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GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

Simon Fishilevich, Ron Nudel, Noa Rappaport, Rotem Hadar, Inbar Plaschkes, Tsippi Iny Stein, Naomi Rosen, Asher Kohn, Michal Twik, Marilyn Safran, Doron Lancet, Dana Cohen
2017 Database: The Journal of Biological Databases and Curation  
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards.  ...  We present GeneHancer, a novel database of human enhancers and their inferred target genes, in the framework of GeneCards.  ...  (Massachusetts, USA); Crown Human Genome Center at the Weizmann Institute of Science.  ... 
doi:10.1093/database/bax028 pmid:28605766 pmcid:PMC5467550 fatcat:xslg453wargdbalhgq7rmj73pq

Genome analysis and knowledge-driven variant interpretation with TGex

Dvir Dahary, Yaron Golan, Yaron Mazor, Ofer Zelig, Ruth Barshir, Michal Twik, Tsippi Iny Stein, Guy Rosner, Revital Kariv, Fei Chen, Qiang Zhang, Yiping Shen (+3 others)
2019 BMC Medical Genomics  
This is enabled by GeneCards' recently developed GeneHancer, a novel integrative and fully annotated database of human enhancers and promoters.  ...  VarElect leverages the widely used GeneCards knowledgebase, which integrates information from > 150 automatically-mined data sources.  ...  GeneHancer provides a unique non-redundant and comprehensive genome-wide map of scored~400,000 enhancers and promoters ("GeneHancers"), and their gene associations.  ... 
doi:10.1186/s12920-019-0647-8 pmid:31888639 pmcid:PMC6937949 fatcat:ixi7j3mqqzflrgzaj5wwwb3xjm

Computational biology solutions to identify enhancers-target gene pairs

Judith Mary Hariprakash, Francesco Ferrari
2019 Computational and Structural Biotechnology Journal  
In this review we focus on computational methods for genome-wide definition of enhancer-target gene pairs.  ...  Their characterization still remains elusive especially due to challenges in achieving a comprehensive pairing of enhancers and target genes.  ...  Acknowledgements We thank Mattia Forcato and Pierre-Luc Germain for critical feedback on an earlier version of the manuscript.  ... 
doi:10.1016/j.csbj.2019.06.012 pmid:31316726 pmcid:PMC6611831 fatcat:zez36sa5qvdtfaxitmid73gase

Quantitative prediction of enhancer-promoter interactions [article]

Polina Belokopytova, Evgeniy Mozheiko, Miroslav Nuriddinov, Daniil Fishman, Veniamin Fishman
2019 bioRxiv   pre-print
Recent experimental and computational efforts provided large datasets describing 3-dimensional organization of mouse and human genomes and showed interconnection between expression profile, epigenetic  ...  We proposed an alternative approach, which gives high-quality predictions of chromatin interactions using only information about gene expression and CTCF-binding.  ...  All computations were performed with support from the Computational Cluster of the Novosibirsk State University and  ... 
doi:10.1101/541011 fatcat:vxexjklxdvfeli52khogkzbfsa

HACER: an atlas of human active enhancers to interpret regulatory variants

2018 Nucleic Acids Research  
The HACER atlas catalogues and annotates in-vivo transcribed cell-type-specific enhancers, as well as placing enhancers within transcriptional regulatory networks by integrating ENCODE TF ChIP-Seq and  ...  To identify, interpret, and prioritize such risk variants, we must identify the enhancers active in disease-relevant cell types, their upstream transcription factor (TF) binding, and their downstream target  ...  GeneHancer is a database of enhancer and enhancer-gene associations derived from multiple sources, embedded in the framework of GeneCards (35) .  ... 
doi:10.1093/nar/gky864 pmid:30247654 pmcid:PMC6323890 fatcat:henwcocizneotot3tawkmj52b4

SNPs in lncRNA Regions and Breast Cancer Risk

Maija Suvanto, Jonathan Beesley, Carl Blomqvist, Georgia Chenevix-Trench, Sofia Khan, Heli Nevanlinna
2020 Frontiers in Genetics  
genome-wide data, and also by in silico functional analyses using Integrated Expression Quantitative trait and in silico prediction of GWAS targets (INQUISIT) and expression quantitative trait loci (eQTL  ...  In addition, putative breast cancer risk associated SNPs (p < 1 × 10-5) in the region of two T-UCRs, uc.184 and uc.313, located in protein coding genes CPEB4 and TIAL1, respectively, targeted these genes  ...  Kristiina Aittomäki and research nurse Outi Malkavaara for the help with the Helsinki patient data, Taru Muranen for text editing and bioinformatical assistance, and Liisa Pelttari for assistance in data  ... 
doi:10.3389/fgene.2020.00550 pmid:32714364 pmcid:PMC7340126 fatcat:yxwitohepfgrnkluu6serntnt4

