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Possible pathways used to predict different stages of lung adenocarcinoma

Xiaodong Chen, Qiongyu Duan, Ying Xuan, Yunan Sun, Rong Wu
2017 Medicine  
The specific coexpression network in every stage was constructed with cytoscape software.  ...  Furthermore, these pathways except thyroid hormone signaling pathway may be able to predict the prognosis.  ...  In the state of disease, the decrease of network efficiency and signal transmission efficiency led to the reduction of some important function, particularly functions related with disease response or self-activated  ... 
doi:10.1097/md.0000000000006736 pmid:28445293 pmcid:PMC5413258 fatcat:pwcqc5vodndx3jfohorhn3k6yu

Construction of disease-specific cytokine profiles by associating disease genes with immune responses

Tianyun Liu, Shiyin Wang, Michael Wornow, Russ B. Altman, Ferhat Ay
2022 PLoS Computational Biology  
this creates a unique profile of inflammatory genes (both known and predicted) for each disease.  ...  The predicted cytokine profiles correlate (p-value<0.0003) with the known ones in 95 diseases.  ...  Six sets of close interactors are suggested by the dendrogram of the hierarchical cluster tree (names as SIG1-SIG6 in Table 1 ) and allow us to capture the function of each cluster with a gene signature  ... 
doi:10.1371/journal.pcbi.1009497 pmid:35404985 pmcid:PMC9022887 fatcat:kqoh5mv3oza4fjrv7365hpaw4i

Construction of disease-specific cytokine profiles by associating disease genes with immune responses [article]

Tianyun Liu, Shiyin Wang, Russ B Altman
2021 bioRxiv   pre-print
this creates a unique profile of inflammatory genes (both known and predicted) for each disease.  ...  of a full map of predicted associations for all possible pairs between 14,707 human genes.  ...  Six sets of close interactors are suggested by the dendrogram of the hierarchical cluster tree (names as SIG1-SIG6 in Table 1 ) and allow us to capture the function of each cluster with a gene signature  ... 
doi:10.1101/2021.09.10.459816 fatcat:2v4zc4537bbdxfgv3nnwhsnpwe

Application of Bioinformatics Tools in Gel-Based Proteomics [chapter]

Kah Wai, Min Jia, Serhiy Souchelnytskyi
2012 Integrative Proteomics  
Besides, hierarchical clustering facilitates the discovery of protein signature for prediction of disease progression.  ...  In directed network, the link between two nodes has a defined direction, for example, the induction of activation of a protein by an enzyme.  ...  However, simply taking a straight verbatim approach to catalog all proteins in all tissues of different organisms is not viable.  ... 
doi:10.5772/31275 fatcat:ypwoadb465evlpt3nnaorr7uie

Transcriptomics of Long-Term Meditation Practice: Evidence for Prevention or Reversal of Stress Effects Harmful to Health

Supaya Wenuganen, Kenneth G. Walton, Shilpa Katta, Clifton L. Dalgard, Gauthaman Sukumar, Joshua Starr, Frederick T. Travis, Robert Keith Wallace, Paul Morehead, Nancy K. Lonsdorf, Meera Srivastava, John Fagan
2021 Medicina  
The largest expression differences were shown by six genes related to erythrocyte function that appeared to reflect a condition of lower energy efficiency in the control group.  ...  in anxiety, post-traumatic stress disorder (PTSD), cardiovascular disease (CVD), and other chronic disorders and diseases.  ...  We thank the staff of the Center for Prostate Disease Research, Rockville, Maryland, and Shiv Srivastava, Scientific Director, for use of their facilities and for assistance in RNA extraction.  ... 
doi:10.3390/medicina57030218 pmid:33804348 fatcat:yab4s4ysufg4jkjycirc77eouq

Assessment of the key regulatory genes and their Interologs for Turner Syndrome employing network approach

