteins from the user; By using the plurality of starting protein name information, the signaling pathway information and the interaction distance information, at least one starting protein associated with the signaling pathway among the plurality of starting proteins according to the interaction distance with the final protein. It provides a method for deriving a relationship between a protein and a signaling pathway comprising a step of displaying.

In addition, to achieve the above object, the present invention comprises the steps of obtaining a plurality of starting protein name information from the user; Obtaining desired signaling path information from the user; Obtaining interaction distance information between a final protein located on the signaling pathway and the plurality of starting proteins from the user; And using the plurality of protein name information, the signaling pathway information, and the interaction distance information, the starting proteins and the final proteins within the interaction distance on a signaling pathway map indicating the signaling pathway. It provides a method for deriving a relationship between a protein and a signaling pathway comprising the step of displaying a pathway interacting with the protein on the signaling pathway map.

In addition, to achieve the above object, the present invention comprises the steps of obtaining a plurality of starting protein name information from the user; Obtaining interaction distance information between a final protein located on the signaling pathway and the plurality of starting proteins from the user; Obtain interaction relationship information between the plurality of starting proteins and the final protein from a first database storing interaction relationship information between proteins, and obtain signaling path information from a second database storing signaling path information. Making; And a signaling pathway in which the plurality of starting proteins and the final protein interact with each other by the interaction distances using the plurality of protein name information, the interaction distance information, the interaction relationship information, and the signaling path information. It provides a method for deriving a relationship between a protein and a signaling pathway comprising a step of displaying.

In addition, to achieve the above object, the present invention provides a network generation system for deriving a relationship between a protein and a signaling pathway, comprising a module for executing at least one of the methods.

In addition, to achieve the above object, the present invention provides a computer readable recording medium having recorded thereon a program for executing at least one of the above methods.

The present invention derives not only the interaction relationship between proteins but also the related signaling pathways, thereby efficiently deriving the interaction relationship between proteins that can provide a basis for the direction of protein biological function research.

In addition, the present invention is to provide a more accurate and reliable information to the user, the species (Organism), interaction type (Interaction Type), Interaction detection method (interaction detection method), the number of information (provided) Information can be retrieved through efficient filtering of the number of DBs, the number of related papers, and the number of interaction detection methods).

In addition, the present invention is to efficiently analyze the interaction relationship between proteins that can be provided to the user to determine the common signaling pathway information or commonly interacting protein information for the identified protein by proceeding proteome analysis to determine the priority On the screen.

The terminology used in the present invention is a general term that is currently widely used as possible, but in certain cases, the term is arbitrarily selected by the applicant, in which case the meaning of the term is described in the detailed description of the invention. It should be understood that the present invention in terms of terms other than these terms.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS Hereinafter, exemplary embodiments of the present invention will be described in detail with reference to the accompanying drawings. The present invention is not limited or limited by the above embodiments, and various modifications may be made to the technical spirit of the present invention. All implementations including the present invention should be included in the scope of the present invention.

1 is an overall system configuration diagram of the present invention. Referring to FIG. 1, the system includes a user interface (UI) module 100, a screen configuration module 200, a main engine module, a filtration module 800, a database manager module 900, a protein information database 1000, and matching. An information database 1100, an interaction information database 1200, and a signal transmission path information database 1300, wherein the main engine module includes a protein-protein interaction (PPI) module 300 and a path-finder. The module 400 includes a path-linker module 500, a path-marker module 600, and a path-lister module 700.

The UI module 100 manages input / output from a user, and the screen configuration module 200 arranges nodes and edges for proteins and signal transmission paths on the screen. The present invention uses the GraphiViz engine or the Tulip engine as the screen configuration module 200, but is not limited thereto.

The PPI module 300 plots a protein interacting with a protein of interest (hereinafter referred to as "first protein") (hereinafter referred to as "last protein") on the screen and the pathfinder. Module 400 provides the function of finding a signaling pathway that includes a final protein that interacts with a single starting protein.

The passlinker module 500 provides a function of representing an interaction distance between a plurality of starting proteins and a final protein present on a signaling pathway of interest. The passmarker module 600 provides a function of displaying a location and frequency of final proteins interacting with a plurality of starting proteins on a signal transduction map.

The passlister module 700 finds a signal transmission path associated with a plurality of starting proteins according to an interaction distance, and provides a signal transmission path and a signal transmission path according to the number of paths between the starting protein and the final protein. It provides the ability to statistically prioritize, such as my final protein share (or frequency).

