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DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes

Mariano J. Alvarez, James C. Chen, Andrea Califano
2015 Bioinformatics  
Identification of driver mutations in human diseases is often limited by cohort size and availability of appropriate statistical models. We propose a method for the systematic discovery of  ...  Activity quantitative trail loci are then inferred by computing the statistical association between F-CNV and VIPER-inferred MR protein activity by MI or correlation analysis.  ...  Finally, a conditional association analysis is performed to determine which, among multiple genes affected by the same amplified or deleted regions, are the most probable drivers of MR dysregulation.  ... 
doi:10.1093/bioinformatics/btv499 pmid:26338767 pmcid:PMC4692968 fatcat:cz7xuu7i7rehfmhrflzffx6lve

Identification of regulatory SNPs associated with genetic modifications in lung adenocarcinoma

Tzu-Pin Lu, Chuhsing K Hsiao, Liang-Chuan Lai, Mong-Hsun Tsai, Chung-Ping Hsu, Jang-Ming Lee, Eric Y Chuang
2015 BMC Research Notes  
A major challenge to improve the understanding of lung cancer is the difficulty of identifying reproducible differentially expressed genes across independent studies, due to their low consistency.  ...  Results: A total of 505 differentially expressed genes were identified, and their dysregulated patterns moderately correlated with CNVs and methylation alterations based on the hierarchical clustering  ...  Acknowledgments This research was supported in part by grants from the Department of Health, Taiwan  ... 
doi:10.1186/s13104-015-1053-8 pmid:25889623 pmcid:PMC4384239 fatcat:4fbhanfjyveb3j4pgnyjq4ntly

Identifying Causal Genes and Dysregulated Pathways in Complex Diseases

Yoo-Ah Kim, Stefan Wuchty, Teresa M. Przytycka, Markus W. Covert
2011 PLoS Computational Biology  
First, we identified a representative set of genes that are differentially expressed in cancer compared to non-tumor control cases.  ...  Combining an expression Quantitative Trait Loci (eQTL) analysis with pathway information, our approach allowed us not only to identify potential causal genes but also to find intermediate nodes and pathways  ...  i ), which are affected by cg k (i.e., with P,0.05) and differentially expressed in case s i .  ... 
doi:10.1371/journal.pcbi.1001095 pmid:21390271 pmcid:PMC3048384 fatcat:ek6ffpeelzfv3bf54dt4deedwu

Convergence of dispersed regulatory mutations predicts driver genes in prostate cancer [article]

Richard C. Sallari, Nicholas A. Sinnott-Armstrong, Juliet D. French, Ken J. Kron, Jason Ho, Jason H. Moore, Vuk Stambolic, Stacey L. Edwards, Mathieu Lupien, Manolis Kellis
2016 bioRxiv   pre-print
We experimentally validate the PLCB4 plexus and its ability to affect the canonical PI3K cancer pathway.  ...  Using 55 matched tumor-normal prostate genomes, we predict 15 driver genes by convergence of dispersed, low-frequency mutations into high-frequency dysregulatory events along prostate-specific plexi, controlling  ...  Dysregulated gene analysis Core scores -We identify dysregulated instances of genes in specific patients across 16 cancer transcriptomes by normalizing every gene's expression using an aggregate of values  ... 
doi:10.1101/097451 fatcat:nlnlg4i2sngbzn2o5hk4i6i6fu

Bridging the Gap between Genotype and Phenotype via Network Approaches

Yoo-Ah Kim, Teresa M. Przytycka
2013 Frontiers in Genetics  
as a quantitative phenotype and genetic loci controlling the phenotypic changes are identified by comparing gene expression and genotypic data from the same set of samples and determining the associations  ...  A useful link between the two can be provided by expression quantitative trait loci (eQTL) analysis (Stranger et al., 2005 (Stranger et al., , 2007 ) -a technique in which gene expression level is treated  ... 
doi:10.3389/fgene.2012.00227 pmid:23755063 pmcid:PMC3668153 fatcat:hbj7ddx5sjf3hha5gluhywha2a

