Background: A great number of data mining methods have been widely made such as gene regulatory n... more Background: A great number of data mining methods have been widely made such as gene regulatory networks and gene set analyses to connect genes that reveal similar expression patterns. These methods generally fail to unveil gene-gene interactions in the same cluster. The aim of this study is to use several nonparametric correlation coefficient methods to transform the linear rank statistics into distance metrics on a Saccharomyces cerevisiae data set. Methods: These nonparametric correlation coefficients, Kendall’s tau index and Gini rank correlation, were compared with common Pearson correlation method. The reliability and advantages of our proposed is satisfied using genetic website, http://www.yeast genome .org/. To address the interactions and characterize the gene–gene biological processes explicitly, the gene relationships are shown as a Pajek graph topology. Result: The results of biological interactions and characteristics demonstrated that the proposed nonparametric correlation coefficient methods have a strong capability to identify interaction genes. Moreover, suggested techniques could accurately detect the main genes and functional interactions in comparison to generally used Pearson correlation coefficient. Conclusion: The two non-linear correlation coefficient techniques are proposed to measure the gene interactions more precisely.
Aim: Efforts to explore biomarkers and biological pathways involved in the disease are needed to ... more Aim: Efforts to explore biomarkers and biological pathways involved in the disease are needed to improve colorectal cancer (CRC) diagnosis and alternative treatments. Background: The fourth common malignancy in the world is colorectal cancer. The over-all burden is predicted to rise by 2030. Methods: In the current study, nine genes were selected. Previously, a panel of genes by Agendia, a classifier of robust gene expression (ColoPrint), was determined to significantly improve the prognostic accuracy of pathologic factors in stage II and III colorectal cancer patients. Five genes, including Ppara, Mctp1, Pyroxd1, Il2r, and Cyfip2, from this panel and four other genes which were not in this panel but were cited abundantly in the literature were selected. Then, expression levels of the selected genes in CRC tissue were compared with levels in adjacent normal tissue. To identify the pathways involved in CRC, gene set enrichment analysis was subsequently performed. Furthermore, to illustrate the relationship between genes in this disease, the cross-shaped co-expression pattern and gene regulatory network were determined using computational methods. Results: This research found that the pairs of genes: {IL2R, CYFIP2}, {FOXM1, PPARA}, {MCTP1, CTSC}, and {PYROXD1, CYF1P2} are functionally related. Furthermore, two differentially expressed gene pairs ({FOXM1, PPARA} and {IL2R, CYFIP2}) are involved in the vascular endothelial growth factor receptor signaling pathway and the purine ribonucleoside diphosphate metabolic process, respectively. Conclusion: This research found that the combination of computational analysis and laboratory data provided the opportunity to better characterize the relation between central colorectal cancer genes as well as possible pathways involved in the colorectal cancer.
In biology, homeostasis is a central cellular phenomenon that plays a crucial role in survival. T... more In biology, homeostasis is a central cellular phenomenon that plays a crucial role in survival. The central nervous system (CNS) is controlled by exquisitely sensitive homeostatic mechanisms when facing inflammatory or pathological insults. Mast cells and microglia play a crucial role in CNS homeostasis by eliminating damaged or unnecessary neurons and synapses. Therefore, decoding molecular circuits that regulate CNS homeostasis may lead to more effective therapeutic strategies that specifically target particular subsets for better therapy of Alzheimer’s disease (AD). Based on a computational analysis of a microarray dataset related to AD, the H2-Ob gene was previously identified as a potential modulator of the homeostatic balance between mast cells and microglia. Specifically, it plays such a role in the presence of a three-way gene interaction in which the H2-Ob gene acts as a switch in the co-expression relationship of two genes, Csf1r and Milr1. Therefore, the importance of the...
Background Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy associated with a poor ... more Background Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy associated with a poor prognosis. High-throughput disease-related-gene expression data provide valuable information on gene interaction, which consequently lead to deeper insight about pathogenesis. The co-expression analysis is a common approach that is used to investigate gene interaction. However, such an approach solely is inadequate to reveal the complexity of the gene interaction. The three-way interaction model is known as a novel approach applied to decode the complex relationship between genes. Methods In the current study, the liquid association method was used to capture the statistically significant triplets involved in the PDAC pathogenesis. Subsequently, gene set enrichment and gene regulatory network analyses were performed to trace the biological relevance of the statistically significant triplets. Results The results of the current study suggest that “response to estradiol” and “Regulation of ...