The filtration module 800 provides the user with more accurate and reliable information in order to provide information about an organism, interaction type, interaction detection method, and number of information. It provides a filtering function for the number of DBs, the number of related papers and the number of interaction detection methods).

The database manager module 900 handles connection to a database and data input / output. The database manager module 900 may include a plurality of processors such as a protein information processor 910, a protein interaction processor 920, a signal path processor 930, and the like. It includes.

The protein interaction processor processes interaction relationship information for a specific protein based on the interaction information database 1200 such as IntAct, BioGrid, DIP, HPRD, MINT DB, and the like. The display information database 1300 processes information on a specific signal transmission path.

The protein information database 1000 stores protein information such as a protein name, a protein type, and a gene sequence. The present invention uses UniprotKB DB and / or SwissProt DB as the protein information database 1000, but is not limited thereto. The signaling pathway database 1300 stores signaling pathways and gene information of proteins. The present invention uses KEGG DB as the signaling path database 1300, but is not limited thereto.

The matching information database 1100 can easily obtain the desired protein information by matching the unique number and protein name of the protein. The present invention uses iProClass DB as the matching information database 1100, but is not limited thereto. The iProClass DB provides matching information between NCBI gi and UniprotKB / SwissProt.

The interaction information database 1200 stores interaction relationship information between proteins. The present invention uses the DB of IntAct, BioGrid, DIP, HPRD, MINT DB as the interaction information database 1200, but is not limited thereto. The signaling information database 1300 stores display information such as a signaling path map and a protein name. The present invention uses a KEGG DB as the signal transmission information database 1300, but is not limited thereto. In addition, the present invention may include other databases in addition to the above-described database. Hereinafter, the functions of each module constituting the main engine module will be described.

2 is a diagram illustrating a flow chart for explaining the function of the PPI module 300 and the database used in accordance with an embodiment of the present invention. The PPI module 300 plots the final proteins interacting with the starting protein of interest on the screen. First, in order to input name information of a starting protein, a user inputs a search word (S310), and selects a starting protein name among proteins listed according to the search word (S320). At this time, the database manager module 900 uses the protein name information stored in the UniProtKB / SwissProt DB 1000.

Then, in order to receive more accurate and reliable information, the user sets filtering conditions for filtering and obtaining information stored in the database (S330). For example, the user may be able to determine the species, the interaction type, the interaction detection method, the number of information (the number of DBs provided, the number of related articles, and the number of interaction detection methods). Filter conditions may be set for the display (S330).

Then, when the user inputs the interaction distance of the final protein interacting with the starting protein (S340), the PPI module 300 through the protein interaction processor 920 IntAct, BioGrid, DIP, HPRD, MINT Search for the final protein information interacting with the starting protein within the interaction distance from the DB 1200 (S350), and the screen configuration module 200 arranges the protein information according to the interaction distance on the screen (S360). ).

In this case, optionally, the final protein search may be performed according to filtration conditions set by a user using the filtration module 800. That is, the present invention includes a filter application step so that biologically useful information can be obtained, and the information can be filtered and searched in a process of searching for interaction relationship information and signal transmission information of the starting protein. Therefore, it is possible to help design the user's experiment by improving the reliability and high accuracy of the information obtained through filtration.

3 is a diagram illustrating a PPI module displayed on a screen according to an embodiment of the present invention. Referring to FIG. 3, reference numeral 301 is a place for inputting a search word, and reference numeral 302 shows protein names listed according to the search word. Reference numeral 303 denotes an input of an interaction distance, and reference numeral 304 denotes a result performed by the PPI module 300. The square box on the left represents the starting protein, and the plurality of square boxes on the right represent the final proteins that interact with the starting protein. 3 shows the case where the interaction distance is set to one.

4 is a flowchart illustrating a function of the pathfinder module 400 according to an embodiment of the present invention and a database used. The pathfinder module 400 finds the relationship between one starting protein and all known signaling pathways and provides information on signaling pathways involving the starting protein as well as the final protein interacting with the starting protein. The selected signal transmission path is displayed on the screen directly. It is possible to search without limiting the interaction distance, and it is possible to sort the signaling path list by the interaction distance or the signaling path.

Referring to FIG. 4, first, a starting protein is searched for (S410). In the search method, when a user inputs a search word, the protein information processor 910 finds protein information matching the search word from the UniProtKB / SwissProt DB 1000, and provides the search result to the user through the UI, and the user searches for the search result. Select the desired starting protein (S420).

