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Phenotypic Subtyping and Re-analyses of Existing Transcriptomic Data from Autistic Probands in Simplex Families Reveal Differentially Expressed and ASD Trait-Associated Genes

Valerie W. Hu, Chongfeng Bi
2020 Frontiers in Neurology  
The comparison reveals overlapping trait-associated pathways as well as upstream regulators of the module-associated genes that may serve as useful targets for a precision medicine approach to ASD.  ...  Finally, we compare the WGCNA-derived data on autistic traits in simplex families with analogous data from multiplex families using transcriptomic data from our previous studies.  ...  ACKNOWLEDGMENTS We are grateful to both the SSC and AGRE for ADI-R scoresheets from individuals with ASD in both the simplex and multiplex families, respectively, as well as to the families who have generously  ... 
doi:10.3389/fneur.2020.578972 pmid:33281715 pmcid:PMC7689346 fatcat:xfnb75dwefbj5i4kobze3mtqfu

Using Gene Expression Signatures to Dissect Insulin Resistance Subtypes [chapter]

Brad Hayward, Nicky Konstantopoulos, Ken R.
2011 Medical Complications of Type 2 Diabetes  
'Omics' approaches The development of powerful platform technologies such as microarrays has led to a vast increase in the utilisation of the 'omics' type studies.  ...  The set of differentially expressed genes can also be used for a diagnostic approach to the disease.  ...  The book concludes with several chapters on the treatments for this disease offering us hope in prevention and successful alleviation of the co-morbidities associated with obesity and type 2 diabetes.  ... 
doi:10.5772/22889 fatcat:a72dhmzczbfjzmycnkmh4dsueq

Artificial Intelligence (AI)-Based Systems Biology Approaches in Multi-Omics Data Analysis of Cancer

Nupur Biswas, Saikat Chakrabarti
2020 Frontiers in Oncology  
Based on the research trends and significance in patient treatment, we have primarily focused on the AI-based analysis for determining cancer subtypes, disease prognosis, and therapeutic targets.  ...  As these bio-entities are very much correlated, integrative analysis of different types of omics data, multi-omics data, is required to understanding the disease from the tumorigenesis to the disease progression  ...  The authors acknowledge the CSIR-Indian Institute of Chemical Biology for infrastructural support.  ... 
doi:10.3389/fonc.2020.588221 pmid:33154949 pmcid:PMC7591760 fatcat:5kfd6jid6vcx7h4qvk52pngo5m

Genetic alterations defining NSCLC subtypes and their therapeutic implications

Larissa A. Pikor, Varune R. Ramnarine, Stephen Lam, Wan L. Lam
2013 Lung Cancer  
treatments based on a tumor's molecular alterations with the hope of improving patient response and survival.  ...  While treatment decisions are determined primarily by stage, therapeutically non small cell lung cancer (NSCLC) has traditionally been treated as a single disease.  ...  Acknowledgements We thank Emily Vucic and Kelsie Thu for insightful comments.  ... 
doi:10.1016/j.lungcan.2013.07.025 pmid:24011633 fatcat:i6uz4druhveq5odyhafs4ybv5u

Multi-dimensional data integration algorithm based on random walk with restart

Yuqi Wen, Xinyu Song, Bowei Yan, Xiaoxi Yang, Lianlian Wu, Dongjin Leng, Song He, Xiaochen Bo
2021 BMC Bioinformatics  
Results Here, we propose a multi-omics data integration algorithm based on random walk with restart (RWR) on multiplex network.  ...  However, the algorithm development for multi-omics data integration remains a pressing challenge.  ...  Ethics approval and consent to participate No ethics approval was required for the study. Consent for publication Not applicable.  ... 
doi:10.1186/s12859-021-04029-3 pmid:33639858 fatcat:xehcfth76bem7o5vttqqoeru3m

