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Predicting pathogenic genes for primary myelofibrosis based on a system‑network approach

Shu‑Cai Xu, Peng Ning
2017 Molecular Medicine Reports  
The aim of the present study was to predict pathogenic genes for primary myelofibrosis (PMF) using a system-network approach by combining protein-protein interaction (PPI) network and gene expression data  ...  Subsequently, a pathogenic network was extracted from the new network, and contained genes that interacted with at least two seed genes, and the candidate pathogenic genes were predicted based on the cohesion  ...  genes for primary myelofibrosis based on a system-network approach pathogenic process (11) .  ... 
doi:10.3892/mmr.2017.7847 pmid:29115418 pmcid:PMC5780125 fatcat:i4c6ubb3bvfpzcrjh27sskow7e

Pathogenic Network Analysis Predicts Candidate Genes for Cervical Cancer

Yun-Xia Zhang, Yan-Li Zhao
2016 Computational and Mathematical Methods in Medicine  
The objective of our study was to predicate candidate genes in cervical cancer (CC) using a network-based strategy and to understand the pathogenic process of CC.Methods.  ...  A pathogenic network of CC was extracted based on known pathogenic genes (seed genes) and differentially expressed genes (DEGs) between CC and normal controls.  ...  To overcome this difficulty, a potentially more effective approach is to employ a network-based strategy to evaluate the disease-related biomarkers.  ... 
doi:10.1155/2016/3186051 pmid:27034707 pmcid:PMC4789371 fatcat:xrtl2m5h65bnvn2pwdbqssuu6a

Multilayer View of Pathogenic SNVs in Human Interactome through In Silico Edgetic Profiling

Hongzhu Cui, Nan Zhao, Dmitry Korkin
2018 Journal of Molecular Biology  
We show that pathogenic SNVs are more likely to cause gene pleiotropy than pathogenic frameshift mutations and are enriched on the protein interaction interfaces.  ...  an edge-based alternative should be used instead.  ...  When applying this approach to study a disease network centered around the genes associated with Type 2 Diabetes Mellitus (T2DM), we have identified systems enriched with disruptive mutations and determined  ... 
doi:10.1016/j.jmb.2018.07.012 pmid:30017919 fatcat:ddwczbvtsjfbrfezea2o5cknym

Analyzing of Molecular Networks for Human Diseases and Drug Discovery

Tong Hao, Qian Wang, Lingxuan Zhao, Dan Wu, Edwin Wang, Jinsheng Sun
2018 Current Topics in Medicinal Chemistry  
and sub-network biomarkers for diseases.  ...  Especially in the research on human disease and drugs, as an emerging tool, the PIN provides a platform to systematically explore the molecular complexities of specific diseases and the references for  ...  Traditional methods for identifying biomarkers include expression-data-based and pathway-based approaches.  ... 
doi:10.2174/1568026618666180813143408 pmid:30101711 pmcid:PMC6174636 fatcat:en2t3a4v7ffivbfqrsqhcln25q

Multilayer view of pathogenic SNVs in human interactome through in-silico edgetic profiling [article]

Hongzhu Cui, Nan Zhao, Dmitry Korkin
2018 bioRxiv   pre-print
Non-synonymous mutations linked to the complex diseases often have a global impact on a biological system, affecting large biomolecular networks and pathways.  ...  We show that pathogenic SNVs are more likely to cause gene pleiotropy than pathogenic frameshift mutations and are enriched on the protein interaction interfaces.  ...  When applying this approach to study a disease network centered around the genes associated with Type 2 Diabetes Mellitus (T2DM), we have identified systems enriched with disruptive mutations and determined  ... 
doi:10.1101/299891 fatcat:anni3epyxbdsxb6ftrj3nhxiq4

Identification of osteosarcoma driver genes using a network method

Zebing Si, Konghe Hu
2019 Oncology Letters  
OS-related genes were extracted from the Catalogue Of Somatic Mutations In Cancer and subsequently ranked by virtue of their effect on a set of functional genes using a network-based algorithm.  ...  In addition, compared with the Mutations For Functional Impact on Network Neighbors algorithm, the results obtained using the aforementioned network-based algorithm revealed that the proposed method is  ...  The present study performed a systematic exploration of somatic mutations by mining datasets for OS-associated driver genes using a network-based approach.  ... 
doi:10.3892/ol.2019.11212 pmid:31966051 pmcid:PMC6956419 fatcat:iqjmwmzjprcu7esbrqbwxwzuza

Protein-protein interaction networks: probing disease mechanisms using model systems

Uros Kuzmanov, Andrew Emili
2013 Genome Medicine  
In this review, we examine the application of MS-based approaches for the experimental analysis of PPI networks and protein complexes, focusing on the diff erent model systems (including human cells) used  ...  In humans, disruptions of the normal patterns of PPIs and protein complexes can be causative or indicative of a disease state.  ...  A protein kinase-phosphatase interaction network encompassing transient dynamic regulatorsubstrate interactions has also been mapped using a modified AP-MS-based approach [35] .  ... 
doi:10.1186/gm441 pmid:23635424 pmcid:PMC3706760 fatcat:62p2wi4mqzfudlr73lasftwb2q

Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches

Anna Onisiforou, George M Spyrou
2021 Briefings in Bioinformatics  
Afterwards, we present our theoretical-driven integrative network-based bioinformatics approach that accounts for pathogen–genes–disease-related PPIs with the aim to identify viral-mediated pathogenic  ...  Finally, our analysis highlighted the Th17 differentiation pathway, a disease communicator node and part of the 12 underlined KEGG pathways, as a key viral-mediated pathogenic mechanism and a possible  ...  We then presented our integrative network-based bioinformatics pipeline approach that accounts for pathogen-genes-disease PPIs with the aim to identify possible viral-mediated pathogenic mechanisms in  ... 
doi:10.1093/bib/bbab141 pmid:34237135 pmcid:PMC8574625 fatcat:ismaywei3jdpfmiyygr3hg2vem

New approach for understanding genome variations in KEGG

Minoru Kanehisa, Yoko Sato, Miho Furumichi, Kanae Morishima, Mao Tanabe
2018 Nucleic Acids Research  
Thus, we have introduced a new approach where human gene variants are explicitly incorporated into what we call 'network variants' in the recently released KEGG NETWORK database.  ...  This allows accumulation of knowledge about disease-related perturbed molecular networks caused not only by gene variants, but also by viruses and other pathogens, environmental factors and drugs.  ...  ACKNOWLEDGEMENTS Computational resources were provided by the Bioinformatics Center, Institute for Chemical Research, Kyoto University.  ... 
doi:10.1093/nar/gky962 pmid:30321428 fatcat:bfng7d23g5arzbx7tsuj6ptemm

NCCN Guidelines Insights: Genetic/Familial High-Risk Assessment: Colorectal, Version 2.2019

Samir Gupta, Dawn Provenzale, Xavier Llor, Amy L. Halverson, William Grady, Daniel C. Chung, Sigurdis Haraldsdottir, Arnold J. Markowitz, Thomas P. Slavin Jr, Heather Hampel, Reid M. Ness, Jennifer M. Weiss (+20 others)
2019 The Journal of the National Comprehensive Cancer Network  
Identifying individuals with hereditary syndromes allows for improved cancer surveillance, risk reduction, and optimized management.  ...  Establishing criteria for assessment allows for the identification of individuals who are carriers of pathogenic genetic variants.  ...  reduction for those with identified pathogenic variants and CRC syndromes.  ... 
doi:10.6004/jnccn.2019.0044 pmid:31487681 fatcat:vpgnksvzjrex3of5h2c3kia3e4

