Methodology: data regarding protein-protein interaction network data of

 

Methodology:

·       
Literature mining  and data retrieval of dengue:

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Literature
mining is the study of that data which is already studied to clarify the topic
more and another words the literature mining is the study of research papers of
the same topics.

 

·       
Protein-protein interaction network
construction:

There
are several databases having protein-protein interaction network data like
string, bio grid, mint, intact. All the data regarding protein-protein
interaction network data of dengue were found in string database.

o  
Literature studying string

 

 

o  
Using Cytoscape:

 

Cytoscape is an open source software project for
integrating biomolecular interaction networks with high-throughput expression
data and other molecular states into a unified conceptual framework. Although
applicable to any system of molecular components and interactions, Cytoscape is
most powerful when used in conjunction with large databases of protein-protein,
protein-DNA, and genetic interactions that are increasingly available for
humans and model organisms.cytoscape  (version 3.0) was installed from that
official website.

o  
Network construction: prepare file for
network construction which was downloaded from string database.extract file and
save in exel  format then remove all
duplicates in exel and upload this file to cytoscape.select one protein as
source node and aone as target node.the network was constructed.

o  
 

 

·       
Functional enrichment analysis of
protein-protein interaction:

o  
Bingo:

o  
Cytohubba:

BiNGO : The Biological Networks Gene Ontology tool (BiNGO) is an
open-source Java tool to determine which Gene Ontology (GO) terms are
significantly overrepresented in a set of genes. BiNGO can be used either on a
list of genes, pasted as text, or interactively on subgraphs of biological
networks visualized in Cytoscape(22).

Cytohubba: Explore
important nodes/hubs and fragile motifs in an interactome network by several
topological algorithms including Degree, and centralities based on shortest
paths, s, Closeness, Radiality, Betweenness, and Stress(http://apps.cytoscape.org/apps/cytohubba).

·       
Identification of hub protein:

Hub
proteins are essential protein which perfom functions.100 proteins were
identified  which are highly connected
nodes in the network.

·       
Sub network construction of hub protein: The
sub network of hub proteins was constructed in string database. open string
database clicked on search the search window was opened and  select multiple protein past        names of 100 hub proteins in search and
choose organism name aedes aegypyi  clicked on search the sub network was
constructed.

 

 

 

 

 

 

·       
Clustering:

o  
Kmean algorithm: Apply kmean algorithm on
sub network on string database.

o  
Clicked on 
clustering then clicked on Kmean algorithm the kmean algorithm was
applied.

  

Methodology:

·       
Literature mining  and data retrieval of dengue:

Literature
mining is the study of that data which is already studied to clarify the topic
more and another words the literature mining is the study of research papers of
the same topics.

 

·       
Protein-protein interaction network
construction:

There
are several databases having protein-protein interaction network data like
string, bio grid, mint, intact. All the data regarding protein-protein
interaction network data of dengue were found in string database.

o  
Literature studying string

 

 

o  
Using Cytoscape:

 

Cytoscape is an open source software project for
integrating biomolecular interaction networks with high-throughput expression
data and other molecular states into a unified conceptual framework. Although
applicable to any system of molecular components and interactions, Cytoscape is
most powerful when used in conjunction with large databases of protein-protein,
protein-DNA, and genetic interactions that are increasingly available for
humans and model organisms.cytoscape  (version 3.0) was installed from that
official website.

o  
Network construction: prepare file for
network construction which was downloaded from string database.extract file and
save in exel  format then remove all
duplicates in exel and upload this file to cytoscape.select one protein as
source node and aone as target node.the network was constructed.

o  
 

 

·       
Functional enrichment analysis of
protein-protein interaction:

o  
Bingo:

o  
Cytohubba:

BiNGO : The Biological Networks Gene Ontology tool (BiNGO) is an
open-source Java tool to determine which Gene Ontology (GO) terms are
significantly overrepresented in a set of genes. BiNGO can be used either on a
list of genes, pasted as text, or interactively on subgraphs of biological
networks visualized in Cytoscape(22).

Cytohubba: Explore
important nodes/hubs and fragile motifs in an interactome network by several
topological algorithms including Degree, and centralities based on shortest
paths, s, Closeness, Radiality, Betweenness, and Stress(http://apps.cytoscape.org/apps/cytohubba).

·       
Identification of hub protein:

Hub
proteins are essential protein which perfom functions.100 proteins were
identified  which are highly connected
nodes in the network.

·       
Sub network construction of hub protein: The
sub network of hub proteins was constructed in string database. open string
database clicked on search the search window was opened and  select multiple protein past        names of 100 hub proteins in search and
choose organism name aedes aegypyi  clicked on search the sub network was
constructed.

 

 

 

 

 

 

·       
Clustering:

o  
Kmean algorithm: Apply kmean algorithm on
sub network on string database.

o  
Clicked on 
clustering then clicked on Kmean algorithm the kmean algorithm was
applied.

 

o  
MCL algorithm: Apply MCL algorithm on sub
network in string database.

Clicked on  clustering then clicked on Kmean algorithm
the kmean algorithm was applied. 

Methodology:

·       
Literature mining  and data retrieval of dengue:

Literature
mining is the study of that data which is already studied to clarify the topic
more and another words the literature mining is the study of research papers of
the same topics.

