ArticleExperimental hematology2013
Gene set control analysis predicts hematopoietic control mechanisms from genome-wide transcription factor binding data.
Article in Experimental hematology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
- Disease-specific epigenetic deregulation of enhancers, transposons, and polycomb targets in acute promyelocytic leukemia.Genome medicine · 2025Article
- Unlocking hematopoietic stem cell potential: integrative computational approaches for genomic and transcriptomic analysis.Frontiers in cell and developmental biology · 2025Review
- Inhibiting the RNA helicase DDX3X in Burkitt lymphoma induces oxydative stress and impedes tumor progression in xenografts.Frontiers in cell and developmental biology · 2025Article
- Article
- Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation.Developmental cell · 2016Article
- CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities.Nucleic acids research · 2015Article
- Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs.BMC bioinformatics · 2014Article
- Concerted bioinformatic analysis of the genome-scale blood transcription factor compendium reveals new control mechanisms.Molecular bioSystems · 2014Article
- ChIP-Enrich: gene set enrichment testing for ChIP-seq data.Nucleic acids research · 2014Article
- A regulatory circuit comprising GATA1/2 switch and microRNA-27a/24 promotes erythropoiesis.Nucleic acids research · 2014Article
- Article
- Building an ENCODE-style data compendium on a shoestring.Nature methods · 2013Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Transcription factors are key regulators of both normal and malignant hematopoiesis. Chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-Seq) has become the method of choice to interrogate the genome-wide effect of transcription factors. We have collected and integrated 142 publicly available ChIP-Seq datasets for both normal and leukemic murine blood cell types. In addition, we introduce the new bioinformatic tool Gene Set Control Analysis (GSCA). GSCA predicts likely upstream regulators for lists of genes based on statistical significance of binding event enrichment within the gene loci of a user-supplied gene set. We show that GSCA analysis of lineage-restricted gene sets reveals expected and previously unrecognized candidate upstream regulators. Moreover, application of GSCA to leukemic gene sets allowed us to predict the reactivation of blood stem cell control mechanisms as a likely contributor to LMO2 driven leukemia. It also allowed us to clarify the recent debate on the role of Myc in leukemia stem cell transcriptional programs. As a result, GSCA provides a valuable new addition to analyzing gene sets of interest, complementary to Gene Ontology and Gene Set Enrichment analyses. To facilitate access to the wider research community, we have implemented GSCA as a freely accessible web tool (http://bioinformatics.cscr.cam.ac.uk/GSCA/GSCA.html).
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Registered trials
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