A generalized kernel machine approach to identify higher-order composite effects in multi-view datasets [article]

Md Ashad Alam, Chuan Qiu, Hui Shen, Yu-Ping Wang, Hong-Wen Deng
2020 arXiv   pre-print
In recent years, a comprehensive study of multi-view datasets (e.g., multi-omics and imaging scans) has been a focus and forefront in biomedical research.  ...  Our experiments demonstrate that the proposed method can effectively identify higher-order composite effects and suggest that corresponding features (genes, region of interests, and chemical taxonomies  ...  Acknowledgments This work was partially supported by grants from National Institutes of Health (NIH) [U19AG05537301, R01AR069055, P20GM109036, R01MH104680, R01AG061917], and the Edward G.  ... 
arXiv:2004.14031v1 fatcat:qjbuwayz4bejpgsdsca7wtzpxy

MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search

Noa Rappaport, Michal Twik, Inbar Plaschkes, Ron Nudel, Tsippi Iny Stein, Jacob Levitt, Moran Gershoni, C. Paul Morrey, Marilyn Safran, Doron Lancet
2016 Nucleic Acids Research  
This is accompanied by other gene-related disease information such as pathways, mouse phenotypes and GO-terms, stemming from MalaCards' affiliation with the GeneCards Suite of databases.  ...  rich disease annotation landscape, and facilitates systems analyses and genome sequence interpretation.  ...  The authors also thank MalaCards users for their feedback and support and the anonymous reviewersfor their valuable comments and suggestions.  ... 
doi:10.1093/nar/gkw1012 pmid:27899610 pmcid:PMC5210521 fatcat:gc65doqdurcxrdfs4fbqhanxbi

Targeting the Non-Coding Genome for the Diagnosis of Disorders of Sex Development

Gabby Atlas, Rajini Sreenivasan, Andrew Sinclair
2021 Sexual Development  
We will also review the current in vitro and in vivo techniques available to demonstrate the functionality of the identified enhancers.  ...  Here, we review how variants in the non-coding genome of DSD patients can be identified using techniques such as array comparative genomic hybridization (CGH) to detect copy number variants (CNVs), and  ...  Conflict of Interest Statement The authors have no conflicts of interest to declare. Funding Sources  ... 
doi:10.1159/000519238 pmid:34634785 fatcat:pdmgcllzi5fx7lypjnstcfhjca

Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci

Charles E Breeze, Anna Batorsky, Mi Kyeong Lee, Mindy D Szeto, Xiaoguang Xu, Daniel L McCartney, Rong Jiang, Amit Patki, Holly J Kramer, James M Eales, Laura Raffield, Leslie Lange (+31 others)
2021 Genome Medicine  
We aimed to identify trans-ethnic and ethnic-specific differentially methylated positions (DMPs) associated with eGFR using an agnostic, genome-wide approach.  ...  Identified DMPs showed significant overlap enrichment with DNase I hypersensitive sites in kidney tissue, sites associated with the expression of proximal genes, and transcription factor motifs and pathways  ...  We are grateful to all the families who took part, the general practitioners and the Scottish School of Primary Care for their help in recruiting them, and the whole Generation Scotland team that includes  ... 
doi:10.1186/s13073-021-00877-z pmid:33931109 pmcid:PMC8088054 fatcat:xt6ymbrwbffaflswni6lazvvta

Detection of new drivers of frequent B-cell lymphoid neoplasms using an integrated analysis of whole genomes