Then, in order to be provided with more accurate and reliable information, the user sets filtration conditions for obtaining and filtering information stored in the protein interaction DB 1200 (430). For example, the user may be able to determine the species, the interaction type, the interaction detection method, the number of information (the number of DBs provided, the number of related articles, and the number of interaction detection methods). A filter condition for the setting is set (S430).

Then, when the interaction distance of the final protein interacting with the starting protein (S440), the pathfinder module 400 uses the protein interaction processor 920, such as IntAct, BioGrid, DIP, HPRD, MINT, etc. The interaction relationship information is obtained from the DB 1200, and the signaling path processor 930 retrieves the signaling path from the KEGG DB 1300 (S450). In this case, optionally, the interaction relationship information acquisition may be performed according to the filtering conditions set by the user using the filtering module 800.

The search for the signaling path is as follows. 1) Collect the final protein within a defined range of interaction distances among the proteins associated with the starting protein. 2) The matching between the starting protein and / or the final protein information and Gene information of the KEGG DB 1300 is performed. 3) KEGG DB (1300) brings the detailed information on the signaling pathway of the matched gene information. 4) The result obtained by repeating the process of 2 ~ 3 times within the defined interaction distance range is displayed on the screen.

Then, the user selects a signaling pathway in which the desired final protein is raised among the signaling pathway search results (S460), and the screen configuration module 200 uses the interaction relationship information to start the protein in the selected signaling pathway. And the final protein interaction relationship is output (S470).

The method of outputting a signal transmission path is as follows. 1) Find the signal transmission path map corresponding to the selected signal transmission path and output it on the screen. 2) Get the location information on the map of the final protein selected in the KEGG DB (1300). 3) The final protein is displayed on the signaling pathway map using the location information. 4) Obtain the interaction pathway from the starting protein to the final protein.

The method for obtaining the interaction path is as follows. 4-1) Search for the related protein starting from the final protein in the hierarchy of the final protein collected in the signaling pathway search step in the direction of decreasing village number. 4-2) Repeat 4-1 until you reach a starting protein with zero interaction distance. 4-3) The search results are converted into node and edge forms, and then passed to the screen configuration module 200 (eg, the GraphViz engine) to determine respective positions. 4-4) Display on the screen based on the arrangement result in 4-3.

5 is a diagram of a pathfinder module 400 displayed on a screen according to an embodiment of the present invention. Referring to FIG. 5, reference numeral 401 is for selecting a starting protein, 402 is for inputting an interaction distance, 403 is for selecting a signaling pathway of interest, and 404 is for selecting an initial protein. The protein pathway output by the pathfinder module 400 is shown. Of the plurality of square boxes on the right, a thick square box 405 represents the final protein.

6 is a diagram illustrating a flow chart for explaining the function of the pass linker module 500 and the database used in accordance with an embodiment of the present invention. The passlinker module 500 inputs a plurality of starting proteins to plot the relationship with the signaling pathway of interest. At this time, the number of starting proteins can be input without limitation, and if the parameters for the signaling pathway and the interaction distance of interest are set, the result is displayed on the screen.

Referring to FIG. 6, first, a protein list is prepared (S510). There are two ways to create a protein list. The first is when the user enters the protein's NCBI gi. 1) Search the iProClass DB 1100 through the protein information processor 910 to search for the presence of a protein corresponding to the NCBI gi, 2) obtain the UniprotKB ID corresponding to the NCBI gi from the search results, and 3) the UniprotKB DB. At 1000 we get all the information corresponding to the UniprotKB ID.

The second method is when the user enters the name of the protein. 1) Fulltext Search for the protein corresponding to the search word in UniprotKB DB (1000) through the protein information processor (910), 2) Display the search results in a list for the user to select, and 3) UniprotKB DB At 1000, all information corresponding to the search result is obtained.

Next, the user selects a target signaling path (S520), and the user sets filtration conditions for filtering and obtaining information stored in the protein interaction DB 1200 (S530). For example, the user may be able to determine the species, the interaction type, the interaction detection method, the number of information (the number of DBs provided, the number of related articles, and the number of interaction detection methods). A filter condition for the back is set (S530).

When the minimum interaction distance between the starting protein and the final protein on the target signaling path is input (S540), the pass linker module 500 outputs a link result (S550).

