Benchmarking pathway interaction network for colorectal cancer to identify dysregulated pathways

Abstract Discovering driver pathways is an essential step to uncover the molecular mechanism underlying cancer and to explore precise treatments for cancer patients. However, due to the difficulties of mapping genes to pathways and the limited knowledge about pathway interactions, most previous work focus on identifying individual pathways. In practice, two (or even more) pathways interplay and often cooperatively trigger cancer. In this study, we proposed a new approach called CDPathway to discover cooperative driver pathways. First, CDPathway introduces a driver impact quantification function to quantify the driver weight of each gene. CDPathway assumes that genes with larger weights contribute more to the occurrence of the target disease and identifies them as candidate driver genes. Next, it constructs a heterogeneous network composed of genes, miRNAs and pathways nodes based on the known intra(inter)-relations between them and assigns the quantified driver weights to gene–pathway and gene–miRNA relational edges. To transfer driver impacts of genes to pathway interaction pairs, CDPathway collaboratively factorizes the weighted adjacency matrices of the heterogeneous network to explore the latent relations between genes, miRNAs and pathways. After this, it reconstructs the pathway interaction network and identifies the pathway pairs with maximal interactive and driver weights as cooperative driver pathways. Experimental results on the breast, uterine corpus endometrial carcinoma and ovarian cancer data from The Cancer Genome Atlas show that CDPathway can effectively identify candidate driver genes [area under the receiver operating characteristic curve (AUROC) of $\geq $0.9] and reconstruct the pathway interaction network (AUROC of>0.9), and it uncovers much more known (potential) driver genes than other competitive methods. In addition, CDPathway identifies 150% more driver pathways and 60% more potential cooperative driver pathways than the competing methods. The code of CDPathway is available at http://mlda.swu.edu.cn/codes.php?name=CDPathway.

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Predicting the Mechanism of the Analgesic Property of Yanhusuo Based on Network Pharmacology

Natural Product Communications ◽

10.1177/1934578x19883071 ◽

2019 ◽

Vol 14 (10) ◽

pp. 1934578X1988307

Author(s):

Wen-Ping Xiao ◽

Yan-Fang Yang ◽

He-Zhen Wu ◽

Yi-yi Xiong

Keyword(s):

Molecular Docking ◽

Metabolic Pathways ◽

Interaction Network ◽

Binding Activity ◽

Network Pharmacology ◽

Active Components ◽

Network Diagram ◽

Pathway Interaction ◽

Pathway Interaction Network ◽

Pathway Analyses

Yanhusuo (Corydalis Rhizoma) extracts are widely used for the treatment of pain and inflammation. The effects of Yanhusuo in pain assays were assessed in a few studies. However, there are few studies on its analgesic mechanism. In this paper, network pharmacology was used to explore the analgesic components of Yanhusuo and its analgesic mechanism. The active components of Yanhusuo were screened by TCMSP database, combined with literature data. PharmMapper and GeneCards databases were used for screening the analgesic targets of the components. The protein interaction network diagram was drawn by String database and Cytoscape software, the gene ontology and KEGG pathway analyses of the target were performed by DAVID database, and the component–target–pathway interaction network diagram was further drawn by Cytoscape3.6.1 software. System Dock Web Site verified the molecular docking among components and targets. Finally, an interaction network of the component–target–pathway of Yanhusuo was constructed, and the functions and pathways were analyzed for preliminarily investigating the mechanism of Yanhusuo in analgesia. The results showed that the active components of analgesic in Yanhusuo were Corynoline, 13-methylpalmatrubine, dehydrocorydaline, saulatine, 2,3,9,10-tetramethoxy-13-methyl-5,6-dihydroisoquinolino[2,1-b]isoquinolin-8-on-e, and Capaurine. The mechanisms were involved in metabolic pathways, PI3k-Akt signaling pathway, pathways in cancer, and so on. The top 3 targets were NOS3, glucose-6-phosphate dehydrogenase, and glucose-6-phosphate isomerase in components-target-pathways network, and they were all enriched in metabolic pathways. Meanwhile the molecular docking showed that there was a high binding activity between the 6 components and the important target proteins, as a further certification for the subsequent network analysis. This study reveals the relationship of the components, targets, and pathways of active components in Yanhusuo, and provides new ideas and methods for further research on the analgesic mechanism of Yanhusuo.

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Molecular characterization, biological function, tumor microenvironment association and clinical significance of m6A regulators in lung adenocarcinoma

Briefings in Bioinformatics ◽

10.1093/bib/bbaa225 ◽

2020 ◽

Author(s):

Yin Li ◽

Jie Gu ◽

Fengkai Xu ◽

Qiaoliang Zhu ◽

Yiwei Chen ◽

...

Keyword(s):

