Results 141 to 150 of about 928,240 (334)

Expresso: A database and web server for exploring the interaction of transcription factors and their target genes in Arabidopsis thaliana using ChIP-Seq peak data [version 1; referees: 2 approved, 1 approved with reservations]

F1000Research, 2017
Motivation: The increasing availability of chromatin immunoprecipitation sequencing (ChIP-Seq) data enables us to learn more about the action of transcription factors in the regulation of gene expression.
Delasa Aghamirzaie, Karthik Raja Velmurugan, Shuchi Wu, Doaa Altarawy, Lenwood S. Heath, Ruth Grene   +5 more
doaj   +1 more source

FOXA1 mutations alter pioneering activity, differentiation and prostate cancer phenotypes. [PDF]

, 2019
Mutations in the transcription factor FOXA1 define a unique subset of prostate cancers but the functional consequences of these mutations and whether they confer gain or loss of function is unknown1-9. Here, by annotating the landscape of FOXA1 mutations
Adams, Elizabeth J, Barbieri, Christopher E, Bose, Rohit, Chhangawala, Sagar, Cho, Hyunwoo, Davicioni, Elai, DiLoreto, Rose, Gruet, Antoine, Hoover, Elizabeth, Karthaus, Wouter R, Leslie, Christina S, Liu, Deli, Liu, Yang, Sawyers, Charles L, Sboner, Andrea, Watson, Philip A, Zhang, Zeda   +16 more
core   +1 more source

Inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data

bioRxiv, 2019
We developed Lisa (http://lisa.cistrome.org) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input gene sets, Lisa first uses compendia of public histone mark ChIP-seq and chromatin ...
Qian Qin, Jingyu Fan, Rongbin Zheng, Changxin Wan, S. Mei, Qiu Wu, Hanfei Sun, Jing Zhang, Myles A. Brown, Clifford A. Meyer, X. Shirley Liu   +10 more
semanticscholar   +1 more source

ChIP-Seq in Candida albicans

BIO-PROTOCOL, 2014
Systems biology approaches can be used to study the regulatory interactions occurring between many components of the biological system at the whole-genome level and decipher the circuitries implicated in the regulation of cellular processes, including those imparting virulence to opportunistic fungi. Candida albicans (C.
Sadri Znaidi, Caroline PROUX, Sandra Weber, Simon Drouin, François Robert, Martine Raymond, Jean-Yves Coppée, Christophe d'Enfert   +7 more
openaire   +2 more sources

ERK‐Mediated Phosphorylation of YAP Defines a Noncanonical FGF Signaling Mechanism in Stem Cells

Advanced Science, EarlyView.
With a powerful combination of in vivo, ex vivo, and in vitro models, the authors highlight a novel FGF‐ERK signaling regulation of YAP at the S128 site in neural crest‐derived stem cells. This study opens exciting new directions in stem cell biology and craniofacial biology, paving the way for potential innovations in the treatment of craniofacial ...
Xiaolei Zhao, Shannon Erhardt, Li Tang, Xiaotong Chen, Stephen M Farmer, Zixiu Cheng, Wen Chen, Ella Ziyuan Lu, Kihan Sung, Chang‐Ru Tsai, Mingjie Zheng, Sheng Zhang, Yang Liu, Jianxin Wang, Min Li, James F Martin, Jun Wang   +16 more
wiley   +1 more source

Bioinformatic Analysis for Profiling Drug-induced Chromatin Modification Landscapes in Mouse Brain Using ChlP-seq Data

Bio-Protocol, 2017
Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a powerful technology to profile genome-wide chromatin modification patterns and is increasingly being used to study the molecular mechanisms of brain diseases such as ...
Yong-Hwee Loh, Jian Feng, Eric Nestler , Li Shen   +3 more
doaj   +1 more source

ChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy

Tree Genetics & Genomes, 2019
Chromatin immunoprecipitation-sequencing (ChIP-seq) is a robust technique to study interactions between proteins, such as histones or transcription factors and DNA.
N. Vimont, Fu Xiang Quah, David Guillaume Schöepfer, F. Roudier, E. Dirlewanger, P. Wigge, B. Wenden, S. Cortijo   +7 more
semanticscholar   +1 more source

Integrated Single‐Cell and Spatial Transcriptomics Reveal Cell‐Type‐Specific Immune Regulatory Networks in Maize Responding to Southern Corn Rust

Advanced Science, EarlyView.
By integrating single‐nuclei and spatial transcriptomics, this study presents a stereoscopic landscape of maize leaf to Puccinia polysora infection. Epidermal and mesophyll cells initiate primary defenses via RLPs/RLKs and jasmonic acid signaling. Cell‐cell communication analyses further reveal the underlying the dynamics of the underlying immune ...
Qiongqiong Wang, Xinyan Sun, Yingchao Sun, Zeqiang Cheng, Zixiang Cheng, Shengbo Han, Ying Feng, Wenbo Yang, Huimin Li, Meichen Zhu, Xiaoling Wu, Jinghua Zhang, Jihua Tang, Honglian Li, Yanyong Cao, Canxing Duan, Yan Shi   +16 more
wiley   +1 more source

The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing. [PDF]

, 2019
Transcriptional regulation in eukaryotes occurs at promoter-proximal regions wherein transcriptionally engaged RNA polymerase II (Pol II) pauses before proceeding toward productive elongation.
Ablondi, Eileen, Adelman, Karen, Chang, Andrew, Choi, Jee-Eun, Etchegaray, Jean-Pierre, Ferrer, Christina, Goren, Alon, Henriques, Telmo, Ji, Fei, Li, Catherine, Mostoslavsky, Raul, Nakadai, Tomoyoshi, Nechaev, Sergei, Ramaswamy, Sridhar, Roeder, Robert G, Ross, Kenneth N, Sadreyev, Ruslan I, Samarakkody, Ann, Van Rechem, Capucine, Whetstine, Johnathan R, Zhong, Lei   +20 more
core   +1 more source

GATA4‐Driven Transcription of HtrA1 Promotes Cellular Senescence in Ménière's Disease and Age‐Related Audio‐Vestibular Dysfunction

Advanced Science, EarlyView.
This study identifies the HDAC6/GATA4/HtrA1 axis as a critical driver of cellular senescence in the inner ear. GATA4 nuclear translocation, facilitated by HDAC6 downregulation, transcriptionally activates HtrA1, promoting hair cell senescence, SASP, and audio‐vestibular dysfunction in models of Ménière's disease and age‐related audio‐vestibular ...
Na Zhang, Na Li, Yan Wang, Jing Zhang, Jiahui Liu, Lei Chen, Yongdong Song, Yurong Mu, Yuechen Han, Yafeng Lyu, Xiaofei Li, Hanyue Wang, Jing Wang, Yao Lu, Zhaomin Fan, Daogong Zhang, Haibo Wang   +16 more
wiley   +1 more source