The following example shows how to output the link result. 1) obtain the final protein within the interaction distance range for each protein in the starting protein list, and 2) climb through the signaling pathway processor 930 on the target signaling pathway from the KEGG DB 1300 to the final signaling pathway. 3) the interaction relationship information between the starting protein and the final protein from the DB 1200 such as IntAct, BioGrid, DIP, HPRD, MINT, etc. through the protein interaction processor 920, e.g., each starting protein. Obtain the minimum interaction distance for the final proteins of 4, 4) each node with the starting signal and the target signaling pathway, and edge the minimum distance between the starting protein and the target signaling pathway. And determine the position where the node and the edge are to be arranged on the screen by passing it to the screen configuration module 200 (for example, the GraphViz engine), and 5) output the result to the screen. In this case, optionally, the interaction relationship information may be obtained according to the filtering conditions set by the user using the filtering module 800.

7 is a diagram of a pass linker module 500 displayed on the screen according to an embodiment of the present invention. Referring to FIG. 7, reference numeral 501 is a place where a starting protein is prepared, reference 502 is a place where an interaction distance is input, and reference numeral 503 is a place where a target signal transmission path is selected. Reference numeral 504 denotes a result performed by the pass linker module 500. The square box on the left shows the target signaling pathway, and the plurality of square boxes on the right shows the starting protein list. The distance between the signaling pathway and the starting proteins represents the distance of interaction. That is, interaction distance 1 is direct interaction, and interaction distance 2 is interaction with a protein interacting with a starting protein.

8 is a diagram illustrating a flow chart for explaining the function of the pass marker module 600 and the database used in accordance with an embodiment of the present invention. The passmarker module 600 represents which protein on the signaling pathway of interest the starting protein interacts with. The number of starting proteins can be entered without limitation, and after setting parameters for the target signaling pathway and the interaction distance, the result is displayed on the screen.

If the pass linker module 500 displays the protein and signaling pathway interaction distance relationship, the pass marker module 600 expands the signaling pathway map and displays on which protein the starting protein interacts.

Referring to FIG. 8, first, a start protein list is prepared (S610). As described with reference to FIG. 6, there are two methods for preparing a starting protein list, and the two methods may be equally used.

Next, a target signal transmission path is selected (S620). The method of selecting a signaling path is as follows. 1) From the KEGG DB 1300 through the signaling path processor 930 to get all the signaling path existing on the DB, 2) Display the signaling path on the screen, 3) The user wants the signal transmission path Choose.

Then, in order to be provided with more accurate and reliable information, the user sets filtering conditions for filtering and obtaining information stored in the protein interaction DB 1200 (S630). For example, the user may be able to determine the species, the interaction type, the interaction detection method, the number of information (the number of DBs provided, the number of related articles, and the number of interaction detection methods). A filter condition for the setting is set (S630).

Next, if the minimum interaction distance between the starting protein list and the final protein on the target signaling path is input (S640), the passmarker module 600 outputs the mark result (S650).

The method of outputting the mark result is as follows. 1) For each protein in the starting protein list, find the final protein within the interaction distance range, 2) Select one of the final proteins that is on the target signaling pathway, and 3) Map the target signaling pathway. On the screen, and 4) bring the final protein data for the signaling pathway targeted by the KEGG DB 1300 through the signaling pathway processor 930, and 5) to the final protein obtained from the KEGG DB 1300. Obtain coordinate data for the data, obtain interaction information from the protein interaction DB 1200 through the protein interaction processor 920, and 6) the final protein for the signaling pathway targeted by the KEGG DB 1300. Find the coordinates of, find the protein that matches the coordinates, 7) the number of final proteins corresponding to each starting protein, 8) the color according to the frequency of the number of input proteins Specified otherwise, and 9) show the interaction between displaying a final protein reached by using the information on the transmission path to the target, and 10) protein information in the form of a list. In this case, optionally, the interaction relationship information may be obtained according to the filtering conditions set by the user using the filtering module 800.

9 is a diagram illustrating a pass marker module displayed on a screen according to an embodiment of the present invention. Referring to FIG. 9, reference numeral 601 is a place for listing a starting protein, reference 602 is a place for selecting a target signaling path, and inputs an interaction distance, and reference numeral 603 is a pass marker. The results performed by module 600 are shown in the protein list. In the figure to the right, the multiple boxes are the final proteins that interact with the starting protein. Reference numeral 605 indicates that the final proteins are displayed in different colors depending on the degree of interaction with the starting protein. That is, the protein 604 shown in dark color indicates that it interacts a lot with the starting proteins.

