Results 11 to 20 of about 5,375,401 (399)

Functional Enrichment Analysis of Regulatory Elements [PDF]

Biomedicines, 2022
Statistical methods for enrichment analysis are important tools to extract biological information from omics experiments. Although these methods have been widely used for the analysis of gene and protein lists, the development of high-throughput ...
Adrián García-Moreno, R. López-Domínguez, J. Villatoro-García, A. Ramírez-Mena, E. Aparicio-Puerta, M. Hackenberg, A. Pascual-Montano, P. Carmona-Sáez   +7 more
semanticscholar   +6 more sources

Regulatory transposable elements in the encyclopedia of DNA elements

Nature Communications, 2023
Transposable elements (TEs) make up about half of the human genome and many have the biochemical hallmarks of tissue- or cell type-specific cis-regulatory elements.
Alan Y. Du, Jason D. Chobirko, Xiaoyu Zhuo, C. Feschotte, Ting Wang   +4 more
semanticscholar   +5 more sources

Information capacity of genetic regulatory elements [PDF]

Physical Review E, 2007
Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need to perform ...
A. P. Gasch, C. E. Shannon, C. E. Shannon, C. E. Shannon, Curtis G. Callan, Gašper Tkačik, H. B. Barlow, J. D. Watson, N. G. van Kampen, P. A. Lawrence, S. B. Laughlin, T. M. Cover, William Bialek   +12 more
core   +3 more sources

cis-Regulatory Elements in Plant Development, Adaptation, and Evolution.

Annual Review of Plant Biology, 2022
cis-Regulatory elements encode the genomic blueprints that ensure the proper spatiotemporal patterning of gene expression necessary for appropriate development and responses to the environment.
Alexandre P. Marand, A. Eveland, K. Kaufmann, Nathan M. Springer   +3 more
semanticscholar   +1 more source

Integration of Alzheimer’s disease genetics and myeloid genomics identifies disease risk regulatory elements and genes

Nature Communications, 2021
Genome-wide association studies (GWAS) have identified more than 40 loci associated with Alzheimer’s disease (AD), but the causal variants, regulatory elements, genes and pathways remain largely unknown, impeding a mechanistic understanding of AD ...
Gloriia Novikova, Manav Kapoor, J. Tcw, Edsel Abud, Anastasia G. Efthymiou, S. Chen, Haoxiang Cheng, J. Fullard, J. Bendl, Yiyuan Liu, Panagiotis Roussos, J. Björkegren, Yunlong Liu, W. Poon, K. Hao, Edoardo Marcora, A. Goate   +16 more
semanticscholar   +1 more source

Cis-Regulatory Elements in Mammals

International Journal of Molecular Sciences, 2023
In cis-regulatory elements, enhancers and promoters with complex molecular interactions are used to coordinate gene transcription through physical proximity and chemical modifications. These processes subsequently influence the phenotypic characteristics of an organism.
Xingyu Liu, Mengjie Chen, Xiuwen Qu, Wenjing Liu, Yuting Dou, Qingyou Liu, Deshun Shi, Mingsheng Jiang, Hui Li   +8 more
openaire   +2 more sources

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Nature Genetics, 2022
Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models.
Damir Baranasic, Matthias Hörtenhuber, Piotr J. Balwierz, T. Zehnder, A. K. Mukarram, Chirag Nepal, C. Várnai, Yavor Hadzhiev, Ada Jimenez-Gonzalez, Nan Li, J. Wragg, Fabio M. D’Orazio, Dorde Relic, M. Pachkov, Noelia Díaz, Benjamín Hernández-Rodríguez, Zelin Chen, Marcus H. Stoiber, Michael Dong, Irene Stevens, Samuel E. Ross, Anne E. Eagle, Ryan Martin, Oluwapelumi Obasaju, S. Rastegar, Alison C. McGarvey, W. Kopp, Emily Chambers, Dennis Wang, Hyejeong Kim, R. D. Acemel, Silvia Naranjo, Maciej Łapiński, Vanessa Chong, S. Mathavan, B. Peers, T. Sauka-Spengler, M. Vingron, Piero Carninci, U. Ohler, S. Lacadie, S. Burgess, C. Winata, F. V. van Eeden, Juan M. Vaquerizas, J. Gómez-Skarmeta, D. Onichtchouk, B. Brown, O. Bogdanović, E. van Nimwegen, M. Westerfield, F. Wardle, C. Daub, B. Lenhard, F. Müller   +54 more
semanticscholar   +1 more source

A multi‐omics framework reveals strawberry flavor genes and their regulatory elements

New Phytologist, 2022
Summary Flavor is essential to consumer preference of foods and is an increasing focus of plant breeding programs. In fruit crops, identifying genes underlying volatile organic compounds has great promise to accelerate flavor improvement, but polyploidy ...
Zhen Fan, D. Tieman, S. Knapp, P. Zerbe, Randi A. Famula, Christopher R. Barbey, K. Folta, R. Amadeu, Manbo Lee, Youngjae Oh, Seonghee Lee, V. Whitaker   +11 more
semanticscholar   +1 more source

A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome

Nature Communications, 2021
Although major advances in genomics have initiated an exciting new era of research, a lack of information regarding cis-regulatory elements has limited the genetic improvement or manipulation of pigs as a meat source and biomedical model.
Yunxia Zhao, Ye Hou, Yueyuan Xu, Yu Luan, Huanhuan Zhou, Xiaolong Qi, Mingyang Hu, Daoyuan Wang, Zhangxu Wang, Yuhua Fu, Jingjin Li, Saixian Zhang, Jianhai Chen, Jianlin Han, Xinyun Li, Shuhong Zhao   +15 more
semanticscholar   +1 more source

Sequence determinants of human gene regulatory elements

Nature Genetics, 2021
DNA can determine where and when genes are expressed, but the full set of sequence determinants that control gene expression is unknown. Here, we measured the transcriptional activity of DNA sequences that represent an ~100 times larger sequence space ...
Biswajyoti Sahu, T. Hartonen, Päivi Pihlajamaa, Bei Wei, Kashyap Dave, F. Zhu, Eevi Kaasinen, Katja Lidschreiber, Michael Lidschreiber, C. Daub, P. Cramer, Teemu Kivioja, J. Taipale   +12 more
semanticscholar   +1 more source