Tumor Microenvironment ◽

Lung Adenocarcinoma ◽

Web Application ◽

Molecular Mechanisms ◽

Treatment Strategies ◽

Interaction Network ◽

Pathway Interaction ◽

Clinical Benefits ◽

Pathway Interaction Network ◽

Scoring Tool

Abstract N6-methyladenosine (m6A) modification can regulate a variety of biological processes. However, the implications of m6A modification in lung adenocarcinoma (LUAD) remain largely unknown. Here, we systematically evaluated the m6A modification features in more than 2400 LUAD samples by analyzing the multi-omics features of 23 m6A regulators. We depicted the genetic variation features of m6A regulators, and found mutations of FTO and YTHDF3 were linked to worse overall survival. Many m6A regulators were aberrantly expressed in tumors, among which FTO, IGF2BP3, YTHDF1 and RBM15 showed consistent alteration features across 11 independent cohorts. Besides, the regulator-pathway interaction network demonstrated that m6A modification was associated with various biological pathways, including immune-related pathways. The correlation between m6A regulators and tumor microenvironment was also assessed. We found that LRPPRC was negatively correlated with most tumor-infiltrating immune cells. On the other hand, we established a scoring tool named m6Sig, which was positively correlated with PD-L1 expression and could reflect both the tumor microenvironment characterization and prognosis of LUAD patients. Comparison of CNV between high and low m6Sig groups revealed differences on chromosome 7. Application of m6Sig on an anti-PD-L1 immunotherapy cohort confirmed that the high m6Sig group demonstrated therapeutic advantages and clinical benefits. Our study indicated that m6A modification is involved in many aspects of LUAD and contributes to tumor microenvironment formation. A better understanding of m6A modification will provide more insights into the molecular mechanisms of LUAD and facilitate developing more effective personalized treatment strategies. A web application was built along with this study (http://www.bioinfo-zs.com/luadexpress/).

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Pathway Interaction Network Analysis Identifies Dysregulated Pathways in Human Monocytes Infected by Listeria monocytogenes

Computational and Mathematical Methods in Medicine ◽

10.1155/2017/3195348 ◽

2017 ◽

Vol 2017 ◽

pp. 1-8

Author(s):

Wufeng Fan ◽

Yuhan Zhou ◽

Hao Li

Keyword(s):

Listeria Monocytogenes ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Interaction Network ◽

Principal Component ◽

Centrality Measures ◽

Network Centrality ◽

Human Monocytes ◽

Pathway Interaction ◽

Pathway Interaction Network

In our study, we aimed to extract dysregulated pathways in human monocytes infected by Listeria monocytogenes (LM) based on pathway interaction network (PIN) which presented the functional dependency between pathways. After genes were aligned to the pathways, principal component analysis (PCA) was used to calculate the pathway activity for each pathway, followed by detecting seed pathway. A PIN was constructed based on gene expression profile, protein-protein interactions (PPIs), and cellular pathways. Identifying dysregulated pathways from the PIN was performed relying on seed pathway and classification accuracy. To evaluate whether the PIN method was feasible or not, we compared the introduced method with standard network centrality measures. The pathway of RNA polymerase II pretranscription events was selected as the seed pathway. Taking this seed pathway as start, one pathway set (9 dysregulated pathways) with AUC score of 1.00 was identified. Among the 5 hub pathways obtained using standard network centrality measures, 4 pathways were the common ones between the two methods. RNA polymerase II transcription and DNA replication owned a higher number of pathway genes and DEGs. These dysregulated pathways work together to influence the progression of LM infection, and they will be available as biomarkers to diagnose LM infection.

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An integrated pathway interaction network for the combination of four effective compounds from ShengMai preparations in the treatment of cardio-cerebral ischemic diseases

Acta Pharmacologica Sinica ◽

10.1038/aps.2015.70 ◽

2015 ◽

Vol 36 (11) ◽

pp. 1337-1348 ◽

Cited By ~ 14

Author(s):

Fang Li ◽

Yan-ni Lv ◽

Yi-sha Tan ◽

Kai Shen ◽

Ke-feng Zhai ◽

...

Keyword(s):

Interaction Network ◽

Pathway Interaction ◽

Integrated Pathway ◽

Ischemic Diseases ◽

Pathway Interaction Network ◽

Cerebral Ischemic

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PINTnet: construction of condition-specific pathway interaction network by computing shortest paths on weighted PPI

BMC Systems Biology ◽

10.1186/s12918-017-0387-3 ◽

2017 ◽

Vol 11 (S2) ◽

Cited By ~ 6

Author(s):

Ji Hwan Moon ◽

Sangsoo Lim ◽

Kyuri Jo ◽

Sangseon Lee ◽

Seokjun Seo ◽

...

Keyword(s):

Shortest Paths ◽

Interaction Network ◽

Pathway Interaction ◽

Pathway Interaction Network ◽

Specific Pathway

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The use of gene interaction networks to improve the identification of cancer driver genes

PeerJ ◽

10.7717/peerj.2568 ◽

2017 ◽

Vol 5 ◽

pp. e2568 ◽

Cited By ~ 5

Author(s):

Emilie Ramsahai ◽

Kheston Walkins ◽

Vrijesh Tripathi ◽

Melford John

Keyword(s):

Interaction Network ◽

Gene Interaction ◽

Driver Genes ◽

Genomic Libraries ◽

Cancer Driver ◽

Gene Interaction Networks ◽

Combining Data ◽

Pathway Interaction ◽

Cancer Driver Genes ◽

Pathway Interaction Network

Bioinformaticians have implemented different strategies to distinguish cancer driver genes from passenger genes. One of the more recent advances uses a pathway-oriented approach. Methods that employ this strategy are highly dependent on the quality and size of the pathway interaction network employed, and require a powerful statistical environment for analyses. A number of genomic libraries are available in R. DriverNet and DawnRank employ pathway-based methods that use gene interaction graphs in matrix form. We investigated the benefit of combining data from 3 different sources on the prediction outcome of cancer driver genes by DriverNet and DawnRank. An enriched dataset was derived comprising 13,862 genes with 372,250 interactions, which increased its accuracy by 17% and 28%, respectively, compared to their original networks. The study identified 33 new candidate driver genes. Our study highlights the potential of combining networks and weighting edges to provide greater accuracy in the identification of cancer driver genes.

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