Searching journal content for articles similar to Morin et al. 33 (5): 763.

Displaying results 1-10 of 81

For checked items

view abstracts
download to citation manager

Select this article
Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...in silico perturbation methods for drug repurposing. Network proximity analysis identifies potential drugs by assessing the proximity between the drug target set and AD-related gene set. Drug efficacy is evaluated based on the proximity distance and Z-score. GSEA leverages drug–gene signatures from the CMap...
OPEN ACCESS ARTICLE
Select this article
Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
- Jonas de Tribolet-Hardy,
- Christian W. Thorball,
- Romain Forey,
- Evarist Planet,
- Julien Duc,
- Alexandre Coudray,
- Bara Khubieh,
- Sandra Offner,
- Cyril Pulver,
- Jacques Fellay,
- Michael Imbeault,
- Priscilla Turelli,
- and Didier Trono
Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
...results by the ChIP-seq technique, we generally saw several TE subfamilies significantly enriched with a given KZFP bait. However, in most cases a few subfamilies stood out as much more enriched than others. We defined the identified sequences as primary targets of the ChIP'ed KZFPs if within an arbitrary...
OPEN ACCESS ARTICLE
Select this article
Research: Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions
- Eric L. Van Nostrand and
- Stuart K. Kim
Genome Res. June 2013 23: 941-953; Published in Advance March 26, 2013, doi:10.1101/gr.152876.112
...perturbation, we find that low-complexity ChIP-seq targets are more likely to be factor-responsive than are high-complexity targets. Second, we use the large number of data sets to identify transcription factors that have different sets of targets identified in multiple developmental stages. Analysis...
Select this article
Research: Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
- Belle A. Moyers,
- E. Christopher Partridge,
- Mark Mackiewicz,
- Michael J. Betti,
- Roshan Darji,
- Sarah K. Meadows,
- Kimberly M. Newberry,
- Laurel A. Brandsmeier,
- Barbara J. Wold,
- Eric M. Mendenhall,
- and Richard M. Myers
Genome Res. November 2023 33: 1879-1892; Published in Advance October 18, 2023, doi:10.1101/gr.278205.123
...unique ChIP-seq DAP targets in HepG2 and nine histone modifications. This expanded catalog of DAPs and associated gene regulatory data sets provides a rich resource to characterize and understand the functional impact of DAP binding on gene regulation.DAP associations at cCREs reveal the interaction...
OPEN ACCESS ARTICLE
Select this article
Research: CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors
- Joseph C. Corbo,
- Karen A. Lawrence,
- Marcus Karlstetter,
- Connie A. Myers,
- Musa Abdelaziz,
- William Dirkes,
- Karin Weigelt,
- Martin Seifert,
- Vladimir Benes,
- Lars G. Fritsche,
- Bernhard H.F. Weber,
- and Thomas Langmann
Genome Res. November 2010 20: 1512-1525; Published in Advance August 6, 2010, doi:10.1101/gr.109405.110
...immunoprecipitation with massively parallel sequencing (ChIP-seq) on CRX to identify thousands of cis -regulatory regions around photoreceptor genes in adult mouse retina. CRX directly regulates downstream photoreceptor transcription factors and their target genes via a network of spatially distributed regulatory...
Select this article
Research: The role of insulators and transcription in 3D chromatin organization of flies
- Keerthi T. Chathoth,
- Liudmila A. Mikheeva,
- Gilles Crevel,
- Jareth C. Wolfe,
- Ioni Hunter,
- Saskia Beckett-Doyle,
- Sue Cotterill,
- Hongsheng Dai,
- Andrew Harrison,
- and Nicolae Radu Zabet
Genome Res. April 2022 32: 682-698; Published in Advance March 30, 2022, doi:10.1101/gr.275809.121
...with transcriptional changes (Li et al. 2015). Recent evidence points to defective 3D architecture as a major contributor for diseases, developmental defects, and even aging (Chandra et al. 2015; Lupiáñez et al. 2015; Flavahan et al. 2016; Hnisz et al. 2016; Sun et al. 2018; Kraft et al. 2019; Akdemir et al. 2020...
OPEN ACCESS ARTICLE
Select this article
Method: A Bayesian inference transcription factor activity model for the analysis of single-cell transcriptomes
- Shang Gao,
- Yang Dai,
- and Jalees Rehman
Genome Res. July 2021 31: 1296-1311; Published in Advance June 30, 2021, doi:10.1101/gr.265595.120
...factor's predicted target gene set that is obtained from GTRD databases of ChIP-seq data that has more than 17,485 transcription factor ChIP-seq samples (Yevshin et al. 2019). This information of known ChIP-seq data is used as a prior probability to guide the factorization of scRNA-seq data in a Bayesian...
OPEN ACCESS ARTICLE
Select this article
Research: Enhancer RNA profiling predicts transcription factor activity
- Joseph G. Azofeifa,
- Mary A. Allen,
- Josephina R. Hendrix,
- Timothy Read,
- Jonathan D. Rubin,
- and Robin D. Dowell
Genome Res. March 2018 28: 334-344; Published in Advance February 15, 2018, doi:10.1101/gr.225755.117
...” by a distance <10 kb. (D) Log base 10 FPKM fold change of “neighboring” genes related to eRNA-grouped NR2F2 binding peaks. (E) Histogram of Log base 10 FPKM fold change of “neighboring” genes for all possible eRNA-grouped TF ChIP-seq data sets (n = 255).Given the strong relationship between active chromatin...
OPEN ACCESS ARTICLE
Select this article
Research: Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors
- Martin Cusack,
- Hamish W. King,
- Paolo Spingardi,
- Benedikt M. Kessler,
- Robert J. Klose,
- and Skirmantas Kriaucionis
Genome Res. October 2020 30: 1393-1406; Published in Advance September 22, 2020, doi:10.1101/gr.257576.119
...perturbations (Supplemental Fig. S4E).Although all five transcription factors predominantly occupy gene promoter regions, the majority of ChIP-seq peaks that showed significant increases in occupancy upon DNA methylation loss or HDAC inhibition were situated at promoter distal genomic sites (Supplemental Fig. S...
OPEN ACCESS ARTICLE
Select this article
Resource: Integration of high-resolution promoter profiling assays reveals novel, cell type–specific transcription start sites across 115 human cell and tissue types
- Jill E. Moore,
- Xiao-Ou Zhang,
- Shaimae I. Elhajjajy,
- Kaili Fan,
- Henry E. Pratt,
- Fairlie Reese,
- Ali Mortazavi,
- and Zhiping Weng
Genome Res. February 2022 32: 389-402; Published in Advance December 23, 2021, doi:10.1101/gr.275723.121
...asymmetric pattern corresponding to transcriptional direction, chromatin accessibility, and Pol II ChIP-seq signals compared with the matched GENCODE TSSs (Fig. 4C).View larger version: In this window In a new window Figure 4. RAMPAGE-verified rPeaks are enriched for regulatory signatures. (A) Bar plots...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Morin et al. 33 (5): 763.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: