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Uncovering Effective Explanations for Interactive Genomic Data Analysis
2020
Patterns
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Better tools are needed to enable researchers to quickly identify and explore effective and interpretable feature-based explanations for discriminating multi-class genomic datasets, e.g., healthy versus ...
With its generalizable optimizations and framework, GENVISAGE opens up real-time feature-based explanation generation to data from massive sequencing efforts, as well as many other scientific domains. ...
ACKNOWLEDGMENTS The authors gratefully acknowledge funding support for this work from the Na-
DECLARATION OF INTERESTS The authors declare no competing interests. ...
doi:10.1016/j.patter.2020.100093
pmid:33205133
pmcid:PMC7660438
fatcat:nwyywzog4nbqjnne46a6f53ote
Understanding Genotype-Phenotype Effects in Cancer via Network Approaches
2016
PLoS Computational Biology
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Indeed, network-centric approaches have proven to be helpful for finding genotypic causes of diseases, classifying disease subtypes, and identifying drug targets. ...
In this review, we discuss how networks can be used to help understand patientto-patient variations and how one can leverage this variability to elucidate interactions between cancer drivers. ...
Illustrations of how gene networks can be used in cancer data analysis. ...
doi:10.1371/journal.pcbi.1004747
pmid:26963104
pmcid:PMC4786343
fatcat:p2zqfax3gfag7jutp3tq52tqve
dcVar: a method for identifying common variants that modulate differential correlation structures in gene expression data
2015
Frontiers in Genetics
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We apply dcVar to the HapMap3 eQTL dataset and demonstrate the utility of this methodology at uncovering novel function of variants of interest with examples from a height genome-wide association and cancer ...
Recent studies have implicated the role of differential co-expression or correlation structure in gene expression data to help explain phenotypic differences. ...
Our implementation of a framework to compute differential correlation from variants in C++ provides a tool for researchers to uncover these effects in a genome-wide eQTL or RNA-Seq analysis. ...
doi:10.3389/fgene.2015.00312
pmid:26539209
pmcid:PMC4609883
fatcat:n6b6lmy43vgyvfk5opqbgydfmq
Perspective on the genetics of attention deficit/hyperactivity disorder
2008
American Journal of Medical Genetics Part B: Neuropsychiatric Genetics
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One hope for genetic studies is the potential for the discovery of new biological pathways and new targets for treatment. ...
This set of articles recapitulates the major trends in the field of complex psychiatric genetics, underscoring how genetic studies of ADHD have evolved, and what approaches are needed to uncover the genetic ...
None of the SNPs tested achieved genome-wide significance on the main effect of the moderator or the test for the interaction between the moderator and ADHD diagnosis. ...
doi:10.1002/ajmg.b.30875
pmid:18951432
fatcat:w2jkxzopczgkpayohg3vm64koi
Learning to swim in a sea of genomic data
2013
Genome Biology
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Acknowledgements The author thanks Chris Tyler-Smith (Wellcome Trust Sanger Institute, UK), Jieming Chen and Suganthi Balasubramanian (Yale University, USA) for comments and suggestions. ...
These talks highlighted the importance of integrating functional genomics studies with whole-genome sequencing data to uncover the effects of sequence variants. ...
A likely explanation for this observation is that dominant mutations tend to be gain-offunction and mostly cause the gain of different functions in interacting proteins, as opposed to recessive mutations ...
doi:10.1186/gb4144
pmid:24314026
pmcid:PMC4053704
fatcat:72nxemflxzgr5kyx4c2y5pmrp4
Toward the dynamic interactome: it's about time
2010
Briefings in Bioinformatics
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conditions, is increasingly helpful in elucidating interaction dynamics. ...
Dynamic molecular interactions play a central role in regulating the functioning of cells and organisms. ...
We thank her for many illuminating discussions, and the organizers of the PSB conference for supporting our session. ...
doi:10.1093/bib/bbp057
pmid:20061351
pmcid:PMC2810115
fatcat:xbj7ugs6nbed7guys2ie5z3efa
Pathway-based classification of genetic diseases
2019
Molecular Cytogenetics
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However, recent achievements in systems biology have offered a possibility to explore the consequences of a genetic defect from genomic variations to molecular/cellular pathway alterations unique to a ...
The basic idea of our classification is to propose pathways as parameters for designating a genetic disease. ...
Focusing on uncovering underlying disease mechanisms using high-resolution genomic data, pathway-based analysis has provided numerous discoveries in the field of molecular medicine. ...
doi:10.1186/s13039-019-0418-4
pmid:30766616
pmcid:PMC6362588
fatcat:csahwgl3rfhqvox7zungdlkgdq
Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements
2016
Nucleic Acids Research
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Motif analyses uncovered candidate Negative Regulatory Sequences (NRSs) that interfere with genomic GR binding. ...