Gastroenterology and hepatology from bed to bench, 2017
The aim of this study is to present the oral Squamous Cell Cancer protein-protein interaction net... more The aim of this study is to present the oral Squamous Cell Cancer protein-protein interaction network interpretation in comparison to esophageal adenocarcinoma. Oral squamous cell cancer (OSCC) is a common disease worldwide, with poor prognosis and limited treatment. Thus, introducing molecular markers through network analysis can be helpful. STRING database (DB) was applied for network construction through Cytoscape 3.4.0. Clue GO handled the gene annotation for the retrieved clusters. Eight proteins were indicated to be differential in the network constitution. The centrality and clustering analysis indicate that TP53 plays an over-significant role in network integrity among eight most central proteins including TP53, AKT1, EGFR, MYC, JUN, CDH1, CCND1, and CTNNB1. The suggested biomarker set is very similar to the related biomarker panel of esophageal adenocarcinoma. The ontology analysis implies that the prominent proteins are involved in regulation of smooth muscle cell prolifer...
Gastroenterology and Hepatology From Bed to Bench, 2021
Aim: Efforts to explore biomarkers and biological pathways involved in the disease are needed to ... more Aim: Efforts to explore biomarkers and biological pathways involved in the disease are needed to improve colorectal cancer (CRC) diagnosis and alternative treatments Background: The fourth common malignancy in the world is colorectal cancer. The over-all burden is predicted to rise by 2030. Methods: In the current study, nine genes were selected. Previously, a panel of genes by Agendia, a classifier of robust gene expression (ColoPrint), was determined to significantly improve the prognostic accuracy of pathologic factors in stage II and III colorectal cancer patients. Five genes, including Ppara, Mctp1, Pyroxd1, Il2r, and Cyfip2, from this panel and four other genes which were not in this panel but were cited abundantly in the literature were selected. Then, expression levels of the selected genes in CRC tissue were compared with levels in adjacent normal tissue. To identify the pathways involved in CRC, gene set enrichment analysis was subsequently performed. Furthermore, to illus...
Background: A great number of data mining methods have been widely made such as gene regulatory n... more Background: A great number of data mining methods have been widely made such as gene regulatory networks and gene set analyses to connect genes that reveal similar expression patterns. These methods generally fail to unveil gene-gene interactions in the same cluster. The aim of this study is to use several nonparametric correlation coefficient methods to transform the linear rank statistics into distance metrics on a Saccharomyces cerevisiae data set. Methods: These nonparametric correlation coefficients, Kendall’s tau index and Gini rank correlation, were compared with common Pearson correlation method. The reliability and advantages of our proposed is satisfied using genetic website, http://www.yeast genome .org/. To address the interactions and characterize the gene–gene biological processes explicitly, the gene relationships are shown as a Pajek graph topology. Result: The results of biological interactions and characteristics demonstrated that the proposed nonparametric correla...
Non-functioning pituitary adenomas (NFPAs) are typical pituitary macroadenomas in adults that are... more Non-functioning pituitary adenomas (NFPAs) are typical pituitary macroadenomas in adults that are associated with increased mortality and morbidity. Although pituitary adenomas are commonly considered slow-growing benign brain tumors, numerous of them possess an invasive nature. Such tumors destroy sella turcica and invade the adjacent tissues such as the cavernous sinus and sphenoid sinus. The most critical obstacle for complete surgical removal in these cases is the high risk of damaging adjacent vital structures. Therefore, the development of novel therapeutic strategies for either early diagnosis through biomarkers or medical therapies to reduce the recurrence rate of NFPAs is imperative. Identification of gene interactions has paved the way for decoding complex molecular mechanisms, including disease-related pathways, and identifying the most momentous genes involved in a specific disease. Currently, our knowledge of the invasion of the pituitary adenoma at the molecular level ...
Gastroenterology and hepatology from bed to bench, 2017
The aim of this study is to present the oral Squamous Cell Cancer protein-protein interaction net... more The aim of this study is to present the oral Squamous Cell Cancer protein-protein interaction network interpretation in comparison to esophageal adenocarcinoma. Oral squamous cell cancer (OSCC) is a common disease worldwide, with poor prognosis and limited treatment. Thus, introducing molecular markers through network analysis can be helpful. STRING database (DB) was applied for network construction through Cytoscape 3.4.0. Clue GO handled the gene annotation for the retrieved clusters. Eight proteins were indicated to be differential in the network constitution. The centrality and clustering analysis indicate that TP53 plays an over-significant role in network integrity among eight most central proteins including TP53, AKT1, EGFR, MYC, JUN, CDH1, CCND1, and CTNNB1. The suggested biomarker set is very similar to the related biomarker panel of esophageal adenocarcinoma. The ontology analysis implies that the prominent proteins are involved in regulation of smooth muscle cell prolifer...
