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Identification of Differentially Expressed Gene Modules in Heterogeneous Diseases [article]

Olga Zolotareva, Sahand Khakabimamaghani, Olga I Isaeva, Zoe Chervontseva, Alexey Savchik, Martin Ester
2020 bioRxiv   pre-print
Results: Here we present DESMOND, a new method for identification of Differentially ExpreSsed gene MOdules iN Diseases.  ...  Motivation: Identification of differentially expressed genes is necessary for unraveling disease pathogenesis.  ...  Iterative signature algorithm for the analysis of large-scale gene expression data. Physical Review E, 67(3). Bollobás, B., Borgs, C., Chayes, J. et al (2003). Directed scale-free graphs.  ... 
doi:10.1101/2020.04.23.055004 fatcat:nar2ms7gb5hgdpy26unvlblsoa

Identification of Differentially Expressed Gene Modules in Heterogeneous Diseases

Olga Zolotareva
They are capable of identifying genes with a similar expression pattern in a previously unknown subset of samples. After an overview [...]  ...  It further focuses on biclustering methods which seem to be very promising in the context of disease heterogeneity.  ...  To solve the formulated problem, a new method for identification of Differentially ExpreSsed gene MOdules iN Diseases called DESMOND has been developed [298] .  ... 
doi:10.4119/unibi/2954162 fatcat:56wt3qyycbapfldgqeir45xzj4

Analysis of gene expression and connectivity on hippocampus of Alzheimer's disease by a new comprehensive approach [article]

Shan Jiang
2020 bioRxiv   pre-print
Our results suggest that changes of gene expression in hippocampus of AD patients are highly heterogeneous at the individual gene level, while biological pathways annotated for PPI modules identified based  ...  Gene expression and gene connectivity describe two different functional aspects of a gene. These two different measures reveal different information about the involvement of genes in disorders.  ...  (3) AD is heterogeneous at individual gene level, but many differential genes are involved in the same nucleus-associated pathways and disease regulatory modules.  ... 
doi:10.1101/2020.01.14.906446 fatcat:4du7wpojzvb5zffgvkuxgariqu

Novel meta-analysis pipeline of heterogeneous high-throughput gene expression datasets reveals dysregulated interactions and pathways in asthma [article]

Brandon Guo, Abhinav Kaushik, Kari C. Nadeau
2019 medRxiv   pre-print
Then, The datasets are pre-processed and subjected to Weighted Gene Co-expression Network Analysis (WGCNA) for identification of functional modules.  ...  However, there is a poor consensus in our understanding of the molecular factors involved in the mechanism of this disease due to inherent genetic heterogeneity.  ...  The funders had no role in the designing of the research, decision to publish, or authoring of manuscript. Figure S1 . Box plots of quantile-normalized gene expression matrices. File 1.  ... 
doi:10.1101/19012377 fatcat:z4o372ksgrcmjfufzgdpvmbbq4

Integrative Analysis for Elucidating Transcriptomics Landscapes of Glucocorticoid-Induced Osteoporosis

Xiaoxia Ying, Xiyun Jin, Pingping Wang, Yuzhu He, Haomiao Zhang, Xiang Ren, Songling Chai, Wenqi Fu, Pengcheng Zhao, Chen Chen, Guowu Ma, Huiying Liu
2020 Frontiers in Cell and Developmental Biology  
Differential expression analysis revealed 1047 and 844 differentially expressed genes in the two datasets.  ...  After integrating differentially expressed glucocorticoid-related genes, we found that most of the robust differentially expressed genes were up-regulated.  ...  Differential Expression Analysis of Glucocorticoid-Related Genes The occurrence of diseases is often accompanied by gene expression disorders.  ... 
doi:10.3389/fcell.2020.00252 pmid:32373610 pmcid:PMC7176994 fatcat:ekhfkk2o6bfvpewnuchhwgov7m

Identifying dysfunctional miRNA-mRNA regulatory modules by inverse activation, cofunction, and high interconnection of target genes: A case study of glioblastoma

