TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets
Sign Up to like & getrecommendations! Published in 2019 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btz573
Abstract: SUMMARY The computational identification of the transcription factors (more generally, transcription regulators, TR) responsible for the co-regulation of a specific set of genes is a common problem found in genomic analysis. Herein, we describe TFEA.ChIP,… read more here.
Keywords: chip seq; seq datasets; transcription; tfea chip ... See more keywords
Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btz975
Abstract: MOTIVATION The availability of thousands of genome-wide ChIP-Seq datasets across hundreds of transcriptional factors (TFs) and cell lines provides an unprecedented opportunity to jointly analyze large-scale transcription factor binding in vivo, making possible the discovery… read more here.
Keywords: chip seq; seq datasets; topic models; tflda ... See more keywords
GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets
Sign Up to like & getrecommendations! Published in 2022 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkac1066
Abstract: Abstract Gene knock-out/down methods are commonly used to explore the functions of genes of interest, but a database that systematically collects perturbed data is not available currently. Manual curation of all the available human cell… read more here.
Keywords: seq datasets; rna seq; gpsadb; genetic perturbation ... See more keywords
Population size estimation for quality control of ChIP-Seq datasets
Sign Up to like & getrecommendations! Published in 2019 at "PLoS ONE"
DOI: 10.1371/journal.pone.0221760
Abstract: Chromatin immunoprecipitation followed by sequencing, i.e. ChIP-Seq, is a widely used experimental technology for the identification of functional protein-DNA interactions. Nowadays, such databases as ENCODE, GTRD, ChIP-Atlas and ReMap systematically collect and annotate a large… read more here.
Keywords: chip seq; seq datasets; quality control; chip ... See more keywords
Integration of Single-Cell RNA-Seq Datasets: A Review of Computational Methods
Sign Up to like & getrecommendations! Published in 2023 at "Molecules and Cells"
DOI: 10.14348/molcells.2023.0009
Abstract: With the increased number of single-cell RNA sequencing (scRNA-seq) datasets in public repositories, integrative analysis of multiple scRNA-seq datasets has become commonplace. Batch effects among different datasets are inevitable because of differences in cell isolation… read more here.
Keywords: cell; seq datasets; integration; single cell ... See more keywords
Identification of Transcription Factors Differentially Expressed under Neuroinflammatory Conditions: Analysis of RNA-Seq Datasets Combined with an Unconventional Exploratory Approach.
Sign Up to like & getrecommendations! Published in 2022 at "Critical reviews in eukaryotic gene expression"
DOI: 10.1615/critreveukaryotgeneexpr.2022044272
Abstract: Neuroinflammation, the inflammatory process of the brain or peripheral nervous system, is mediated by various chemokines, cytokines, and other secondary messengers. Just like any other physiological process, transcription factors (TFs) lie at the core of… read more here.
Keywords: seq datasets; rna seq; identification; brain ... See more keywords
Grape-RNA: A Database for the Collection, Evaluation, Treatment, and Data Sharing of Grape RNA-Seq Datasets
Sign Up to like & getrecommendations! Published in 2020 at "Genes"
DOI: 10.3390/genes11030315
Abstract: Since its inception, RNA sequencing (RNA-seq) has become the most effective way to study gene expression. After more than a decade of development, numerous RNA-seq datasets have been created, and the full utilization of these… read more here.
Keywords: seq datasets; rna seq; rna; grape rna ... See more keywords