FIG. 10 is a diagram illustrating a flow chart and a database used for describing the function of the pass thruster module 700 according to an embodiment of the present invention. Referring to FIG. 10, the function of the passlister module 700 is performed through the following process.

First, a start protein list is prepared (S710), and a folder for storing a result is designated (S720). At this time, the UniprotKB DB 1000 and the iProClass DB 1100 are used through the protein information processor 910.

Then, in order to be provided with more accurate and reliable information, the user sets filtering conditions for filtering and obtaining information stored in the protein interaction DB 1200 (S730). For example, the user may be able to determine the species, the interaction type, the interaction detection method, the number of information (the number of DBs provided, the number of related articles, and the number of interaction detection methods). A filter condition for the setting is set (S730).

Next, when the interaction distance is determined (S740), the passlister module 700 uses the KEGG DB 1300 and the IntAct DB 1200 through the signal transfer processor 930 and the protein interaction processor 920. Obtaining the delivery path search and interaction relationship information (S750), storing the search results (S760), calculating the statistics for each signal transmission path of the search results (S770), and outputting and storing the statistical results (S780). . In this case, the interaction relationship information may be obtained according to the filtering conditions set by the user using the filtering module 800. The process between acquiring the signal transmission path (S750) and outputting and storing the statistical result (S780) may be repeated.

The passlister module 700 displays detailed results for each input protein as a tap, provides signaling path priority statistics for each interaction distance, and provides priority statistics of proteins interacting with the input protein.

FIG. 11 is a diagram illustrating a pathistor module 700 displayed on a screen according to an embodiment of the present invention. Referring to FIG. 11, reference numeral 701 denotes a place for inputting a plurality of proteins, and reference numeral 702 denotes a folder for designating a folder for storing the output result by the passlister module 700. Reference numeral 703 is for inputting an interaction distance, reference 704 is a tab showing detailed results for each input protein, and reference numeral 705 is for providing signaling path priority statistics for each interaction distance. , 706, is where it provides priority statistics of proteins interacting with the input protein.

The invention also includes a computer readable recording medium having recorded thereon a program for executing at least one of the above methods.

In the present invention as described above has been described by the limited embodiment and the drawings, but this is provided only to help a more general understanding of the present invention, the present invention is not limited to the above embodiments, it is common in the field of the present invention Those skilled in the art can make various modifications and variations from this description.

Accordingly, the spirit of the present invention should not be limited to the described embodiments, and all of the equivalents and equivalents of the claims, as well as the claims described below, belong to the scope of the present invention. will be.

1 is an overall system configuration of the present invention

Figure 2 shows a flow chart for explaining the functionality of the PPI module of the present invention and the database used;

3 is a diagram of a PPI module displayed on a screen according to an embodiment of the present invention;

4 is a flowchart illustrating a function of the Path-Finder module of the present invention and a database used.

5 is a diagram of a path finder module displayed on a screen according to an embodiment of the present invention;

FIG. 6 shows a flow chart for explaining the function of the Path-Linker module of the present invention and a database used. FIG.

7 is a diagram of a Path-Linker module displayed on a screen according to an embodiment of the present invention.

FIG. 8 shows a flow chart for explaining the function of the Path-Marker module of the present invention and a database used.

9 is a diagram of a Path-Marker module displayed on a screen according to an embodiment of the present invention.

FIG. 10 is a flowchart illustrating a function of the Path-Lister module of the present invention and a database used. FIG.

11 is a diagram of a Path-Lister module 700 displayed on a screen according to an embodiment of the present invention.

<Description of the symbols for the main parts of the drawings>

100: UI module 200: screen configuration module

300: PPI module 400: Path-Finder module

500: Path-Linker Module 600: Path-Marker Module

700: Path-Lister Module 800: Filtration Module

900: database manager module 1000: protein information database

1100: Matching database

1200: Interactive Information Database

1300: Signaling Pathway and Gene Information Database

Claims (27)

