scholarly journals Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility

2017 ◽  
Vol 13 (1) ◽  
pp. e1005311 ◽  
Author(s):  
David Lamparter ◽  
Daniel Marbach ◽  
Rico Rueedi ◽  
Sven Bergmann ◽  
Zoltán Kutalik
Keyword(s):  
Transcription Factor ◽  
Chromatin Accessibility ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Factor Expression ◽  
Transcription Factor Expression

scholarly journals High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sarah E. Pierce ◽  
Jeffrey M. Granja ◽  
William J. Greenleaf
Keyword(s):  
Transcription Factor ◽  
Single Cell ◽  
Cancer Cells ◽  
High Throughput ◽  
Regulatory Networks ◽  
Temporal Dynamics ◽  
Chromatin Accessibility ◽  
Regulatory Regions ◽  
Factor Binding ◽  
Genome Wide

AbstractChromatin accessibility profiling can identify putative regulatory regions genome wide; however, pooled single-cell methods for assessing the effects of regulatory perturbations on accessibility are limited. Here, we report a modified droplet-based single-cell ATAC-seq protocol for perturbing and evaluating dynamic single-cell epigenetic states. This method (Spear-ATAC) enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at once. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations reveals the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles.

scholarly journals The Transcriptional Cascade in the Heat Stress Response of Arabidopsis Is Strictly Regulated at the Level of Transcription Factor Expression

2015 ◽  
Vol 28 (1) ◽  
pp. 181-201 ◽  
Author(s):  
Naohiko Ohama ◽  
Kazuya Kusakabe ◽  
Junya Mizoi ◽  
Huimei Zhao ◽  
Satoshi Kidokoro ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Heat Stress ◽  
Stress Response ◽  
Heat Stress Response ◽  
Factor Expression ◽  
Transcription Factor Expression

Differential cytokine and transcription factor expression in patients with allergic reactions to drugs

Allergy ◽  
2007 ◽  
Vol 62 (12) ◽  
pp. 1429-1438 ◽  
Author(s):  
J. A. Cornejo-Garcia ◽  
T. D. Fernandez ◽  
M. J. Torres ◽  
M. Carballo ◽  
I. Hernan ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Allergic Reactions ◽  
Factor Expression ◽  
Transcription Factor Expression

scholarly journals TFutils: Data structures for transcription factor bioinformatics

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 152
Author(s):  
Benjamin J. Stubbs ◽  
Shweta Gopaulakrishnan ◽  
Kimberly Glass ◽  
Nathalie Pochet ◽  
Celine Everaert ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Data Structures ◽  
Binding Sites ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Bioconductor Package ◽  
Genome Wide ◽  
Study Results ◽  
Integrative Analyses

DNA transcription is intrinsically complex. Bioinformatic work with transcription factors (TFs) is complicated by a multiplicity of data resources and annotations. The Bioconductor package TFutils includes data structures and functions to enhance the precision and utility of integrative analyses that have components involving TFs. TFutils provides catalogs of human TFs from three reference sources (CISBP, HOCOMOCO, and GO), a catalog of TF targets derived from MSigDb, and multiple approaches to enumerating TF binding sites. Aspects of integration of TF binding patterns and genome-wide association study results are explored in examples.

scholarly journals Regulation of MAPK Activation, AP-1 Transcription Factor Expression and Keratinocyte Differentiation in Wounded Fetal Skin

2004 ◽  
Vol 122 (3) ◽  
pp. 791-804 ◽  
Author(s):  
Samantha Gangnuss ◽  
Allison J. Cowin ◽  
Ilse S. Daehn ◽  
Nick Hatzirodos ◽  
Joseph A. Rothnagel ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Keratinocyte Differentiation ◽  
Fetal Skin ◽  
Mapk Activation ◽  
Factor Expression ◽  
Transcription Factor Expression
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