Background: A great number of data mining methods have been widely made such as gene regulatory n... more Background: A great number of data mining methods have been widely made such as gene regulatory networks and gene set analyses to connect genes that reveal similar expression patterns. These methods generally fail to unveil gene-gene interactions in the same cluster. The aim of this study is to use several nonparametric correlation coefficient methods to transform the linear rank statistics into distance metrics on a Saccharomyces cerevisiae data set. Methods: These nonparametric correlation coefficients, Kendall’s tau index and Gini rank correlation, were compared with common Pearson correlation method. The reliability and advantages of our proposed is satisfied using genetic website, http://www.yeast genome .org/. To address the interactions and characterize the gene–gene biological processes explicitly, the gene relationships are shown as a Pajek graph topology. Result: The results of biological interactions and characteristics demonstrated that the proposed nonparametric correlation coefficient methods have a strong capability to identify interaction genes. Moreover, suggested techniques could accurately detect the main genes and functional interactions in comparison to generally used Pearson correlation coefficient. Conclusion: The two non-linear correlation coefficient techniques are proposed to measure the gene interactions more precisely.
Aim: Efforts to explore biomarkers and biological pathways involved in the disease are needed to ... more Aim: Efforts to explore biomarkers and biological pathways involved in the disease are needed to improve colorectal cancer (CRC) diagnosis and alternative treatments. Background: The fourth common malignancy in the world is colorectal cancer. The over-all burden is predicted to rise by 2030. Methods: In the current study, nine genes were selected. Previously, a panel of genes by Agendia, a classifier of robust gene expression (ColoPrint), was determined to significantly improve the prognostic accuracy of pathologic factors in stage II and III colorectal cancer patients. Five genes, including Ppara, Mctp1, Pyroxd1, Il2r, and Cyfip2, from this panel and four other genes which were not in this panel but were cited abundantly in the literature were selected. Then, expression levels of the selected genes in CRC tissue were compared with levels in adjacent normal tissue. To identify the pathways involved in CRC, gene set enrichment analysis was subsequently performed. Furthermore, to illustrate the relationship between genes in this disease, the cross-shaped co-expression pattern and gene regulatory network were determined using computational methods. Results: This research found that the pairs of genes: {IL2R, CYFIP2}, {FOXM1, PPARA}, {MCTP1, CTSC}, and {PYROXD1, CYF1P2} are functionally related. Furthermore, two differentially expressed gene pairs ({FOXM1, PPARA} and {IL2R, CYFIP2}) are involved in the vascular endothelial growth factor receptor signaling pathway and the purine ribonucleoside diphosphate metabolic process, respectively. Conclusion: This research found that the combination of computational analysis and laboratory data provided the opportunity to better characterize the relation between central colorectal cancer genes as well as possible pathways involved in the colorectal cancer.
In biology, homeostasis is a central cellular phenomenon that plays a crucial role in survival. T... more In biology, homeostasis is a central cellular phenomenon that plays a crucial role in survival. The central nervous system (CNS) is controlled by exquisitely sensitive homeostatic mechanisms when facing inflammatory or pathological insults. Mast cells and microglia play a crucial role in CNS homeostasis by eliminating damaged or unnecessary neurons and synapses. Therefore, decoding molecular circuits that regulate CNS homeostasis may lead to more effective therapeutic strategies that specifically target particular subsets for better therapy of Alzheimer’s disease (AD). Based on a computational analysis of a microarray dataset related to AD, the H2-Ob gene was previously identified as a potential modulator of the homeostatic balance between mast cells and microglia. Specifically, it plays such a role in the presence of a three-way gene interaction in which the H2-Ob gene acts as a switch in the co-expression relationship of two genes, Csf1r and Milr1. Therefore, the importance of the...
Background Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy associated with a poor ... more Background Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy associated with a poor prognosis. High-throughput disease-related-gene expression data provide valuable information on gene interaction, which consequently lead to deeper insight about pathogenesis. The co-expression analysis is a common approach that is used to investigate gene interaction. However, such an approach solely is inadequate to reveal the complexity of the gene interaction. The three-way interaction model is known as a novel approach applied to decode the complex relationship between genes. Methods In the current study, the liquid association method was used to capture the statistically significant triplets involved in the PDAC pathogenesis. Subsequently, gene set enrichment and gene regulatory network analyses were performed to trace the biological relevance of the statistically significant triplets. Results The results of the current study suggest that “response to estradiol” and “Regulation of ...