Receiving a search word corresponding to a name of a protein to be searched from a user to obtain name information of the starting protein, and selecting a name of the starting protein from among names of one or more proteins searched by the search word; Receiving an interaction distance from the user to obtain interaction distance information between a final protein interacting with the starting protein and the starting protein; To obtain the name information of the final protein interacting with the starting protein, the name information of the final protein interacting with the starting protein within the interaction distance is read from a first database that stores the interaction relationship information between the proteins. Shipping step; Reading interaction relationship information between the starting protein and the final protein from the first database; The searched signaling pathway from the user to obtain desired signal pathway information from the user among the signaling pathway information related to the starting protein and the final protein from a second database storing a signaling pathway; Selecting a signaling pathway on which a desired final protein is raised from among information; And By using the name information of the starting protein, the interaction distance information, the name information of the final protein, the interaction relationship information, and the signaling pathway information, the starting protein and the final protein are within the interaction distance. Displaying the interacting route on a signaling route map displaying the signaling route information and providing the same through the screen to the user; and deriving a relationship between the protein and the signaling route. . The method of claim 1, wherein the obtaining of the starting protein name information comprises: Receiving a search word related to the starting protein from the user; Obtaining protein name information matching the search word from a database storing protein name information and providing the same to the user; And And receiving the starting protein name information selected by the user from the provided protein information. The method of claim 1, wherein the method of deriving a relationship between the protein and a signaling pathway is And receiving a filtering condition to be applied when the interaction relationship information is obtained from the first database from the user. The method of claim 3, wherein The filtration conditions include at least one of an organism, an interaction type, an interaction detection method, a number of DBs provided, a number of related papers, and an interaction detection method. A method of deriving a relationship between a protein and a signaling pathway that is characterized. The method of claim 1, wherein the obtaining of the signaling path information comprises: Using the name information of the start protein and the name information of the final protein, providing the user with signaling path information matching the starting protein and the final protein from a database storing signaling path information; And And inputting signal transmission path information desired by the user among the provided signaling path information. The method of claim 1, wherein the displaying step Outputting the signaling path map; Displaying the location of the final protein on the signaling pathway map; And Displaying the interaction pathway between the starting protein and the final protein on the signaling pathway map. The method of claim 5, wherein the displaying on the signaling path map comprises: Finding an associated protein in the signaling pathway map until the starting protein is reached in a direction that reduces the interaction distance from a final protein; And Determining a location of the starting protein and the associated protein and displaying the signal on a signaling pathway map; and deriving a relationship between a protein and a signaling pathway. Receiving a search word corresponding to a name of a protein to be searched by a user to obtain name information of a plurality of start proteins, and selecting a plurality of names of the start protein among names of one or more proteins searched by the search word; Selecting a desired signaling path from the user to obtain desired signaling path information; Input an interaction distance between the starting protein and the final protein on the selected signaling pathway from the user to obtain interaction distance information between the final protein located on the signaling pathway and the plurality of starting proteins Receiving step; By using the name information of the plurality of starting proteins, the signaling pathway information and the interaction distance information, at least one starting protein associated with the signaling pathway among the plurality of starting proteins is the interaction distance with the final protein. Displaying on the screen according to the method; deriving a relationship between a protein and a signaling pathway. The method of claim 8, wherein the obtaining of the starting protein name information comprises: Receiving a search word related to the starting protein from the user; Obtaining protein information matching the search word from a database storing protein information and providing the same to the user; And Receiving the plurality of starting protein name information from the user among the provided protein information; deriving a relationship between a protein and a signaling pathway. The method of claim 8, wherein the displaying step Obtaining a plurality of final proteins that interact with the plurality of starting proteins within the interaction distance; Selecting a final protein present on the signaling pathway information among the plurality of final proteins; Obtaining minimum interaction distance information between the plurality of starting proteins and the selected final protein from a first database storing interaction relationship information between proteins; And And displaying the plurality of starting protein positions according to the minimum interaction distance using the plurality of starting proteins and the signaling pathway as nodes and the minimum interaction distance as an edge. How to derive the relationship between and signaling pathways. The method of claim 9, wherein the method of deriving a relationship between the protein and a signaling pathway is And receiving a filtering condition to be applied when the interaction relationship information is obtained from the first database from the user. The method of claim 11, The filtration conditions include at least one of an organism, an interaction type, an interaction detection method, a number of DBs provided, a number of related papers, and an interaction detection method. A method of deriving a relationship between a characterized protein and a signaling pathway. The method of claim 8, wherein the obtaining of the signaling path information comprises: Providing