Genome-wide signatures of transcription factor activity: connecting transcription factors, disease, and small molecules
Identifying transcription factors (TF) involved in producing a genome-wide transcriptional
profile is an essential step in building mechanistic model that can explain observed gene …
profile is an essential step in building mechanistic model that can explain observed gene …
Functional transcription factor target discovery via compendia of binding and expression profiles
Genome-wide experiments to map the DNA-binding locations of transcription-associated
factors (TFs) have shown that the number of genes bound by a TF far exceeds the number of …
factors (TFs) have shown that the number of genes bound by a TF far exceeds the number of …
Systematic target function annotation of human transcription factors
Abstract Background Transcription factors (TFs), the key players in transcriptional regulation,
have attracted great experimental attention, yet the functions of most human TFs remain …
have attracted great experimental attention, yet the functions of most human TFs remain …
MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
A Roopra - PLoS computational biology, 2020 - journals.plos.org
Transcriptomic profiling is an immensely powerful hypothesis generating tool. However,
accurately predicting the transcription factors (TFs) and cofactors that drive transcriptomic …
accurately predicting the transcription factors (TFs) and cofactors that drive transcriptomic …
Raw sequence to target gene prediction: An integrated inference pipeline for ChIP-seq and RNA-seq datasets
Abstract Next Generation Sequencing technologies, such as ChIP-seq and RNA-seq are
increasingly being used to understand the genomic mechanisms whereby the interaction …
increasingly being used to understand the genomic mechanisms whereby the interaction …
Cell-type and transcription factor specific enrichment of transcriptional cofactor motifs in ENCODE ChIP-seq data
Background Cell type and TF specific interactions between Transcription Factors (TFs) and
cofactors are essential for transcriptional regulation through recruitment of general …
cofactors are essential for transcriptional regulation through recruitment of general …
Inferring transcription factor complexes from ChIP-seq data
T Whitington, MC Frith, J Johnson… - Nucleic acids …, 2011 - academic.oup.com
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) allows
researchers to determine the genome-wide binding locations of individual transcription …
researchers to determine the genome-wide binding locations of individual transcription …
Discovering transcription factor regulatory targets using gene expression and binding data
M Maienschein-Cline, J Zhou, KP White… - …, 2012 - academic.oup.com
Motivation: Identifying the target genes regulated by transcription factors (TFs) is the most
basic step in understanding gene regulation. Recent advances in high-throughput …
basic step in understanding gene regulation. Recent advances in high-throughput …
Predicting tissue specific transcription factor binding sites
Background Studies of gene regulation often utilize genome-wide predictions of
transcription factor (TF) binding sites. Most existing prediction methods are based on …
transcription factor (TF) binding sites. Most existing prediction methods are based on …
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
Background Transcription factors function by binding different classes of regulatory
elements. The Encyclopedia of DNA Elements (ENCODE) project has recently produced …
elements. The Encyclopedia of DNA Elements (ENCODE) project has recently produced …