ArticleGenome biology2009
Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
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- Reconstructing Dynamic Gene Regulatory Networks Using f-Divergence from Time-Series scRNA-Seq Data.Current issues in molecular biology · 2025Article
- Time-Varying Gene Regulatory Networks Inference Using KL Divergence from Single Cell Data.Proceedings of the ... International Conference on Bioinformatics and Biomedical Technology · 2025Article
- Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation.PLoS computational biology · 2025Article
- Isoform-specific effects of transcription factor TCFL5 on the pluripotency-related genes SOX2 and KLF4 in colorectal cancer development.Molecular oncology · 2022Article
- The AAA+ATPase RUVBL2 is essential for the oncogenic function of c-MYB in acute myeloid leukemia.Leukemia · 2019Article
- SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles.Bioinformatics (Oxford, England) · 2018Article
- Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line.Frontiers in genetics · 2015Article
- A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation.Nucleic acids research · 2014Article
- Temporal dynamics and transcriptional control using single-cell gene expression analysis.Genome biology · 2013Article
- Establishment of single-cell screening system for the rapid identification of transcriptional modulators involved in direct cell reprogramming.Nucleic acids research · 2012Article
- The Myc-ARF-Egr1 pathway: unleashing the apoptotic power of c-Myc.Cell cycle (Georgetown, Tex.) · 2011Article
- Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb.Nucleic acids research · 2011Article
- Nuclear pore complex protein mediated nuclear localization of dicer protein in human cells.PloS one · 2011Article
- Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE.Nucleic acids research · 2010Article
- Systematical detection of significant genes in microarray data by incorporating gene interaction relationship in biological systems.PloS one · 2010Article
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7 authors.
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Abstract
backgroundWith the move towards systems biology, we need sensitive and reliable ways to determine the relationships between transcription factors and their target genes. In this paper we analyze the regulatory relationships between 78 myeloid transcription factors and their coding genes by using the matrix RNAi system in which a set of transcription factor genes are individually knocked down and the resultant expression perturbation is quantified.
resultsUsing small interfering RNAs we knocked down the 78 transcription factor genes in monocytic THP-1 cells and monitored the perturbation of the expression of the same 78 transcription factors and 13 other transcription factor genes as well as 5 non-transcription factor genes by quantitative real-time RT-PCR, thereby building a 78 x 96 matrix of perturbation and measurement. This approach identified 876 cases where knockdown of one transcription factor significantly affected the expression of another (from a potential 7,488 combinations). Our study also revealed cell-type-specific transcriptional regulatory networks in two different cell types.
conclusionsBy considering whether the targets of a given transcription factor are naturally up- or downregulated during phorbol 12-myristate 13-acetate-induced differentiation, we could classify these edges as pro-differentiative (229), anti-differentiative (76) or neither (571) using expression profiling data obtained in the FANTOM4 study. This classification analysis suggested that several factors could be involved in monocytic differentiation, while others such as MYB and the leukemogenic fusion MLL-MLLT3 could help to maintain the initial undifferentiated state by repressing the expression of pro-differentiative factors or maintaining expression of anti-differentiative factors.
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