ArticleBMC bioinformatics2005
Chromosomal clustering of a human transcriptome reveals regulatory background.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it, 39 citations in OpenAlex.
- Pooled it
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- Efficient weighted univariate clustering maps outstanding dysregulated genomic zones in human cancers.Bioinformatics (Oxford, England) · 2020Article
- PLAGL2 and POFUT1 are regulated by an evolutionarily conserved bidirectional promoter and are collaboratively involved in colorectal cancer by maintaining stemness.EBioMedicine · 2019Article
- Article
- Genomic Clustering of differential DNA methylated regions (epimutations) associated with the epigenetic transgenerational inheritance of disease and phenotypic variation.BMC genomics · 2016Article
- Co-expressed genes prepositioned in spatial neighborhoods stochastically associate with SC35 speckles and RNA polymerase II factories.Cellular and molecular life sciences : CMLS · 2014Article
- Functional and genetic analysis of the colon cancer network.BMC bioinformatics · 2014Article
- G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes.BMC bioinformatics · 2012Article
- A novel 4EHP-GIGYF2 translational repressor complex is essential for mammalian development.Molecular and cellular biology · 2012Article
- The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes.PloS one · 2012Article
- Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.PloS one · 2012Article
- Gepoclu: a software tool for identifying and analyzing gene positional clusters in large-scale gene expression analysis.BMC bioinformatics · 2011Article
- Selection upon genome architecture: conservation of functional neighborhoods with changing genes.PLoS computational biology · 2010Article
- A conserved cluster of three PRD-class homeobox genes (homeobrain, rx and orthopedia) in the Cnidaria and Protostomia.EvoDevo · 2010Article
- Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes.BMC genomics · 2010Article
- Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response.BMC genomics · 2009Article
- Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.Nucleic acids research · 2009Article
- Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster.BMC genomics · 2009Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThere has been much evidence recently for a link between transcriptional regulation and chromosomal gene order, but the relationship between genomic organization, regulation and gene function in higher eukaryotes remains to be precisely defined.
resultsHere, we present evidence for organization of a large proportion of a human transcriptome into gene clusters throughout the genome, which are partly regulated by the same transcription factors, share biological functions and are characterized by non-housekeeping genes. This analysis was based on the cardiac transcriptome identified by our genome-wide array analysis of 55 human heart samples. We found 37% of these genes to be arranged mainly in adjacent pairs or triplets. A significant number of pairs of adjacent genes are putatively regulated by common transcription factors (p = 0.02). Furthermore, these gene pairs share a significant number of GO functional classification terms. We show that the human cardiac transcriptome is organized into many small clusters across the whole genome, rather than being concentrated in a few larger clusters.
conclusionOur findings suggest that genes expressed in concert are organized in a linear arrangement for coordinated regulation. Determining the relationship between gene arrangement, regulation and nuclear organization as well as gene function will have broad biological implications.
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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 OpenQuestion graph.