The emerging role of lncRNAs in inflammatory bowel disease

Reza Yarani, Aashiq H Mirza, Simranjeet Kaur, Flemming Pociot
2018 Experimental and Molecular Medicine  
Dysregulation of long noncoding RNA (lncRNA) expression is linked to the development of various diseases.  ...  We also collate potentially immune-relevant, IBD-associated lncRNAs identified through a built-by association analysis with respect to their neighboring protein-coding genes within IBD-susceptible loci  ...  Acknowledgements This work was supported by grants from the Independent Research Fund Denmark (8020-00300B) and the Sehested Hansen Foundation.  ... 
doi:10.1038/s12276-018-0188-9 pmid:30523244 pmcid:PMC6283835 fatcat:i6vnniuvxffyxnijcdezsc6e2y

MiR-886-3p Regulates Cell Proliferation and Migration, and Is Dysregulated in Familial Non-Medullary Thyroid Cancer

Yin Xiong, Lisa Zhang, Alisha K. Holloway, Xiaolin Wu, Ling Su, Electron Kebebew, Marian Ludgate
2011 PLoS ONE  
Methodology/Principal Findings: Genome wide miRNA profiling of sporadic and familial papillary thyroid cancer was performed. Differentially expressed miRNAs were validated by quantitative RT-PCR.  ...  The molecular basis and characteristics of familial non-medullary thyroid cancer are poorly understood.  ...  of dysregulated miRNAs in sporadic versus familial papillary thyroid cancer by quantitative RT-PCR.  ... 
doi:10.1371/journal.pone.0024717 pmid:21998631 pmcid:PMC3187745 fatcat:qivk7eptpfcmtbuw3tl265fw3m

Gene Clusters, Molecular Evolution and Disease: A Speculation

Leah Elizondo, Paymaan Jafar-Nejad, J. Clewing, Cornelius Boerkoel
2009 Current Genomics  
In the context of human disease, we propose that dysregulation of gene expression across genomic neighborhoods will cause highly pleiotropic diseases.  ...  Traditionally eukaryotic genes are considered independently expressed under the control of their promoters and cis-regulatory domains.  ...  Considering the features of these rare Mendelian disorders as quantitative traits provides a model for the variable expressivity and pleiotropism; characteristics which cannot be explained simply by dysregulation  ... 
doi:10.2174/138920209787581271 pmid:19721813 pmcid:PMC2699835 fatcat:ketuspaqxvaurc6cyo5is5gmxe

regQTLs: Single nucleotide polymorphisms that modulate microRNA regulation of gene expression in tumors

Gary Wilk, Rosemary Braun, FJ Slack
2018 PLoS Genetics  
We previously identified pathways-systems of genes conferring specific cell functions-that are dysregulated by miRNAs in cancer, by comparing miRNA-pathway associations between healthy and tumor tissue  ...  We draw on these results as a starting point to assess whether SNPs on dysregulated pathways are responsible for miRNA dysregulation of individual genes in tumors.  ...  Acknowledgments The results published here are in whole or part based upon data generated by The Cancer Genome Atlas managed by the NCI and NHGRI.  ... 
doi:10.1371/journal.pgen.1007837 pmid:30557297 pmcid:PMC6343932 fatcat:uzxipp56anfk5crkcibjdtuxiq

CTCF maintains regulatory homeostasis of cancer pathways

Sarah J. Aitken, Ximena Ibarra-Soria, Elissavet Kentepozidou, Paul Flicek, Christine Feig, John C. Marioni, Duncan T. Odom
2018 Genome Biology  
Furthermore, we observe dysregulation of the expression of several hundred genes, which are concentrated in cancer-related pathways, and are caused by changes in transcriptional regulation.  ...  In contrast, Ctcf hemizygous mice with lifelong reduction of CTCF expression are viable, albeit with increased cancer incidence.  ...  To explore whether fine-scale chromatin organization is affected by reduced levels of CTCF, we merged all Fig. 3 Differentially bound CTCF loci are found near genes, occur in shorter motifs, and have  ... 
doi:10.1186/s13059-018-1484-3 pmid:30086769 pmcid:PMC6081938 fatcat:rfzctzqa3nbsdlrsb3yrkxnl4i

Obesity, Rather Than Diet, Drives Epigenomic Alterations in Colonic Epithelium Resembling Cancer Progression