Anam Farooqui, Safia Tazyeen, Mohd. Murshad Ahmed, Aftab Alam, Shahnawaz Ali, Md. Zubbair Malik, Sher Ali, Romana Ishrat
2018 Scientific Reports  
Though an increase in discovering disease-associated genes have been observed with time, there is still a large fraction of diseases without a known molecular basis.  ...  Network-based approaches serve as potent prognostic tools that have been successfully applied in the characterization of genes in complex diseases such as cancer, ataxia, multiple sclerosis etc. 1-4 .  ...  Analysing the interacting partners of the disease associated genes play an important role in the prediction of genotype-phenotype associations and helps in identifying new disease genes candidates (i.e  ... 
doi:10.1038/s41598-018-28375-0 pmid:29973620 pmcid:PMC6031616 fatcat:jcu57yd2fvdzjme63zo7nzx6km

Cooperative Driver Pathway Discovery by Hierarchical Clustering and Link Prediction

Sufang Li, Jun Wang, Maozu Guo, Xiangliang Zhang
2020 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
In this paper, we proposed a method (CDPLP) based on hierarchical clustering and link prediction.  ...  CDPLP firstly devises a new similarity metric to quantify the exclusivity and co-expression of two gene modules, and thus to obtain gene sets with exclusivity by hierarchical clustering.  ...  Link prediction is a popular method to predict whether two nodes in a network having a link or not and can be used to replenish the interactions between pathways in a biological network composed of pathway  ... 
doi:10.1109/bibm49941.2020.9313174 fatcat:5ci6waf3krawpadsmg3kze7ace

Machine learning analysis of gene expression profile reveals a novel diagnostic signature for osteoporosis

Xinlei Chen, Guangping Liu, Shuxiang Wang, Haiyang Zhang, Peng Xue
2021 Journal of Orthopaedic Surgery and Research  
A gene module consisted of 176 genes predicted to be associated with the occurrence of OP was identified.  ...  A total of 16 significantly enriched GO terms and 1 significantly enriched KEGG pathway were obtained based on the 176 genes. The top 50 key genes in the PPI network were identified.  ...  Then we identified the top 50 genes that were predicted to be closely related to the development of OP according to the score based on the PPI network.  ... 
doi:10.1186/s13018-021-02329-1 pmid:33722258 fatcat:b63nnz4qyvbqzh6skmbyw3x2xy

A seven-gene CpG-island methylation panel predicts breast cancer progression

Yan Li, Anatoliy A. Melnikov, Victor Levenson, Emanuela Guerra, Pasquale Simeone, Saverio Alberti, Youping Deng
2015 BMC Cancer  
Unsupervised hierarchical clustering independently confirmed these findings, in close agreement with the accuracy measurements.  ...  When modelled together, these seven genes reached a sensitivity of 93 %, 100 % specificity, a positive predictive value of 100 % and a negative predictive value of 93 %, with high statistical power.  ...  Notably, most of these prognostic genes and their direct interactors in the network were found to map over key cancer cell-signaling pathways.  ... 
doi:10.1186/s12885-015-1412-9 pmid:25986046 pmcid:PMC4438505 fatcat:ppadaom2vfdelgfoml3reixdnu

Distinct and Competitive Regulatory Patterns of Tumor Suppressor Genes and Oncogenes in Ovarian Cancer

Min Zhao, Jingchun Sun, Zhongming Zhao, Szabolcs Semsey
2012 PLoS ONE  
and the target genes regulated by TSGs only were enriched in the ErbB signaling pathway.  ...  in the ErbB signaling pathway.  ...  Our hypothesis here was that a systematic integration of TFs and their potential modulators (TSGs and OCGs) provides an efficient approach to discover a gene regulatory network in OVC.  ... 
doi:10.1371/journal.pone.0044175 pmid:22952919 pmcid:PMC3431336 fatcat:jjpvpcmgvvg3nglrkwxaw5mxpa

