Diagnosis of pancreatic cancer by pattern recognition methods using gene expression profiles

2017 ◽  
Author(s):  
Derya Arslan ◽  
Merve Erkinay Ozdemir ◽  
Mustafa Turan Arslan
Keyword(s):  
Gene Expression ◽  
Pancreatic Cancer ◽  
Pattern Recognition ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Pattern Recognition Methods

scholarly journals Gene expression profiles of pancreatic cancer and stromal desmoplasia

Oncogene ◽  
2001 ◽  
Vol 20 (50) ◽  
pp. 7437-7446 ◽  
Author(s):  
Tatjana Crnogorac-Jurcevic ◽  
Evangelis Efthimiou ◽  
Paola Capelli ◽  
Ekaterina Blaveri ◽  
Antonella Baron ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pancreatic Cancer ◽  
Expression Profiles ◽  
Gene Expression Profiles

scholarly journals Identify key genes and pathways in pancreatic ductal adenocarcinoma via bioinformatics analysis

2020 ◽  
Author(s):  
Huatian Luo ◽  
Da-qiu Chen ◽  
Jing-jing Pan ◽  
Zhang-wei Wu ◽  
Can Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pancreatic Cancer ◽  
Pancreatic Ductal Adenocarcinoma ◽  
Bioinformatics Analysis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Gene Expression Omnibus ◽  
Ductal Adenocarcinoma ◽  
Hub Genes ◽  
Expression Levels

Abstract Background: Pancreatic cancer has many pathologic types, among which pancreatic ductal adenocarcinoma (PDAC) is the most common one. Bioinformatics has become a very common tool for the selection of potentially pathogenic genes. Methods: Three data sets containing the gene expression profiles of PDAC were downloaded from the gene expression omnibus (GEO) database. The limma package of R language was utilized to explore the differentially expressed genes (DEGs). To analyze functions and signaling pathways, the Database Visualization and Integrated Discovery (DAVID) was used. To visualize the protein-protein interaction (PPI) of the DEGs ,Cytoscape was performed under the utilization of Search Tool for the Retrieval of Interacting Genes (STRING). With the usage of the plug-in cytoHubba in cytoscape software, the hub genes were found out. To verify the expression levels of hub genes, Gene Expression Profiling Interactive Analysis (GEPIA) was performed. Last but not least, UALCAN analysis online tool was implemented to analyze the overall survival. Results: The 376 DEGs were highly enriched in biological processes including signal transduction, apoptotic process and several pathways, mainly associated with Protein digestion and absorption and Pancreatic secretion pathway. The expression levels of nucleolar and spindle associated protein 1 (NUSAP1) and SHC binding and spindle associated 1 (SHCBP1) were discovered highly expressed in pancreatic ductal adenocarcinoma tissues. NUSAP1 and SHCBP1 had a high correlation with prognosis. Conclusions: The findings of this bioinformatics analysis indicate that NUSAP1 and SHCBP1 may be key factors in the prognosis and treatment of pancreatic cancer.

scholarly journals Variability in statin-induced changes in gene expression profiles of pancreatic cancer

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Helena Gbelcová ◽  
Silvie Rimpelová ◽  
Tomáš Ruml ◽  
Marie Fenclová ◽  
Vítek Kosek ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pancreatic Cancer ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Induced Changes

scholarly journals Chemical-induced Gene Expression Ranking and its Application to Pancreatic Cancer Drug Repurposing

2021 ◽  
Author(s):  
Thai-Hoang Pham ◽  
Yue Qiu ◽  
Jiahui Liu ◽  
Steven Zimmer ◽  
Eric O'Neill ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pancreatic Cancer ◽  
Drug Discovery ◽  
Large Scale ◽  
Missing Values ◽  
De Novo ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Drug Repurposing ◽  
Cancer Drug

Chemical-induced gene expression profiles provide critical information on the mode of action, off-target effect, and cellar heterogeneity of chemical actions in a biological system, thus offer new opportunities for drug discovery, system pharmacology, and precision medicine. Despite their successful applications in drug repurposing, large-scale analysis that leverages these profiles is limited by sparseness and low throughput of the data. Several methods have been proposed to predict missing values in gene expression data. However, most of them focused on imputation and classification settings which have limited applications to real-world scenarios of drug discovery. Therefore, a new deep learning framework named chemical-induced gene expression ranking (CIGER) is proposed to target a more realistic but more challenging setting in which the model predicts the rankings of genes in the whole gene expression profiles induced by de novo chemicals. The experimental results show that CIGER significantly outperforms existing methods in both ranking and classification metrics for this prediction task. Furthermore, a new drug screening pipeline based on CIGER is proposed to select approved or investigational drugs for the potential treatments of pancreatic cancer. Our predictions have been validated by experiments, thereby showing the effectiveness of CIGER for phenotypic compound screening of precision drug discovery in practice.

scholarly journals Identify key genes and pathways in pancreatic ductal adenocarcinoma via bioinformatics analysis

2020 ◽  
Author(s):  
Huatian Luo ◽  
Da-qiu Chen ◽  
Jing-jing Pan ◽  
Zhang-wei Wu ◽  
Can Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pancreatic Cancer ◽  
Pancreatic Ductal Adenocarcinoma ◽  
Bioinformatics Analysis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Gene Expression Omnibus ◽  
Ductal Adenocarcinoma ◽  
Hub Genes ◽  
Expression Levels

Abstract Background: Pancreatic cancer has many pathologic types, among which pancreatic ductal adenocarcinoma (PDAC) is the most common one. Bioinformatics has become a very common tool for the selection of potentially pathogenic genes.Methods: Three data sets containing the gene expression profiles of PDAC were downloaded from the gene expression omnibus (GEO) database. The limma package of R language was utilized to explore the differentially expressed genes (DEGs). To analyze functions and signaling pathways, the Database Visualization and Integrated Discovery (DAVID) was used. To visualize the protein-protein interaction (PPI) of the DEGs ,Cytoscape was performed under the utilization of Search Tool for the Retrieval of Interacting Genes (STRING). With the usage of the plug-in cytoHubba in cytoscape software, the hub genes were found out. To verify the expression levels of hub genes, Gene Expression Profiling Interactive Analysis (GEPIA) was performed. Last but not least, UALCAN analysis online tool was implemented to analyze the overall survival.Results: The 376 DEGs were highly enriched in biological processes including signal transduction, apoptotic process and several pathways, mainly associated with Protein digestion and absorption and Pancreatic secretion pathway. The expression levels of nucleolar and spindle associated protein 1 (NUSAP1) and SHC binding and spindle associated 1 (SHCBP1) were discovered highly expressed in pancreatic ductal adenocarcinoma tissues. NUSAP1 and SHCBP1 had a high correlation with prognosis.Conclusions: The findings of this bioinformatics analysis indicate that NUSAP1 and SHCBP1 may be key factors in the prognosis and treatment of pancreatic cancer.

scholarly journals Gene Expression Profiles in Chemokine (C-C Motif) Ligand 21-Overexpressing Pancreatic Cancer Cells

2018 ◽  
Vol 26 (1) ◽  
pp. 201-208
Author(s):  
Kai Cui ◽  
Hongsheng Zou ◽  
Mingliang Shi ◽  
Yang Ou ◽  
Lu Han ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pancreatic Cancer ◽  
Cancer Cells ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Pancreatic Cancer Cells
Sign in / Sign up

Export Citation Format

Share Document