Results 71 to 80 of about 604,881 (306)

ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements.

PLoS Computational Biology, 2021
Transcription factors (TFs) often function as a module including both master factors and mediators binding at cis-regulatory regions to modulate nearby gene transcription.
Xi Chen, Andrew F Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan   +4 more
doaj   +1 more source

SPHINX31 acts as a SRPK1 inhibitor targeting the ATR/DNA‐PKcs/CHK1 replicative checkpoint to inhibit cell growth in non‐small cell lung cancer

Molecular Oncology, EarlyView.
The kinase SRPK1 directly interacts with the protein TOPBP1 and regulates the pre‐mRNA splicing of WIZ thereby contributing to the activation of the ATR/CHK1 replicative checkpoint in response to replicative stress. This allows cancer cells' genomic stability and survival.
Amani Shreim, Aurelie Genoux, Nadiia Zubchuk, Haoyang Zheng, Perla Salameh, Theo Ziegelmeyer, Fabien Dalonneau, Margot Rouchette, Christiane Oddou, Simona Miron, Helene Polveche, Adiilah Mamode Cassim, Carmen Garrido, Eleni Nikolakaki, Didier Auboeuf, Tao Jia, Sophie Zinn‐Justin, Beatrice Eymin   +17 more
wiley   +1 more source

The Role of Genome Accessibility in Transcription Factor Binding in Bacteria. [PDF]

PLoS Computational Biology, 2016
ChIP-seq enables genome-scale identification of regulatory regions that govern gene expression. However, the biological insights generated from ChIP-seq analysis have been limited to predictions of binding sites and cooperative interactions. Furthermore,
Antonio L C Gomes, Harris H Wang
doaj   +1 more source

A Statistical Framework for the Analysis of ChIP-Seq Data [PDF]

Journal of the American Statistical Association, 2011
Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has revolutionalized experiments for genome-wide profiling of DNA-binding proteins, histone modifications, and nucleosome occupancy. As the cost of sequencing is decreasing, many researchers are switching from microarray-based technologies (ChIP-chip) to ChIP-Seq for genome-wide study of ...
Kuan, Pei Fen, Chung, Dongjun, Pan, Guangjin, Thomson, James A., Stewart, Ron, KeleÅŸ, Sündüz   +5 more
openaire   +3 more sources

MagmaFlow: A desktop platform for artificial intelligence‐driven expression analysis

FEBS Open Bio, EarlyView.
MagmaFlow is a free, no‐code platform for gene expression analysis. It generates interactive volcano plots, links genes to literature, pathways, and diseases, prioritizes candidates using millions of publications, identifies affected biological processes, builds network diagrams, and exports publication‐ready figures and reports for macOS and Windows ...
Carlos E. Buss, Ao Li, Eduardo H. Gilglioni, Mayank Bansal, Sumeet Pal Singh, Latifa Bakiri, Alessandra K. Cardozo, Esteban N. Gurzov   +7 more
wiley   +1 more source

Dual native G‐quadruplex folding is associated with chromatin looping at the MYC locus

FEBS Open Bio, EarlyView.
BG4‐detectable G‐quadruplex (G4) in HaCaT and NHEK keratinocytes identified folded and unfolded G4s enriched at promoters/TSSs and active enhancers, whereas unfolded G4s also overlapped weak/poised enhancers. At MYC–PVT1, 3C‐qPCR detected enhancer–promoter looping only when G4s were simultaneously folded at both regulatory elements under native ...
Dieila Giomo de Lima, Gustavo Narvaes Guimarães, Emilyane de Oliveira Santana Amaral, Bianca Caroline Figueiredo Bianco, Manuel Jara‐Espejo, Sérgio Roberto Peres Line, Ana Paula de Souza, Aline Cristiane Planello   +7 more
wiley   +1 more source

ChIP-seq analysis of ZHX3.

, 2022
(A) ChIP-seq analysis showing the distribution of ZHX3 around target gene loci in proliferating IMR-90 cells. TSS, transcription start site; TES, transcription end site.
Naoki Tani (504791), Tomoaki Koga (35204), Tomoka Igata (12009374), Hiroshi Tanaka (3087), Mitsuyoshi Nakao (12822), Seonghyeon Hong (12009380), Kan Etoh (12009377)   +6 more
core   +1 more source

Model-based Analysis of ChIP-Seq (MACS) [PDF]

Genome Biology, 2008
AbstractWe present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites.
Zhang, Yong, Liu, Tao, Meyer, Clifford A., Eeckhoute, Jerome, Johnson, David S., Nusbaum, Chad, Myers, Richard M., Brown, Myles, Li, Wei, Liu, Xiaole S., Bernstein, Bradley E.   +10 more
openaire   +4 more sources

GelMA‐based 3D spheroids recapitulate transcriptomic and functional hallmarks of myeloid sarcoma

FEBS Open Bio, EarlyView.
GelMA 5% hydrogels support the formation of myeloid leukemia spheroids that recapitulate MS‐specific features, including G1 arrest, apoptosis, and ECM‐driven transcriptomic reprogramming. The 3D model mimicked soft‐tissue‐like stiffness and oxygen conditions, and transcriptomic convergence with primary MS samples confirmed its utility as a preclinical ...
Nicolas Germain, Elise Buret, Le Hoang Thanh Nguyen, Marion Cocheteux, Nicolas Touya, Mélanie Dhayer, Romain Dubois, Frank Lafont, Sebastien Janel, Patrice Maboudou, Steve Lancel, Philippe Marchetti   +11 more
wiley   +1 more source

RACS: rapid analysis of ChIP-Seq data for contig based genomes

BMC Bioinformatics, 2019
Background Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely-used molecular method to investigate the function of chromatin-related proteins by identifying their associated DNA sequences on a genomic scale.
Alejandro Saettone, Marcelo Ponce, Syed Nabeel-Shah, Jeffrey Fillingham   +3 more
doaj   +1 more source