ArticleGenome research2003
Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells.
Article in Genome research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 145 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.
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Who cites it
145 citing papers in PubMed, 302 citations in OpenAlex.
- Trial
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- Prostaglandins and calprotectin are genetically and functionally linked to the Inflammatory Bowel Diseases.PLoS genetics · 2022Article
- Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics.PLoS computational biology · 2022Article
- Functional screen of inflammatory bowel disease genes reveals key epithelial functions.Genome medicine · 2021Article
- Nuclear Respiratory Factor 1 Acting as an Oncoprotein Drives Estrogen-Induced Breast Carcinogenesis.Cells · 2018Article
- Interplay between NRF1, E2F4 and MYC transcription factors regulating common target genes contributes to cancer development and progression.Cellular oncology (Dordrecht, Netherlands) · 2018Review
- Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness.Human genomics · 2018Article
- Evolution of Brain Active Gene Promoters in Human Lineage Towards the Increased Plasticity of Gene Regulation.Molecular neurobiology · 2018Article
- ChickenOncotarget · 2017Article
- Aurora A Phosphorylation of YY1 during Mitosis Inactivates its DNA Binding Activity.Scientific reports · 2017Article
- Integrative transcriptome analysis of liver cancer profiles identifies upstream regulators and clinical significance of ACSM3 gene expression.Cellular oncology (Dordrecht, Netherlands) · 2017Article
- The dynamics of early-state transcriptional changes and aggregate formation in a Huntington's disease cell model.BMC genomics · 2017Article
- SWIM: a computational tool to unveiling crucial nodes in complex biological networks.Scientific reports · 2017Article
- E2F transcription factors associated with up-regulated genes in glioblastoma.Cancer biomarkers : section A of Disease markers · 2017Article
- Molecular Characterization of Down Syndrome Embryonic Stem Cells Reveals a Role for RUNX1 in Neural Differentiation.Stem cell reports · 2016Article
- Evidence of TAF1 dysfunction in peripheral models of X-linked dystonia-parkinsonism.Cellular and molecular life sciences : CMLS · 2016Article
- NF-Y loss triggers p53 stabilization and apoptosis in HPV18-positive cells by affecting E6 transcription.Oncotarget · 2016Article
- Tissue-specific targeting of cell fate regulatory genes by E2f factors.Cell death and differentiation · 2016Article
- Bioinformatic Evaluation of Transcriptional Regulation of WNT Pathway Genes with reference to Diabetic Nephropathy.Journal of diabetes research · 2016Article
85 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Dissection of regulatory networks that control gene transcription is one of the greatest challenges of functional genomics. Using human genomic sequences, models for binding sites of known transcription factors, and gene expression data, we demonstrate that the reverse engineering approach, which infers regulatory mechanisms from gene expression patterns, can reveal transcriptional networks in human cells. To date, such methodologies were successfully demonstrated only in prokaryotes and low eukaryotes. We developed computational methods for identifying putative binding sites of transcription factors and for evaluating the statistical significance of their prevalence in a given set of promoters. Focusing on transcriptional mechanisms that control cell cycle progression, our computational analyses revealed eight transcription factors whose binding sites are significantly overrepresented in promoters of genes whose expression is cell-cycle-dependent. The enrichment of some of these factors is specific to certain phases of the cell cycle. In addition, several pairs of these transcription factors show a significant co-occurrence rate in cell-cycle-regulated promoters. Each such pair indicates functional cooperation between its members in regulating the transcriptional program associated with cell cycle progression. The methods presented here are general and can be applied to the analysis of transcriptional networks controlling any biological process.
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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.