Big Data and Network Biology 2015

Shigehiko Kanaya, Md. Altaf-Ul-Amin, Samuel K. Kiboi, Farit Mochamad Afendi
2015 BioMed Research International  
Finally we acknowledge the dedicated works of all reviewers of these papers for their critical and helpful comments.  ...  Acknowledgments Our heartfelt thanks are due to authors for their excellent and fundamental contributions and their patience in communicating with us.  ...  The paper "Discovering Distinct Functional Modules of Specific Cancer Types Using Protein-Protein Interaction Networks" proposes a new graph theory based method to identify distinct functional modules  ... 
doi:10.1155/2015/604623 pmid:26609530 pmcid:PMC4644560 fatcat:vykzxrxdejcbzeot3nuprgcz4u

ENIGMA-Evidence-based network for the interpretation of germline mutant alleles: An international initiative to evaluate risk and clinical significance associated with sequence variation in BRCA1 and BRCA2 genes

Amanda B. Spurdle, Sue Healey, Andrew Devereau, Frans B. L. Hogervorst, Alvaro N. A. Monteiro, Katherine L. Nathanson, Paolo Radice, Dominique Stoppa-Lyonnet, Sean Tavtigian, Barbara Wappenschmidt, Fergus J. Couch, David E. Goldgar
2011 Human Mutation  
However, for many disease genes, including the breast cancer susceptibility genes BRCA1 and BRCA2, a significant fraction of tests result in the detection of a genetic variant for which disease association  ...  As these variants are individually rare, a large collaboration of researchers and clinicians will facilitate studies to assess their association with cancer predisposition.  ...  Participation by KLN is supported by the Breast Cancer Research Foundation. PR is supported by grant from the Italian Association for Cancer Research (AIRC).  ... 
doi:10.1002/humu.21628 pmid:21990146 pmcid:PMC3240687 fatcat:drc7orq2kbb2bfou7uevjlocfa

In silico analyses of metabolic pathway and protein interaction network for identification of next gen therapeutic targets in Chlamydophila pneumoniae

Bilachi S Ravindranath, Venkatappa Krishnamurthy, Venkatarangaiah Krishna, Kahale Vasudevanayaka
2013 Bioinformation  
The understanding of disease and treatment options are limited represents a severe concern and a need for better therapeutics.  ...  A computational comparative metabolic pathway analysis of the host H. sapiens and the pathogen C pneumoniae AR39 has been carried out at three level analyses.  ...  Conclusion: In the present study, comparative metabolic pathway approach and protein interaction network analysis of the causative agent of COPD has been performed to identify the unique pathways present  ... 
doi:10.6026/97320630009605 pmid:23904736 pmcid:PMC3725000 fatcat:4gz32dwodfe47cvlakhhyoebyu

Prediction of key genes in ovarian cancer treated with decitabine based on network strategy

2016 Oncology Reports  
Pathogenic networks of ovarian cancer before and after treatment were identified based on known pathogenic genes (seed genes) and differentially expressed genes (DEGs) detected by Significance Analysis  ...  The objective of the present study was to predict key genes in ovarian cancer before and after treatment with decitabine utilizing a network approach and to reveal the molecular mechanism.  ...  Acknowledgements The present study received no specific grants from any funding agency in public, commercial or not-for-profit sectors.  ... 
doi:10.3892/or.2016.4697 pmid:27035425 fatcat:sefmwdnszzbypld6iaep5pxx2u

Rapid diagnosis and comprehensive bacteria profiling of sepsis based on cell-free DNA

Pei Chen, Shuo Li, Wenyuan Li, Jie Ren, Fengzhu Sun, Rui Liu, Xianghong Jasmine Zhou
2020 Journal of Translational Medicine  
identify the majority of pathogens in all patients.  ...  For comparison, where a culture-based analysis of pathogens takes up to 5 days and is effective for only a third to a half of patients, cfDNA sequencing can be completed in just 1 day and our method can  ...  Results A novel strategy for rapid sepsis diagnosis based on cfDNA Following the procedures shown in Fig. 1a , b, we developed a two-step approach for rapid sepsis diagnosis, which has been validated  ... 
doi:10.1186/s12967-019-02186-x pmid:31906978 pmcid:PMC6943891 fatcat:k6e5hcjq3nhyzcaaijf77wo2ka
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