1.

Introduction
Gastric cancer is the third cause of death by cancer and the fifth most common cancer
worldwide. H. pylori infection in gastric cancer has been verified numerous studies investigate the
causes, genetic and non-genetic factors involved in gastric cancer, where effective proteins have
been identified in the cancer's pathogenesis, and most often the expression level of receptor
tyrosine-protein kinase which increases its levels in gastric cancer. This protein can also prevent
the invasion of cancer cells into other tissues. Some biological molecules prevent the tumor
formation, and its expression level decreases in gastric cancer cells. Proteins interact with other
molecules for their function in the cell and it has been proven that elevated levels of varied proteins
are not due to cancer.
Describing an onset for output data in above-mentioned methods would result in excluding
unchanged level proteins from the study. We assumed that the involved proteins in cancer are
concentrated in limited numbers of cellular signaling pathways which lead to subsequent cellular
changes. Curing method for gastric cancer therapy is surgery, where chemotherapy has limited
effect. Urgent curing strategies are the protein-protein interaction networks.

2. Materials and methods

2.1. Collecting proteins involved in gastric cancer

PubMed database research was made using “gastric cancer” keyword, excluding case
reports.
2.2. Interaction network construction
Interaction information of introduced proteins was gathered from well-known protein-
protein interaction databases and merged in MiMI repository based on an intelligent integration
strategy.
2.3. Identification of sub-networks
Clusters were determined to identify dense areas in the network using Cytoscape plugins
based on Community Clustering (GLay) and Markov Clustering algorithms. algorithms.
Community Clustering (GLay) algorithm performs in three steps including vertex weighting,
molecular complex prediction and post-processing to filter or add proteins to the predicted
complex
 The Markov Cluster defines a sequence of matrices by alternation of two operators on a
generating matrix. It is basically all that is needed for the clustering of graphs, but it is useful to
distinguish between the algorithm and the algebraic process.
2.4. Annotating network with microarray data
Arrayexpress database was searched in order to access to both cancer and non-cancer
samples. Expression data were applied for annotating the network, performing quality control and
pre-processing using ArrayAnalysis modules.
2.5. Gene set analysis
The Database for Annotation, Visualization and Integrated Discovery used to organize
and annotate heterogeneous data from high-throughput techniques such as microarray representing
the gene sets in four different modules.
2.6. Computing centrality parameters
In order to identify hubs, centrality parameters for each node were calculated in the network
and sub-networks. Number of connected edges to each node shows by degree index and role of
node by betweenness.

3. Results

3.1. Collecting the proteins involved in gastric cancer

We found different proteins involved in the pathogenesis of gastric cancer in many articles
based on the defined criteria from PubMed
3.2. Drawing interactive network and determining sub-networks
MiMI algorithm has the ability to show the identified edges between first neighbors of
different seeds. Primary interactive network with nodes and edges was formed using seed proteins.
We used algorithms to identify high-density areas of network, which can be resulted in
subnetworks.
3.3. Loading microarray data in the network
We obtained only two datasets from ArrayExpress database of which one were excluded
because of the low number of samples. Qualitative analysis of other datasets with ArrayAnalysis
found 7 slides due to stains and contamination with cells on slides and hence excluded. Rest of the
slides were analyzed, after adding expression data to our network nodes and calculations the active
expression sub-networks were identified.

3.4. Study of functional relationship and analysis of gene sets

DAVID functional annotation was used to identify biological pathways and Functions
within subnetworks. The enrichment on subnetworks showed that the neurotrophin signaling
pathway, mitotic cell cycle, and other pathways highly involved pathways in the development of
gastric cancer by evaluating main network.

3.5. Network evaluation indices

Evaluation of Betweenness and Degree indicated highest values of the indices in the core
network. we found highest scored cluster algorithms and the most expressed active subnetwork
before and after adding the expression data when calculations were repeated through the
classification by algorithms.

4. Conclusion

We have shown a comprehensive collection of pathways and key proteins which remains
unique to this study, whereas no other study has yet investigated but the exact role of these proteins
in gastric cancer has not been examined. Our methodology offers a systematic insight into the
involvement of particular proteins in gastric cancer which can be applied in order to identify key
proteins and pathways in other diseases. The results of the present study show the pathways and
proteins which are important in the occurrence of gastric cancer and can be introduced as
therapeutic targets and significant biomarkers in this disease.