Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences
C Manzoni, DA Kia, J Vandrovcova… - Briefings in …, 2018 - academic.oup.com
Advances in the technologies and informatics used to generate and process large biological
data sets (omics data) are promoting a critical shift in the study of biomedical sciences. While …
data sets (omics data) are promoting a critical shift in the study of biomedical sciences. While …
Transcription factor–DNA binding: beyond binding site motifs
S Inukai, KH Kock, ML Bulyk - Current opinion in genetics & development, 2017 - Elsevier
Sequence-specific transcription factors (TFs) regulate gene expression by binding to cis-
regulatory elements in promoter and enhancer DNA. While studies of TF–DNA binding have …
regulatory elements in promoter and enhancer DNA. While studies of TF–DNA binding have …
g: Profiler—interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update)
Abstract g: Profiler is a reliable and up-to-date functional enrichment analysis tool that
supports various evidence types, identifier types and organisms. The toolset integrates many …
supports various evidence types, identifier types and organisms. The toolset integrates many …
AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations
WK Shen, SY Chen, ZQ Gan, YZ Zhang… - Nucleic acids …, 2023 - academic.oup.com
Transcription factors (TFs) are proteins that interact with specific DNA sequences to regulate
gene expression and play crucial roles in all kinds of biological processes. To keep up with …
gene expression and play crucial roles in all kinds of biological processes. To keep up with …
Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics
Abstract Knowledge of therapeutic targets and early drug candidates is useful for improved
drug discovery. In particular, information about target regulators and the patented …
drug discovery. In particular, information about target regulators and the patented …
Pathway-based classification of glioblastoma uncovers a mitochondrial subtype with therapeutic vulnerabilities
The transcriptomic classification of glioblastoma (GBM) has failed to predict survival and
therapeutic vulnerabilities. A computational approach for unbiased identification of core …
therapeutic vulnerabilities. A computational approach for unbiased identification of core …
g: Profiler—a web server for functional interpretation of gene lists (2016 update)
Functional enrichment analysis is a key step in interpreting gene lists discovered in diverse
high-throughput experiments. g: Profiler studies flat and ranked gene lists and finds …
high-throughput experiments. g: Profiler studies flat and ranked gene lists and finds …
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants
CN Chow, HQ Zheng, NY Wu, CH Chien… - Nucleic acids …, 2016 - academic.oup.com
Transcription factors (TFs) are sequence-specific DNA-binding proteins acting as critical
regulators of gene expression. The Plant P romoter A nalysis N avigator (PlantPAN; …
regulators of gene expression. The Plant P romoter A nalysis N avigator (PlantPAN; …
PRODORIC: state-of-the-art database of prokaryotic gene regulation
PRODORIC is worldwide one of the largest collections of prokaryotic transcription factor
binding sites from multiple bacterial sources with corresponding interpretation and …
binding sites from multiple bacterial sources with corresponding interpretation and …
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models
IV Kulakovskiy, IE Vorontsov, IS Yevshin… - Nucleic acids …, 2016 - academic.oup.com
Abstract Models of transcription factor (TF) binding sites provide a basis for a wide spectrum
of studies in regulatory genomics, from reconstruction of regulatory networks to functional …
of studies in regulatory genomics, from reconstruction of regulatory networks to functional …