ArticleBioinformatics (Oxford, England)2009
Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster.
Article in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 54 citations in OpenAlex.
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- Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data.Bioinformatics (Oxford, England) · 2023Article
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- Emergence of co-expression in gene regulatory networks.PloS one · 2021Article
- Human-Specific Transcriptome of Ventral and Dorsal Midbrain Dopamine Neurons.Annals of neurology · 2020Article
- Enhanced identification of significant regulators of gene expression.BMC bioinformatics · 2020Article
- A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs.International journal of molecular sciences · 2020Review
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- Environmental and Evolutionary Drivers of the Modular Gene Regulatory Network Underlying Phenotypic Plasticity for Stress Resistance in the NematodeG3 (Bethesda, Md.) · 2019Article
- Network Medicine in the Age of Biomedical Big Data.Frontiers in genetics · 2019Review
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Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
motivationIn functional genomics, it is frequently useful to correlate expression levels of genes to identify transcription factor binding sites (TFBS) via the presence of common sequence motifs. The underlying assumption is that co-expressed genes are more likely to contain shared TFBS and, thus, TFBS can be identified computationally. Indeed, gene pairs with a very high expression correlation show a significant excess of shared binding sites in yeast. We have tested this assumption in a more complex organism, Drosophila melanogaster, by using experimentally determined TFBS and microarray expression data. We have also examined the reverse relationship between the expression correlation and the extent of TFBS sharing.
resultsPairs of genes with shared TFBS show, on average, a higher degree of co-expression than those with no common TFBS in Drosophila. However, the reverse does not hold true: gene pairs with high expression correlations do not share significantly larger numbers of TFBS. Exception to this observation exists when comparing expression of genes from the earliest stages of embryonic development. Interestingly, semantic similarity between gene annotations (Biological Process) is much better associated with TFBS sharing, as compared to the expression correlation. We discuss these results in light of reverse engineering approaches to computationally predict regulatory sequences by using comparative genomics.
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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.