Unsupervised Multi-Omics Data Integration Methods: A Comprehensive Review

Nasim Vahabi, George Michailidis
2022 Frontiers in Genetics  
discovery, disease subtyping, module discovery, and network/pathway analysis.  ...  This review aims to provide an overview of multi-Omics data integration methods with different statistical approaches, focusing on unsupervised learning tasks, including disease onset prediction, biomarker  ...  SNF (Similarity Network Fusion) (Wang et al., 2014 ) is a popular method for multi-Omics data integration and subtype analysis.  ... 
doi:10.3389/fgene.2022.854752 pmid:35391796 pmcid:PMC8981526 fatcat:ijmwfu264rbgtaen66tkbr4sgu

Network Diffusion Promotes the Integrative Analysis of Multiple Omics

Noemi Di Nanni, Matteo Bersanelli, Luciano Milanesi, Ettore Mosca
2020 Frontiers in Genetics  
We present an overview of the state of the art of bioinformatics pipelines that use network diffusion processes for the integrative analysis of omics data.  ...  Current trends suggest that network diffusion is a tool of broad utility in omics data analysis.  ...  to identify disease subtypes.  ... 
doi:10.3389/fgene.2020.00106 pmid:32180795 pmcid:PMC7057719 fatcat:qjbmb6atxndfvgtva62vdvxd4u

Exploring Gene Signatures in Different Molecular Subtypes of Gastric Cancer (MSS/ TP53+, MSS/TP53-): A Network-based and Machine Learning Approach

Mehdi Sadeghi, Nafiseh Ghorbanpour, Abolfazl Barzegar, Iliya Rafiei
2020 Journal of genetic resources  
module was selected for further analysis (modules with 241 genes for TP53+ and 1441 genes for TP53- were identified).  ...  In this study, a three-step methodology was developed to identify important genes and subnetworks in two subtypes of GC (TP53+ and TP53-).  ...  We would like to thank the Research Institute for Fundamental Sciences (RIFS)-University of Tabriz for financial supports.  ... 
doi:10.22080/jgr.2020.19465.1198 doaj:577f5a06ea5042b09b4fd8af38ddb86f fatcat:obdoxmfyrnbitgnvp4uwlo4awm

An integrated multi-omics analysis identifies prognostic molecular subtypes of non-muscle-invasive bladder cancer

Sia Viborg Lindskrog, Frederik Prip, Philippe Lamy, Ann Taber, Clarice S. Groeneveld, Karin Birkenkamp-Demtröder, Jørgen Bjerggaard Jensen, Trine Strandgaard, Iver Nordentoft, Emil Christensen, Mateo Sokac, Nicolai J. Birkbak (+35 others)
2021 Nature Communications  
Here, we perform an integrative multi-omics analysis of patients diagnosed with NMIBC (n = 834).  ...  Transcriptomic analysis identifies four classes (1, 2a, 2b and 3) reflecting tumor biology and disease aggressiveness.  ...  Source data are provided as a Source data file. Furthermore, a similar approach shown in a recent study also documented that high-precision analysis of mutations based on RNA is achievable 50 .  ... 
doi:10.1038/s41467-021-22465-w pmid:33863885 pmcid:PMC8052448 fatcat:q6n5r6btdbeqznf2eerljdvi2m

Orthogonal proteomic platforms and their implications for the stable classification of high-grade serous ovarian cancer subtypes [article]

Stefani N. Thomas, Betty Friedrich, Michael Schnaubelt, Daniel W. Chan, Hui Zhang, Ruedi Aebersold
2019 bioRxiv   pre-print
SWATH-MS, an instance of data-independent acquisition (DIA) proteomic methods, was recently developed as an alternate proteomic approach.  ...  The SWATH-MS results indicated that both methods confidently identified differentially expressed proteins in enriched pathways associated with the robust Mesenchymal subtype of high-grade serous ovarian  ...  described network 4 7 5 propagation approach based on functional enrichment analysis.  ... 
doi:10.1101/793026 fatcat:cboeyjgjdnfk7kd7abbaktci34