Ruifang Li, Sara A. Grimm, Kaliopi Chrysovergis, Justin Kosak, Xingya Wang, Ying Du, Adam Burkholder, Kyathanahalli Janardhan, Deepak Mav, Ruchir Shah, Thomas E. Eling, Paul A. Wade
2014 Cell Metabolism  
Environmental stimuli, including diet, can alter the epigenetic landscape of DNA cis-regulatory elements affecting gene expression and phenotype.  ...  The interrogation of enhancer alterations by diet in colonic epithelium provides insights into the biology underlying high-fat diet and obesity as risk factors for colon cancer.  ...  We express gratitude to Dr. Scott Bultman for many useful suggestions and vigorous discussion throughout the course of this work.  ... 
doi:10.1016/j.cmet.2014.03.012 pmid:24703701 pmcid:PMC4050048 fatcat:qifig3zjezd27djbnojgotsrse

Microsphere-Based Multiplex Analysis of DNA Methylation in Acute Myeloid Leukemia

Gerald B.W. Wertheim, Catherine Smith, Maria E. Figueroa, Michael Kalos, Adam Bagg, Martin Carroll, Stephen R. Master
2014 Journal of Molecular Diagnostics  
We have developed a novel strategy, termed microsphere HpaII tiny fragment enrichment by ligation-mediated PCR (MELP), to simultaneously analyze the DNA methylation pattern at these loci using methylation-specific  ...  Previous studies have demonstrated that the prognosis of patients with acute myeloid leukemia can be predicted by the DNA methylation pattern of 18 loci.  ...  , recent work has unequivocally demonstrated that cancer is also characterized by dysregulation of chromatin structure that involves the DNA itself (eg, CpG methylation) and its associated histones. 2  ... 
doi:10.1016/j.jmoldx.2013.10.010 pmid:24373919 pmcid:PMC3937537 fatcat:w3cdaixervgdjb4fggu4yj4aoq

MicroRNA Dysregulation in Squamous Cell Carcinoma of Head and Neck [chapter]

Thian-Sze Wong, Wei Gao, Wai-Kuen Ho, Jimmy Yu-Wai, William Ignace, Raymond King-Yin
2012 Squamous Cell Carcinoma  
MicroRNA dysregulation by candidate oncogene MicroRNA expression could be controlled by oncogene such as myc. He et al.  ...  Loss of heterozygosity (LOH) in these loci are common in HNSCC (Bauer et al., 2008; Spafford et al., 2001) .  ...  The role of tumor microenvironment in head and neck SCC is specifically discussed. Thirdly, the roles of cancer stem cells (CSC) in cancer therapy of SCC are described.  ... 
doi:10.5772/25376 fatcat:pz4szvv3wrhuhg4ql52wcixawm

The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma

Yanqiang Wang, Huiling He, Sandya Liyanarachchi, Luke K Genutis, Wei Li, Lianbo Yu, John E Phay, Rulong Shen, Pamela Brock, Albert de la Chapelle
2018 Genetics in Medicine  
To identify and characterize the functional variants, regulatory gene networks, and potential binding targets of SMAD3 in the 15q22 thyroid cancer risk locus.  ...  ACKNOWLEDGMENTS This work was supported by National Cancer Institute grants P30CA16058 and P50CA168505. We thank Matthew D. Ringel for helpful discussions and suggestions.  ...  The analysis was done in part by an allocation of computing time from the Ohio Supercomputer Center.  ... 
doi:10.1038/gim.2017.224 pmid:29300379 pmcid:PMC6030507 fatcat:m3kvkav2nzesnimu3wmmepz56m

Single nucleotide polymorphisms that modulate microRNA regulation of gene expression in tumors [article]

Gary Wilk, Rosemary Braun
2018 arXiv   pre-print
We previously identified pathways--systems of genes conferring specific cell functions--that are dysregulated by miRNAs in cancer, by comparing miRNA-pathway associations between healthy and tumor tissue  ...  "regulatory QTLs (regQTLs)": loci whose alleles impact the regulation of genes by miRNAs.  ...  To date, the functional effects of polymorphisms are typically explored by integrating GWAS and gene expression data find expression Quantitative Trait Loci (eQTLs): SNP variants that result in altered  ... 
arXiv:1803.03189v2 fatcat:tuhw4sdd7vcplessrvpfzucsi4
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