Y. Xiao, Y. Ping, H. Fan, C. Xu, J. Guan, H. Zhao, Y. Li, Y. Lv, Y. Jin, L. Wang, X. Li
2013 Neuro-Oncology  
We identified dysfunctional miRNAs, which were differentially expressed and inversely regulated most of their target genes, by integrating paired miRNA and mRNA expression profiles and miRNA target information  ...  In this study, we proposed a multistep method to identify dysfunctional miRNA-mRNA regulatory modules (dMiMRMs) in a specific disease, in which a group of miRNAs cooperatively regulate a group of target  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/neuonc/not018 pmid:23516263 pmcid:PMC3688007 fatcat:grxz6amzdvcbtjnskjvhm3xpuq

Unravelling personalized dysfunctional gene network of complex diseases based on differential network model

Xiangtian Yu, Tao Zeng, Xiangdong Wang, Guojun Li, Luonan Chen
2015 Journal of Translational Medicine  
However, due to the heterogeneity of disease samples, many disease genes are even not always consistently up-/ down-regulated, leading to be under-estimated.  ...  network) even when disease samples are heterogeneous, and thus can provide new features like gene-pairs, in addition to the conventional individual genes, to the analysis of the personalized diagnosis  ...  samples (e.g., heterogeneity of diseases [5] ).  ... 
doi:10.1186/s12967-015-0546-5 pmid:26070628 pmcid:PMC4467679 fatcat:zifnm2ynrvbqzjv4334tbk2qwm

Understanding Genotype-Phenotype Effects in Cancer via Network Approaches

Yoo-Ah Kim, Dong-Yeon Cho, Teresa M. Przytycka, Rachel Karchin
2016 PLoS Computational Biology  
Cancer is now increasingly studied from the perspective of dysregulated pathways, rather than as a disease resulting from mutations of individual genes.  ...  A pathway-centric view acknowledges the heterogeneity between genomic profiles from different cancer patients while assuming that the mutated genes are likely to belong to the same pathway and cause similar  ...  Also, in the case in which alteration refers to differential gene expression, each cancer case will have many differentially expressed genes because of indirect impact.  ... 
doi:10.1371/journal.pcbi.1004747 pmid:26963104 pmcid:PMC4786343 fatcat:p2zqfax3gfag7jutp3tq52tqve

MSIGNET: A Bayesian Approach for Disease-associated Gene Network Identification

Xi Chen, Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA, Jianhua Xuan
2020 OBM Genetics  
MSIGNET integrates disease gene expression data and human protein-protein interactions in a Bayesian network, and identifies interactions of genes specifically expressed under the disease condition.  ...  Yet, for many heterogeneous diseases, the number of known disease-associated genes is limited. Identifying disease-associated genes is still an open challenge.  ...  The conditional probability represents the likelihood of genes in that are differentially expressed between disease subjects and control subjects in the gene expression dataset .  ... 
doi:10.21926/obm.genet.2002107 fatcat:247isvcgk5cjpp3swm4pdoqjmi

Single Cell Atlas of Human Putamen Reveals Disease Specific Changes in Synucleinopathies: Parkinson's Disease and Multiple System Atrophy [article]

Rahul Pande, Yinyin Huang, Erin Teeple, Pooja Joshi, Amilcar Flores-Morales, Martine Latta- Mahieu, S. Pablo Sardi, Angel Cedazo-Minguez, Katherine W. Klinger, Stephen L. Madden, Deepak Rajpal, Dinesh Kumar
2021 bioRxiv   pre-print
Differentially expressed genes in major cell types are enriched for genes associated with PD-GWAS loci.  ...  We also identified disease associated gene modules using a network biology approach.  ...  GFAP and CD44 (B) Differential modulation of enriched biological pathways in MSA and PD clusters compared to Control, underscores contrasting altered heterogeneity in PD and MSA (C) Scaled average expression  ... 
doi:10.1101/2021.05.06.442950 fatcat:2xxhyvajrbdg5lxds5wjcsujwa

Single-Cell RNA Sequencing of the Cardiovascular System: New Looks for Old Diseases

Farhan Chaudhry, Jenna Isherwood, Tejeshwar Bawa, Dhruvil Patel, Katherine Gurdziel, David E. Lanfear, Douglas M. Ruden, Phillip D. Levy
2019 Frontiers in Cardiovascular Medicine  
Cardiovascular disease encompasses a wide range of conditions, resulting in the highest number of deaths worldwide.  ...  a wide variety of diseases.  ...  This was the first study showing a GWAS-identified gene mediating SMC phenotypic modulation in vivo in the setting of coronary artery disease.  ... 
doi:10.3389/fcvm.2019.00173 pmid:31921894 pmcid:PMC6914766 fatcat:5keydeeyw5frtebwit76mf7nkm

An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer

Zhenshu Wen, Zhi-Ping Liu, Zhengrong Liu, Yan Zhang, Luonan Chen
2013 JAMIA Journal of the American Medical Informatics Association  
Many methods have been developed to identify disease genes and further module biomarkers of complex diseases based on gene expression data.  ...  It is generally difficult to distinguish whether the variations in gene expression are causative or merely the effect of a disease.  ...  Acknowledgements The authors would like to thank Dr Tao Zeng (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences) for his helpful discussions and suggestions.  ... 
doi:10.1136/amiajnl-2012-001168 pmid:22967703 pmcid:PMC3721155 fatcat:eipl4asyufabro72mlzkn4lv2u

Deeper insights into long-term survival heterogeneity of Pancreatic Ductal Adenocarcinoma (PDAC) patients using integrative individual- and group-level transcriptome network analyses [article]

Archana Bhardwaj, Claire Josse, Daniel Van Daele, Christophe Poulet, Marcela Chavez, Ingrid Struman, Kristel Van Steen
2020 bioRxiv   pre-print
Findings: We identified 173 differentially expressed genes (DEGs) in ST and LT survivors and five modules (including 38 DEGs) showing associations to clinical traits such as tumor size and chemotherapy  ...  Furthermore, we applied two gene prioritization approaches: random walk-based Degree-Aware disease gene prioritizing (DADA) method to develop PDAC disease modules; Network-based Integration of Multi-omics  ...  Group based DEGs analysis: Differential Gene analysis and functional follow-up We used DEseq2 4 for the identification of differentially expressed genes (DEG), with the thresholds log2 fold change ≥2 and  ... 
doi:10.1101/2020.06.01.116194 fatcat:at46sigm3vh4naqy2qinsbmo3i

Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses

Francesco Monticolo, Emanuela Palomba, Maria Luisa Chiusano
2020 International Journal of Molecular Sciences  
We identified differentially-expressed genes, pathways that are significantly dysregulated across treatments, and characterized genes among those involved in induced cell death.  ...  Here, we analyzed gene expression data from induction of programmed cell death and stress response in Homo sapiens and compared the results with Saccharomyces cerevisiae gene expression during the response  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms21249560 pmid:33334055 fatcat:4astbldnmbh47by4wcp6pfaacq

A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes in asthma

Amitabh Sharma, Jörg Menche, C. Chris Huang, Tatiana Ort, Xiaobo Zhou, Maksim Kitsak, Nidhi Sahni, Derek Thibault, Linh Voung, Feng Guo, Susan Dina Ghiassian, Natali Gulbahce (+13 others)
2015 Human Molecular Genetics  
Recent advances in genetics have spurred rapid progress towards the systematic identification of genes involved in complex diseases.  ...  We find that the asthma disease module is enriched with modest GWAS P-values against the background of random variation, and with differentially expressed genes from normal and asthmatic fibroblast cells  ...  Funding This research received funding from Janssen R&D and was supported in part by National Institutes of Health (NIH) grants P50-HG004233-CEGS, MapGen grant (1U01HL108630-01) and 5P01-HL083069-5, U01  ... 
doi:10.1093/hmg/ddv001 pmid:25586491 pmcid:PMC4447811 fatcat:7iuvo4qqsrbv3g7ipab3pzfh7e
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