ArticlePloS one2019
CiiiDER: A tool for predicting and analysing transcription factor binding sites.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers.
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125 citing papers in PubMed, 234 citations in OpenAlex.
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- The transcriptomes of hypothalamic micropunches reveal sex differences in regulatory processes across hibernation in the Arctic ground squirrel.Physiological genomics · 2025Article
- The ETS-family transcription factor PU.1 is a critical regulator of the inhibitory Fcγ receptor IIB expression in humans.Journal of immunology (Baltimore, Md. : 1950) · 2025Article
- Vitamin D Reshapes Genomic Hierarchies in Skin Cells: lncRNA-Driven Responses in Carcinoma Versus Transcription Factor-Based Regulation in Healthy Skin.International journal of molecular sciences · 2025Article
- Transcript PHF19-207 May Be a Long Non-Coding RNA with Tumor-Promoting Role in Colon Cancer.Biomolecules · 2025Article
- A triple serine motif in the intracellular domain of SorCS2 impacts its cellular signaling.iScience · 2025Article
- LD block disorder-specific pleiotropic roles of novel CRHR1 in type 2 diabetes and depression disorder comorbidity.European archives of psychiatry and clinical neuroscience · 2025Article
- The gene regulatory mechanisms shaping the heterogeneity of venom production in the Cape coral snake.Genome biology · 2025Article
- Dynamic activation of rAAV transgene expression by a small molecule that recruits endogenous transcriptional machinery.Nucleic acids research · 2025Article
65 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The availability of large amounts of high-throughput genomic, transcriptomic and epigenomic data has provided opportunity to understand regulation of the cellular transcriptome with an unprecedented level of detail. As a result, research has advanced from identifying gene expression patterns associated with particular conditions to elucidating signalling pathways that regulate expression. There are over 1,000 transcription factors (TFs) in vertebrates that play a role in this regulation. Determining which of these are likely to be controlling a set of genes can be assisted by computational prediction, utilising experimentally verified binding site motifs. Here we present CiiiDER, an integrated computational toolkit for transcription factor binding analysis, written in the Java programming language, to make it independent of computer operating system. It is operated through an intuitive graphical user interface with interactive, high-quality visual outputs, making it accessible to all researchers. CiiiDER predicts transcription factor binding sites (TFBSs) across regulatory regions of interest, such as promoters and enhancers derived from any species. It can perform an enrichment analysis to identify TFs that are significantly over- or under-represented in comparison to a bespoke background set and thereby elucidate pathways regulating sets of genes of pathophysiological importance.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.