Adrián Mosquera Orgueira, Roi Ferreiro Ferro, José Ángel Díaz Arias, Carlos Aliste Santos, Beatriz Antelo Rodríguez, Laura Bao Pérez, Natalia Alonso Vence, Ággeles Bendaña López, Aitor Abuin Blanco, Paula Melero Valentín, And Res Peleteiro Raindo, Miguel Cid López (+4 others)
2021 PLoS ONE  
Here we present an integrated analysis of 354 B-cell lymphoid disorders. 112 recurrently mutated genes were discovered, of which KMT2D, CREBBP, IGLL5 and BCL2 were the most frequent, and 31 genes were  ...  In the meantime, the aggregation of diverse tumors in pan-cancer genomic studies has become a useful tool to detect new driver genes, while enabling the comparison of mutational patterns across tumors.  ...  Acknowledgments We would like to thank the International Cancer Genome Consortium for facilitating the data, and to the Supercomputing Center of Galicia (CESGA) for providing informatics support for the  ... 
doi:10.1371/journal.pone.0248886 pmid:33945543 pmcid:PMC8096002 fatcat:dpbyigdfjfbmnppz65qidb43x4

Remus: A Web Application for Prioritization of Regulatory Regions and Variants in Monogenic Diseases

Paweł Sztromwasser, Damian Skrzypczak, Arkadiusz Michalak, Wojciech Fendler
2021 Frontiers in Genetics  
Remus searches for regulatory features linked to the known disease-associated genes and filters them using activity status in the target tissues relevant for the studied disorder.  ...  However, the vast size of the regulome, great number of variants, and the difficulty in predicting their phenotypic impact make searching for pathogenic variants in the regulatory genome challenging.  ...  Remus uses a range of tissue-specific genome-wide datasets to identify regulatory regions active in user-selected target tissues and in proximity of the target genes (Figure 1) .  ... 
doi:10.3389/fgene.2021.638960 pmid:33747049 pmcid:PMC7978111 fatcat:vesnlw4ldnexxijafz4n5j4mty

Leveraging linkage evidence to identify low-frequency and rare variants on 16p13 associated with blood pressure using TOPMed whole genome sequencing data

Karen Y. He, Xiaoyin Li, Tanika N. Kelly, Jingjing Liang, Brian E. Cade, Themistocles L. Assimes, Lewis C. Becker, Amber L. Beitelshees, Adam P. Bress, Yen-Pei Christy Chang, Yii-Der Ida Chen, Paul S. de Vries (+41 others)
2019 Human Genetics  
After follow-up analysis of the 25 genes in ten independent TOPMed studies with individuals of European, African, and East Asian ancestry, and Hispanics (N = 29,988), we identified variants in SLX4 (p  ...  Follow-up analysis with GTEx eQTL data shows SLX4 variants are associated with gene expression in coronary artery, multiple brain tissues, and right atrial appendage of the heart.  ...  Whole genome sequencing (WGS) for the Trans-Omics in Precision Medicine (TOPMed) program was supported by the National Heart, Lung and Blood Institute (NHLBI).  ... 
doi:10.1007/s00439-019-01975-0 pmid:30671673 pmcid:PMC6404531 fatcat:4gaqx6ihhfapxpu22brso3kcgi

Integrated in-depth bioinformatic analysis suggests RELCH/KIAA1468, LINC02341, and AKAP11 as candidate genes for ages at menarche and menopause

Volodymyr Dvornyk, Alfaisal University
Results: TNFRSF11A and TNFSF11 are highly pleiotropic genes that play a role in many metabolic processes.  ...  Polymorphisms of the TNFRSF11A and TNFSF11 genes were reported for their association with age at menarche (AAM) and age at natural menopause (ANM).  ...  On the other hand, according to GeneHancer, this gene harbors binding sites of multiple transcription factors targeting the expression of RELCH and TNFRSF11A.  ... 
doi:10.18413/2658-6533-2021-7-3-0-2 fatcat:66bvjmnxpjdelloi4n5ytijl2q

Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance [article]

Soheil Yousefi, Ruizhi Deng, Kristina Lanko, Eva Medico Salsench, Anita Nikoncuk, Herma C. van der Linde, Elena Perenthaler, Tjakko J van Ham, Eskeatnaf Mulugeta, Tahsin Stefan Barakat
2021 bioRxiv   pre-print
Despite immense community-wide efforts to understand the role of the non-coding genome and NCREs, annotating functional NCREs remains challenging.  ...  Many of these DAEs are linked to clinically relevant genes, and functional validation of selected DAEs in cell models and zebrafish confirms their role in gene regulation.  ...  Fishilevich S, Nudel R, Rappaport N, Hadar R, Plaschkes I, Iny Stein T, Rosen N, Kohn A, Twik M, Safran M, et al: GeneHancer: genome-wide integration of enhancers and target genes in GeneCards.  ... 
doi:10.1101/2021.04.05.438382 fatcat:pp2s5euk4febdkwh5edke7zesm
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