Integration strategies of multi-omics data for machine learning analysis

Milan Picard, Marie-Pier Scott-Boyer, Antoine Bodein, Olivier Périn, Arnaud Droit
2021 Computational and Structural Biotechnology Journal  
Multi-omics data integration strategies are needed to combine the complementary knowledge brought by each omics layer.  ...  Most biomarkers obtained to date however only include one omic measurement at a time and thus do not take full advantage of recent multi-omics experiments that now capture the entire complexity of biological  ...  linear regression Bayesian integrative clustering Disease subtyping, biomarker discovery iCluster was used to identify subtypes of esophageal carcinoma from genomic, epigenomic and transcriptomic data  ... 
doi:10.1016/j.csbj.2021.06.030 pmid:34285775 pmcid:PMC8258788 fatcat:n45fkusgnfen3noyrwgklykboq

Orthologous proteins of experimental de- and remyelination are differentially regulated in the CSF proteome of multiple sclerosis subtypes

Nellie A. Martin, Arkadiusz Nawrocki, Viktor Molnar, Maria L. Elkjaer, Eva K. Thygesen, Miklos Palkovits, Peter Acs, Tobias Sejbaek, Helle H. Nielsen, Zoltan Hegedus, Finn Sellebjerg, Tihamer Molnar (+9 others)
2018 PLoS ONE  
Conclusions Pathology-based multi-omics identified four CSF markers that were differentially expressed in MS subtypes.  ...  Objective Here, we applied a multi-omics approach (i) to examine molecular pathways related to deand remyelination in multiple sclerosis (MS) lesions; and (ii) to translate these findings to the CSF proteome  ...  Acknowledgments We thank Ulla Damgaard Munk for expert technical assistance.  ... 
doi:10.1371/journal.pone.0202530 pmid:30114292 fatcat:wks4lbhhjzfb7hzibfpb7pkxtu

Review of Statistical Learning Methods in Integrated Omics Studies (An Integrated Information Science)

Irene Sui Lan Zeng, Thomas Lumley
2018 Bioinformatics and Biology Insights  
Acknowledgements The authors would like to express their gratitude to Ms Vivian Ward who helped to visualize the analytical processes for the review.  ...  Estimating structure of multilayer networks formed by integrated omics data sets Angione et al 19 introduced the multilayer network (multiplex) method for the integrated omics data.  ...  Comparatively, the regularization-based approach iCluster can be used for both categorical and continuous integrated omics data.  ... 
doi:10.1177/1177932218759292 pmid:29497285 pmcid:PMC5824897 fatcat:nbknjl4qq5awrldy7natmg3h6y

How to build personalized multi-omics comorbidity profiles

Mohammad Ali Moni, Pietro Liò
2015 Frontiers in Cell and Developmental Biology  
Methods for integrating multiple types of omics data play an important role to identify integrative biomarkers for stratification of patients into groups with different clinical outcomes.  ...  Starting from an initial diagnosis, omics and clinical data of a patient the software identifies the association risk of disease comorbidities.  ...  Multiplex Network Model for Data Integration We developed multiplex network model to integrate diverse set of omics and clinical data to predict disease comorbidities.  ... 
doi:10.3389/fcell.2015.00028 pmid:26157799 pmcid:PMC4478898 fatcat:i4si7dvtdvagjd4lytuyxosnze

Methods for the integration of multi-omics data: mathematical aspects

Matteo Bersanelli, Ettore Mosca, Daniel Remondini, Enrico Giampieri, Claudia Sala, Gastone Castellani, Luciano Milanesi
2016 BMC Bioinformatics  
Methods for the integrative analysis of multi-omics data are required to draw a more complete and accurate picture of the dynamics of molecular systems.  ...  Results and Conclusions: We review the most advanced strategies for integrating multi-omics datasets, focusing on mathematical and methodological aspects.  ...  Multi-layer network-based frameworks, such as heterogeneous and multiplex networks, allow the definition of novel tools for the integration of omics.  ... 
doi:10.1186/s12859-015-0857-9 pmid:26821531 pmcid:PMC4959355 fatcat:wqbgnui7cnhd3ba6wz22ux2ddy
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