WhichTF is functionally important in your open chromatin data?
Y Tanigawa, ES Dyer, G Bejerano - PLOS Computational Biology, 2022 - journals.plos.org
We present WhichTF, a computational method to identify functionally important transcription
factors (TFs) from chromatin accessibility measurements. To rank TFs, WhichTF applies an …
factors (TFs) from chromatin accessibility measurements. To rank TFs, WhichTF applies an …
Transcription factor dynamics: one molecule at a time
K Wagh, DA Stavreva, A Upadhyaya… - Annual Review of Cell …, 2023 - annualreviews.org
Cells must tightly regulate their gene expression programs and yet rapidly respond to acute
biochemical and biophysical cues within their environment. This information is transmitted to …
biochemical and biophysical cues within their environment. This information is transmitted to …
Proteomic analyses reveal distinct chromatin‐associated and soluble transcription factor complexes
The current knowledge on how transcription factors (TF s), the ultimate targets and executors
of cellular signalling pathways, are regulated by protein–protein interactions remains limited …
of cellular signalling pathways, are regulated by protein–protein interactions remains limited …
Anchor: trans-cell type prediction of transcription factor binding sites
The ENCyclopedia of DNA Elements (ENCODE) consortium has generated transcription
factor (TF) binding ChIP-seq data covering hundreds of TF proteins and cell types; however …
factor (TF) binding ChIP-seq data covering hundreds of TF proteins and cell types; however …
TRRUST: a reference database of human transcriptional regulatory interactions
The reconstruction of transcriptional regulatory networks (TRNs) is a long-standing
challenge in human genetics. Numerous computational methods have been developed to …
challenge in human genetics. Numerous computational methods have been developed to …
CUT&RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis
Motivation Genome-wide profiling of transcription factor binding and chromatin states is a
widely-used approach for mechanistic understanding of gene regulation. Recent technology …
widely-used approach for mechanistic understanding of gene regulation. Recent technology …
Modeling gene regulation from paired expression and chromatin accessibility data
The rapid increase of genome-wide datasets on gene expression, chromatin states, and
transcription factor (TF) binding locations offers an exciting opportunity to interpret the …
transcription factor (TF) binding locations offers an exciting opportunity to interpret the …
IMPACT: genomic annotation of cell-state-specific regulatory elements inferred from the epigenome of bound transcription factors
Despite significant progress in annotating the genome with experimental methods, much of
the regulatory noncoding genome remains poorly defined. Here we assert that regulatory …
the regulatory noncoding genome remains poorly defined. Here we assert that regulatory …
Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction
F Schmidt, N Gasparoni, G Gasparoni… - Nucleic acids …, 2017 - academic.oup.com
The binding and contribution of transcription factors (TF) to cell specific gene expression is
often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays …
often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays …
Pioneer factors and ATP‐dependent chromatin remodeling factors interact dynamically: a new perspective: Multiple transcription factors can effect chromatin pioneer …
Transcription factor (TF) signaling regulates gene transcription and requires a complex
network of proteins. This network includes co‐activators, co‐repressors, multiple TFs …
network of proteins. This network includes co‐activators, co‐repressors, multiple TFs …