A pathways-based prediction model for classifying breast cancer subtypes

Tong Wu, Yunfeng Wang, Ronghui Jiang, Xinliang Lu, Jiawei Tian
2017 OncoTarget  
Based on unsupervised clustering analysis, these 136 core genes efficiently categorized breast cancer patients into the appropriate subtypes.  ...  Functional enrichment based on Kyoto Encyclopedia of Genes and Genomes analysis identified six functional pathways regulated by these genes: JAK-STAT signaling, basal cell carcinoma, inflammatory mediator  ...  and that the network signal transmission efficiency decreased ( Figure 5B ).  ... 
doi:10.18632/oncotarget.18544 pmid:28938599 pmcid:PMC5601695 fatcat:7njqolwqrnf2ndofeffcnstmn4

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

Peter Csermely, Tamás Korcsmáros, Huba J.M. Kiss, Gábor London, Ruth Nussinov
2013 Pharmacology and Therapeutics  
Network description and analysis not only give a systems-level understanding of drug action and disease complexity, but can also help to improve the efficiency of drug design.  ...  The network influence strategy works against other diseases, where an efficient reconfiguration of rigid networks needs to be achieved by targeting the neighbors of central nodes or edges.  ...  Work in the authors' laboratory was supported by research grants from the Hungarian National Science Foundation (OTKA K83314), by the EU (TÁMOP-4.2.2/B-10/1-2010-0013), by a Bolyai Fellowship of the Hungarian  ... 
doi:10.1016/j.pharmthera.2013.01.016 pmid:23384594 pmcid:PMC3647006 fatcat:osjkz6kpr5gzxomqlyenla2fvq

Review on Graph Clustering and Subgraph Similarity Based Analysis of Neurological Disorders

Jaya Thomas, Dongmin Seo, Lee Sael
2016 International Journal of Molecular Sciences  
way to gain a global understanding of the diseases.  ...  We review a wide spectrum of graph representation and graph analysis methods and their application in the study of both the genomic level and the phenotypic level of the neurological disorder.  ...  They also considered two-way hierarchical clustering in order to predict disease phenotype cluster-gene cluster associations.  ... 
doi:10.3390/ijms17060862 pmid:27258269 pmcid:PMC4926396 fatcat:42vgbgz6erg2jaquohdirhw4ge

Stage specific classification of DEGs via statistical profiling and network analysis reveals potential biomarker associated with various stages of TB [article]

Aftab Alam, Nikhat Imam, Mohammad Murshad Ahmed, Safiya Tazyeen, Anam Farooqui, Shahnawaz Ali, Md. Zubbair Malik, Romana Ishrat
2018 bioRxiv   pre-print
In addition, we studied the regulatory networks of these classified genes, network analysis does consider the interactions between genes (specific for TB) or proteins provide us new facts about TB disease  ...  stages of TB were elucidated, which in turn provided a basis for the identification of potential pathways and key regulatory genes that may be involved in progression of TB disease.  ...  Community Analysis: Leading Eigen-vector method In hierarchical network, to distinguish the nature of modular and its properties is important to explaining the predicting about the activities of network  ... 
doi:10.1101/414110 fatcat:vs3mzb7hmrb6voochrsbj62kyi

Bioinformatic Primer for Clinical and Translational Science

Randolph S. Faustino, Anca Chiriac, Andre Terzic
2008 Clinical and Translational Science  
This new biology perspective allows inspection and prediction of disease conditions, not limited to a monogenic challenge, but as a combination of individualized molecular permutations acting in concert  ...  In this context, the network theory has become an invaluable tool to map relationships that integrate discrete elements that collectively direct global function within a particular -omic category, and  ...  Acknowledgments We are grateful for the assistance with the gene array technology by the Mayo Advanced Genomics Technology Center core facility.  ... 
doi:10.1111/j.1752-8062.2008.00038.x pmid:19690627 pmcid:PMC2727724 fatcat:tmlodwbtvnfyrorzajolppot6u
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