 

·       
Protein-protein interaction network
construction:

There
are several databases having protein-protein interaction network data like
string, bio grid, mint, intact. All the data regarding protein-protein
interaction network data of dengue were found in string database.

o  
Literature studying string

 

 

o  
Using Cytoscape:

 

Cytoscape is an open source software project for
integrating biomolecular interaction networks with high-throughput expression
data and other molecular states into a unified conceptual framework. Although
applicable to any system of molecular components and interactions, Cytoscape is
most powerful when used in conjunction with large databases of protein-protein,
protein-DNA, and genetic interactions that are increasingly available for
humans and model organisms.cytoscape  (version 3.0) was installed from that
official website.

o  
Network construction: prepare file for
network construction which was downloaded from string database.extract file and
save in exel  format then remove all
duplicates in exel and upload this file to cytoscape.select one protein as
source node and aone as target node.the network was constructed.

o  
 

 

·       
Functional enrichment analysis of
protein-protein interaction:

o  
Bingo:

o  
Cytohubba:

BiNGO : The Biological Networks Gene Ontology tool (BiNGO) is an
open-source Java tool to determine which Gene Ontology (GO) terms are
significantly overrepresented in a set of genes. BiNGO can be used either on a
list of genes, pasted as text, or interactively on subgraphs of biological
networks visualized in Cytoscape(22).

Cytohubba: Explore
important nodes/hubs and fragile motifs in an interactome network by several
topological algorithms including Degree, and centralities based on shortest
paths, s, Closeness, Radiality, Betweenness, and Stress(http://apps.cytoscape.org/apps/cytohubba).

·       
Identification of hub protein:

Hub
proteins are essential protein which perfom functions.100 proteins were
identified  which are highly connected
nodes in the network.

·       
Sub network construction of hub protein: The
sub network of hub proteins was constructed in string database. open string
database clicked on search the search window was opened and  select multiple protein past        names of 100 hub proteins in search and
choose organism name aedes aegypyi  clicked on search the sub network was
constructed.

 

 

 

 

 

 

·       
Clustering:

o  
Kmean algorithm: Apply kmean algorithm on
sub network on string database.

o  
Clicked on 
clustering then clicked on Kmean algorithm the kmean algorithm was
applied.

 

o  
MCL algorithm: Apply MCL algorithm on sub
network in string database.

Clicked on  clustering then clicked on Kmean algorithm
the kmean algorithm was applied. 

Methodology:

·       
Literature mining  and data retrieval of dengue:

Literature
mining is the study of that data which is already studied to clarify the topic
more and another words the literature mining is the study of research papers of
the same topics.

 

·       
Protein-protein interaction network
construction:

There
are several databases having protein-protein interaction network data like
string, bio grid, mint, intact. All the data regarding protein-protein
interaction network data of dengue were found in string database.

o  
Literature studying string

 

 

o  
Using Cytoscape:

 

Cytoscape is an open source software project for
integrating biomolecular interaction networks with high-throughput expression
data and other molecular states into a unified conceptual framework. Although
applicable to any system of molecular components and interactions, Cytoscape is
most powerful when used in conjunction with large databases of protein-protein,
protein-DNA, and genetic interactions that are increasingly available for
humans and model organisms.cytoscape  (version 3.0) was installed from that
official website.

o  
Network construction: prepare file for
network construction which was downloaded from string database.extract file and
save in exel  format then remove all
duplicates in exel and upload this file to cytoscape.select one protein as
source node and aone as target node.the network was constructed.

o  
 

 

·       
Functional enrichment analysis of
protein-protein interaction:

o  
Bingo:

o  
Cytohubba:

BiNGO : The Biological Networks Gene Ontology tool (BiNGO) is an
open-source Java tool to determine which Gene Ontology (GO) terms are
significantly overrepresented in a set of genes. BiNGO can be used either on a
list of genes, pasted as text, or interactively on subgraphs of biological
networks visualized in Cytoscape(22).

Cytohubba: Explore
important nodes/hubs and fragile motifs in an interactome network by several
topological algorithms including Degree, and centralities based on shortest
paths, s, Closeness, Radiality, Betweenness, and Stress(http://apps.cytoscape.org/apps/cytohubba).

·       
Identification of hub protein:

Hub
proteins are essential protein which perfom functions.100 proteins were
identified  which are highly connected
nodes in the network.

·       
Sub network construction of hub protein: The
sub network of hub proteins was constructed in string database. open string
database clicked on search the search window was opened and  select multiple protein past        names of 100 hub proteins in search and
choose organism name aedes aegypyi  clicked on search the sub network was
constructed.

 

 

 

 

 

 

·       
Clustering:

o  
Kmean algorithm: Apply kmean algorithm on
sub network on string database.

o  
Clicked on 
clustering then clicked on Kmean algorithm the kmean algorithm was
applied.

 

o  
MCL algorithm: Apply MCL algorithm on sub
network in string database.

Clicked on  clustering then clicked on Kmean algorithm
the kmean algorithm was applied.vvv

o  
MCL algorithm: Apply MCL algorithm on sub
network in string database.

Clicked on  clustering then clicked on Kmean algorithm
the kmean algorithm was applied.

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