Detecting changes in the activity of a transcription factor (TF) in response to a perturbation provides insights into the underlying cellular process. Transcription Factor Enrichment Analysis (TFEA) is a robust and reliable computational method that detects positional motif enrichment associated with changes in transcription observed in response to a perturbation. TFEA detects positional motif enrichment within a list of ranked regions of interest (ROIs), typically sites of RNA polymerase initiation inferred from regulatory data such as nascent transcription. Therefore, we also introduce muMerge, a statistically principled method of generating a consensus list of ROIs from multiple replicates and conditions. TFEA is broadly applicable to data that informs on transcriptional regulation including nascent transcription (eg. PRO-Seq), CAGE, histone ChIP-Seq, and accessibility data (e.g., ATAC-Seq). TFEA not only identifies the key regulators responding to a perturbation, but also temporally unravels regulatory networks with time series data. Consequently, TFEA serves as a hypothesis-generating tool that provides an easy, rigorous, and cost-effective means to broadly assess TF activity yielding new biological insights.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8172830PMC
http://dx.doi.org/10.1038/s42003-021-02153-7DOI Listing

Publication Analysis

Top Keywords

transcription factor
12
factor enrichment
8
enrichment analysis
8
analysis tfea
8
detects positional
8
positional motif
8
motif enrichment
8
nascent transcription
8
transcription
7
tfea
6

Similar Publications

BACKGROUND Cleidocranial dysplasia (CCD) is a rare (1: 1 000 000) autosomal dominant congenital skeletal dysplasia characterized by widely patent calvarial sutures, clavicular hypoplasia, supernumerary teeth, and short stature. Only a minority of the cases are diagnosed early after birth. We present another case of proven CCD presenting with typical neonatal phenotype to promote awareness of this rare disorder.

View Article and Find Full Text PDF

Tongue squamous cell carcinoma (TSCC) is a common malignant oral cancer characterized by substantial invasion, a high rate of lymph node and distant metastasis, and a high recurrence rate. This study aims to provide new ideas for the diagnosis and treatment of TSCC patients by exploring the related mechanisms that affect the migration and invasion of TSCC and inhibit the migration and spread of cancer cells. The results indicated the rate of high expression of IL-17 in cancer tissues was greater than that in tongue tissues, and the expression of IL-17 was related to the TNM stage.

View Article and Find Full Text PDF

Aedes mosquitoes transmit pathogenic arthropod-borne (arbo) viruses, putting nearly half the world's population at risk. Blocking virus replication in mosquitoes is a promising approach to prevent arbovirus transmission, the development of which requires in-depth knowledge of virus-host interactions and mosquito immunity. By integrating multi-omics data, we find that heat shock factor 1 (Hsf1) regulates eight small heat shock protein (sHsp) genes within one topologically associated domain in the genome of the Aedes aegypti mosquito.

View Article and Find Full Text PDF

In our research, we performed temporal transcriptomic profiling of host cells infected with Equid alphaherpesvirus 1 (EHV-1) by utilizing direct cDNA sequencing based on nanopore MinION technology. The sequencing reads were harnessed for transcript quantification at various time points. Viral infection-induced differential gene expression was identified through the edgeR package.

View Article and Find Full Text PDF

This study is designed to assess the effect of root extract of P. ginseng on kidney tissue injury attributed to cisplatin and its molecular mechanism involved in this process in the AKI rat model. Twenty-four male Wistar rats were randomly allocated into 4 experimental groups including: the control group, the cisplatin group, the extract 100 mg/kg group, and the extract 200 mg/kg group.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!