all the signaling path information to the user from a database storing the signaling path information; And And receiving the signal transmission path information selected by the user among all the signal transmission path information provided. Receiving a search word corresponding to a name of a protein to be searched by a user to obtain name information of a plurality of start proteins, and selecting a plurality of names of the start protein among names of one or more proteins searched by the search word; Selecting a desired signaling path from the user to obtain desired signaling path information; Input an interaction distance between the starting protein and the final protein on the selected signaling pathway from the user to obtain interaction distance information between the final protein located on the signaling pathway and the plurality of starting proteins Receiving step; And Using the plurality of protein name information, the signaling path information, and the interaction distance information, the starting proteins and the plurality of starting proteins within the interaction distance on a signaling path map displaying the signaling path information. Displaying the interaction pathway with the final protein and providing the same through the screen to the user; deriving a relationship between the protein and the signaling pathway. 15. The method of claim 14, wherein obtaining the starting protein name information Receiving a search word related to the starting protein from the user; Obtaining protein information matching the search word from a database storing protein information and providing the same to the user; And Receiving the plurality of starting protein name information from the user among the provided protein information; deriving a relationship between a protein and a signaling pathway. 15. The method of claim 14, wherein acquiring the signaling path information Providing all signaling path information to the user from a database that stores signaling path information; And And receiving the signal transmission path information selected by the user among all the signal transmission path information provided. The method of claim 14, wherein the displaying step Obtaining a plurality of final proteins that interact with the plurality of starting proteins within the interaction distance; Selecting a final protein present on the signaling pathway information among the plurality of final proteins; Displaying the signaling path map; Obtaining interaction relationship information between the plurality of starting proteins and the selected final protein from a first database storing interaction relationship information between proteins, and transmitting the signal from a second database storing signaling pathway information. Obtaining final protein information on a pathway and location information of the final protein; And And displaying the final protein on the signaling pathway map by using the interaction relationship information, the final protein information, and the positional information of the final protein. How to. The method of claim 17, wherein the method of deriving a relationship between the protein and a signaling pathway is And receiving a filtering condition to be applied when the interaction relationship information is obtained from the first database from the user. The method of claim 18, The filtration conditions include at least one of an organism, an interaction type, an interaction detection method, a number of DBs provided, a number of related papers, and an interaction detection method. A method of deriving a relationship between a characterized protein and a signaling pathway. 18. The method of claim 17, wherein the displaying step Obtaining a final number of proteins interacting with each starting protein; And A method of deriving a relationship between a protein and a signaling pathway, the method further comprising: differently expressing colors on the signal transduction map of the final protein according to the number. Receiving a search word corresponding to a name of a protein to be searched from the user to obtain a plurality of starting protein name information, and selecting a plurality of names of the starting protein from among names of one or more proteins searched by the search word; Selecting a desired signaling path from the user to obtain desired signaling path information; Input an interaction distance between the starting protein and the final protein on the selected signaling pathway from the user to obtain interaction distance information between the final protein located on the signaling pathway and the plurality of starting proteins Receiving step; Obtain interaction relationship information between the plurality of starting proteins and the final protein from a first database storing interaction relationship information between proteins, and read signaling pathway information from a second database storing signaling pathway information. Shipping step; And By using the plurality of protein name information, the interaction distance information, the interaction relationship information and the signaling path information, a signaling path for the interaction between the plurality of starting proteins and the final protein for each interaction distance Displaying and providing to the user through the screen; Deriving a relationship between the protein and the signaling pathway comprising a. The method of claim 21, wherein the method of deriving a relationship between the protein and a signaling pathway is And receiving a filtering condition to be applied when the interaction relationship information is obtained from the first database from the user. The method of claim 22, The filtration conditions include at least one of an organism, an interaction type, an interaction detection method, a number of DBs provided, a number of related papers, and an interaction detection method. A method of deriving a relationship between a characterized protein and a signaling pathway. The method of claim 21, wherein obtaining the starting protein name information comprises: Receiving a search word related to the starting protein from the user; Obtaining protein information matching the search word from a database storing protein information and providing the same to the user; And Receiving the plurality of starting protein name information from the user among the provided protein information; deriving a relationship between a protein and a signaling pathway. The method of claim 21, Acquiring the signaling pathway and displaying the signaling pathway may be repeated. 26. A signaling pathway derivation system for deriving a relationship between a protein and a signaling pathway comprising at least one module for carrying out the method according to any one of claims 1 to 25. A computer-readable recording medium having recorded thereon a program for executing the method according to any one of claims 1 to 25.

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