ArticleNucleic acids research2012
i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 147 papers.
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Who cites it
147 citing papers in PubMed.
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- The transcription factor IRF8 drives tumor-specific exhaustion in CD8+ T cells.The Journal of experimental medicine · 2026Article
- Single cell transcriptomic analysis by deep learning identifies novel microglial transcription regulations in Alzheimer's Disease.AI in neuroscience · 2026Article
- ChEA-KG and ChEA-KG-TS: a network-based transcription factor enrichment analysis tool with an accompanying time-series workflow.Nucleic acids research · 2026Article
- Single-nucleus interrogation of primate small intestinal aging reveals NCoR1 decline as a conserved feature that is reversed by metformin.Nature aging · 2026Article
- Proteome-wide prediction of the functional impact of missense variants with ProteoCast.Nature communications · 2026Article
- Inferring gene-regulatory networks using epigenomic priors.iScience · 2026Article
- Heterogeneous NF-κB activation and enhancer features shape transcription in Drosophila immunity.Biophysical journal · 2026Article
- Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding.Nature genetics · 2026Article
- Ectopic expression of BEX genes in T-cell acute lymphoblastic leukemia.Blood advances · 2026Article
- Key Concepts in Transcriptomics Data Analysis in the Era of Next-Gen Sequencing.Advances in experimental medicine and biology · 2026Review
- Aging-associated transcriptional programs in T cells signify constituents of TGF-β signaling for immunosenescence.BMC biology · 2025Article
- InCURA: integrative gene clustering based on transcription factor binding sites.Nucleic acids research · 2025Article
- Regulatory logic of neuronal identity specification inbioRxiv : the preprint server for biology · 2025Article
- The sex-biased chromatin modifier SMC1A promotes autoimmunity by shaping inflammatory pathways in patients with SLE.Nature communications · 2025Article
- Improved gene regulatory network inference from single cell data with dropout augmentation.PLoS computational biology · 2025Article
- Differentiation, ageing and leukaemia alter the metabolic profile of human bone marrow haematopoietic stem and progenitor cells.Nature cell biology · 2025Article
- Mitigating Cell Cycle Effects in Multi-Omics Data: Solutions and Analytical Frameworks.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
87 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The field of regulatory genomics today is characterized by the generation of high-throughput data sets that capture genome-wide transcription factor (TF) binding, histone modifications, or DNAseI hypersensitive regions across many cell types and conditions. In this context, a critical question is how to make optimal use of these publicly available datasets when studying transcriptional regulation. Here, we address this question in Drosophila melanogaster for which a large number of high-throughput regulatory datasets are available. We developed i-cisTarget (where the 'i' stands for integrative), for the first time enabling the discovery of different types of enriched 'regulatory features' in a set of co-regulated sequences in one analysis, being either TF motifs or 'in vivo' chromatin features, or combinations thereof. We have validated our approach on 15 co-expressed gene sets, 21 ChIP data sets, 628 curated gene sets and multiple individual case studies, and show that meaningful regulatory features can be confidently discovered; that bona fide enhancers can be identified, both by in vivo events and by TF motifs; and that combinations of in vivo events and TF motifs further increase the performance of enhancer prediction.
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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 Socratic graph.