Gastroenterology and hepatology from bed to bench, 2017
The aim of this study is to present the oral Squamous Cell Cancer protein-protein interaction net... more The aim of this study is to present the oral Squamous Cell Cancer protein-protein interaction network interpretation in comparison to esophageal adenocarcinoma. Oral squamous cell cancer (OSCC) is a common disease worldwide, with poor prognosis and limited treatment. Thus, introducing molecular markers through network analysis can be helpful. STRING database (DB) was applied for network construction through Cytoscape 3.4.0. Clue GO handled the gene annotation for the retrieved clusters. Eight proteins were indicated to be differential in the network constitution. The centrality and clustering analysis indicate that TP53 plays an over-significant role in network integrity among eight most central proteins including TP53, AKT1, EGFR, MYC, JUN, CDH1, CCND1, and CTNNB1. The suggested biomarker set is very similar to the related biomarker panel of esophageal adenocarcinoma. The ontology analysis implies that the prominent proteins are involved in regulation of smooth muscle cell prolifer...
Gastroenterology and Hepatology From Bed to Bench, 2021
Aim: Efforts to explore biomarkers and biological pathways involved in the disease are needed to ... more Aim: Efforts to explore biomarkers and biological pathways involved in the disease are needed to improve colorectal cancer (CRC) diagnosis and alternative treatments Background: The fourth common malignancy in the world is colorectal cancer. The over-all burden is predicted to rise by 2030. Methods: In the current study, nine genes were selected. Previously, a panel of genes by Agendia, a classifier of robust gene expression (ColoPrint), was determined to significantly improve the prognostic accuracy of pathologic factors in stage II and III colorectal cancer patients. Five genes, including Ppara, Mctp1, Pyroxd1, Il2r, and Cyfip2, from this panel and four other genes which were not in this panel but were cited abundantly in the literature were selected. Then, expression levels of the selected genes in CRC tissue were compared with levels in adjacent normal tissue. To identify the pathways involved in CRC, gene set enrichment analysis was subsequently performed. Furthermore, to illus...
Background: A great number of data mining methods have been widely made such as gene regulatory n... more Background: A great number of data mining methods have been widely made such as gene regulatory networks and gene set analyses to connect genes that reveal similar expression patterns. These methods generally fail to unveil gene-gene interactions in the same cluster. The aim of this study is to use several nonparametric correlation coefficient methods to transform the linear rank statistics into distance metrics on a Saccharomyces cerevisiae data set. Methods: These nonparametric correlation coefficients, Kendall’s tau index and Gini rank correlation, were compared with common Pearson correlation method. The reliability and advantages of our proposed is satisfied using genetic website, http://www.yeast genome .org/. To address the interactions and characterize the gene–gene biological processes explicitly, the gene relationships are shown as a Pajek graph topology. Result: The results of biological interactions and characteristics demonstrated that the proposed nonparametric correla...
Non-functioning pituitary adenomas (NFPAs) are typical pituitary macroadenomas in adults that are... more Non-functioning pituitary adenomas (NFPAs) are typical pituitary macroadenomas in adults that are associated with increased mortality and morbidity. Although pituitary adenomas are commonly considered slow-growing benign brain tumors, numerous of them possess an invasive nature. Such tumors destroy sella turcica and invade the adjacent tissues such as the cavernous sinus and sphenoid sinus. The most critical obstacle for complete surgical removal in these cases is the high risk of damaging adjacent vital structures. Therefore, the development of novel therapeutic strategies for either early diagnosis through biomarkers or medical therapies to reduce the recurrence rate of NFPAs is imperative. Identification of gene interactions has paved the way for decoding complex molecular mechanisms, including disease-related pathways, and identifying the most momentous genes involved in a specific disease. Currently, our knowledge of the invasion of the pituitary adenoma at the molecular level ...
Gastroenterology and hepatology from bed to bench, 2017
The aim of this study is to present the oral Squamous Cell Cancer protein-protein interaction net... more The aim of this study is to present the oral Squamous Cell Cancer protein-protein interaction network interpretation in comparison to esophageal adenocarcinoma. Oral squamous cell cancer (OSCC) is a common disease worldwide, with poor prognosis and limited treatment. Thus, introducing molecular markers through network analysis can be helpful. STRING database (DB) was applied for network construction through Cytoscape 3.4.0. Clue GO handled the gene annotation for the retrieved clusters. Eight proteins were indicated to be differential in the network constitution. The centrality and clustering analysis indicate that TP53 plays an over-significant role in network integrity among eight most central proteins including TP53, AKT1, EGFR, MYC, JUN, CDH1, CCND1, and CTNNB1. The suggested biomarker set is very similar to the related biomarker panel of esophageal adenocarcinoma. The ontology analysis implies that the prominent proteins are involved in regulation of smooth muscle cell prolifer...
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