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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
2020
Frontiers in Neurology
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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]
2011
Medical Complications of Type 2 Diabetes
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'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
2020
Frontiers in Oncology
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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
2013
Lung Cancer
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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
2021
BMC Bioinformatics
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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
2022
Frontiers in Genetics
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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
2020
Frontiers in Genetics
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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
2020
Journal of genetic resources
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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
2021
Nature Communications
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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]
2019
bioRxiv
pre-print
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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
2021
Computational and Structural Biotechnology Journal
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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
2018
PLoS ONE
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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)
2018
Bioinformatics and Biology Insights
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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
2015
Frontiers in Cell and Developmental Biology
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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
2016
BMC Bioinformatics
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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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