Instead, we find that NRSs interact with proteins found at sub-nuclear structures called paraspeckles and that these proteins might mediate the repressive effects of NRSs. ...
Thus, one explanation for the effect of NRSs could be that they render nearby genomic regions inaccessible. ...
doi:10.1093/nar/gkw203
pmid:27016732
pmcid:PMC5291246
fatcat:mpaex2heofcidbfwtlt3qhkrpy
Reworking GWAS Data to Understand the Role of Nongenetic Factors in MS Etiopathogenesis
2020
Genes
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We then surveyed studies on the bioinformatic reworking of genome-wide association studies (GWAS) data, with aggregate analyses of many GWAS loci, each contributing with a small effect to the overall disease ...
This complexity poses at least two challenges: the definition of an etiological model including the impact of nongenetic factors, and the clinical translation of genomic data that may be drivers for new ...
which are known to interact with the genetic signals resulting from genome-scale data. ...
doi:10.3390/genes11010097
pmid:31947683
pmcid:PMC7017269
fatcat:l62b4ntdn5cazpp3m23mvektji
Highly polygenic architecture of antidepressant treatment response: Comparative analysis of SSRI and NRI treatment in an animal model of depression
2016
American Journal of Medical Genetics Part B: Neuropsychiatric Genetics
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Highly Polygenic Architecture of Antidepressant Treatment Response: Comparative Analysis of SSRI and NRI Treatment in an Animal Model of Depression. Am J Med Genet Part B 9999:1-16. ...
ACKNOWLEDGMENTS The Genome-Based Therapeutic Drugs for Depression study was funded by a European Commission ...
The same analysis was repeated for probe sets uncovered from the escitalopram versus saline classification analysis. ...
doi:10.1002/ajmg.b.32494
pmid:27696737
pmcid:PMC5434854
fatcat:pzvtelvifffg3nvubhgjb6o4bu
Computational solutions for omics data
2013
Nature reviews genetics
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Finally, efficient means for storing, searching and retrieving data are of foremost concern as they are necessary for any analysis to proceed. ...
Several software platforms and database systems have been developed for basic data analysis and integration 1-3 (BOX 1). ...
Cowen for valuable feedback. B.B. thanks the US National Institutes of Health (NIH) for grant GM081871. ...
doi:10.1038/nrg3433
pmid:23594911
pmcid:PMC3966295
fatcat:b7n6xwzyc5gqzo7plgyoe257iq
Defining the genetic architecture of the predisposition to obesity: a challenging but not insurmountable task
2009
American Journal of Clinical Nutrition
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However, a meta-analysis of 37 genome scan studies with data on 31,000 individuals from .10,000 families could not implicate unequivocally a single genetic locus for obesity or body mass index (BMI) ( ...
I see 2 possible avenues of explanation for this extraordinary discrepancy. ...
doi:10.3945/ajcn.2009.28933
pmid:19939981
fatcat:aq2leka22zaihdgs4cof7ob6x4
In the pursuit of complexity: Systems medicine in cancer biology
2006
Cancer Cell
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This work shows that the intersect analysis of gene amplification and transcriptional expression on a genome-wide scale can uncover complex conditional interactions embedded in the systems map of transcriptional ...
This work by Adler et al. highlights the fact that the intersection of two genome-wide scans (expression and chromosomal amplification) can yield interesting higher-order mechanistic explanations for biological ...
doi:10.1016/j.ccr.2006.03.026
pmid:16616330
fatcat:udnasembbzdynno5qkrayiq3ga
Expanding the uses of genome‐scale models with protein structures
2019
Molecular Systems Biology
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In contrast, systems biology and genome-scale modeling have organically grown out of the wealth of data now being generated by diverse omics measurements. ...
In this commentary, we highlight the challenges of integrating these two fields, with a focus on genome-scale metabolic modeling, and the novel findings that are made possible from such a merger. ...
The authors graciously thank Marc Abrams for his help editing and proofreading this document.
Conflict of interest The authors declare that they have no conflict of interest. ...
doi:10.15252/msb.20188601
pmid:31777175
pmcid:PMC6880182
fatcat:um26g7wm3bfojjcox5eie4f66y
Genome-wide analysis of interactions between ATP-dependent chromatin remodeling and histone modifications
2009
BMC Genomics
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Analysis of the genome-wide picture revealed that transcription-related modifications tend to interact with more chromatin remodelers. ...
Our method succeeds in identifying known interactions and uncovers many previously unknown interactions between these two activities. ...
Acknowledgements We thank Martin Kupiec for providing the chromatin modifier compendium and Euan Ashley for providing the Heatmap Builder. ...
doi:10.1186/1471-2164-10-304
pmid:19586523
pmcid:PMC2713269
fatcat:l6b37uif4femdd2cyeendqyun4
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