ArticlePLoS genetics2013
Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
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- BLSSpeller to discover novel regulatory motifs in maize.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Transposable Elements: Distribution, Polymorphism, and Climate Adaptation inFrontiers in plant science · 2022Article
- Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family inFrontiers in plant science · 2022Article
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- Genome- and transcriptome-wide association studies reveal the genetic basis and the breeding history of seed glucosinolate content in Brassica napus.Plant biotechnology journal · 2022Article
- Transcripts switched off at the stop of phloem unloading highlight the energy efficiency of sugar import in the ripening V. vinifera fruit.Horticulture research · 2021Article
- The Seed Development FactorsGenes · 2021Article
- Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example.Plant physiology · 2021Article
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- Identification of ABA-Mediated Genetic and Metabolic Responses to Soil Flooding in Tomato (Frontiers in plant science · 2021Article
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- Co-expression Networks From Gene Expression Variability Between Genetically Identical Seedlings Can Reveal Novel Regulatory Relationships.Frontiers in plant science · 2020Article
- Recent advances in gene function prediction using context-specific coexpression networks in plants.F1000Research · 2019Review
- Coactivation of MEP-biosynthetic genes and accumulation of abietane diterpenes in Salvia sclarea by heterologous expression of WRKY and MYC2 transcription factors.Scientific reports · 2018Article
- Structure and transcriptional regulation of the major intrinsic protein gene family in grapevine.BMC genomics · 2018Article
- Co-expression network analysis and cis-regulatory element enrichment determine putative functions and regulatory mechanisms of grapevine ATL E3 ubiquitin ligases.Scientific reports · 2018Article
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5 authors.
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Abstract
Understanding of gene regulatory networks requires discovery of expression modules within gene co-expression networks and identification of promoter motifs and corresponding transcription factors that regulate their expression. A commonly used method for this purpose is a top-down approach based on clustering the network into a range of densely connected segments, treating these segments as expression modules, and extracting promoter motifs from these modules. Here, we describe a novel bottom-up approach to identify gene expression modules driven by known cis-regulatory motifs in the gene promoters. For a specific motif, genes in the co-expression network are ranked according to their probability of belonging to an expression module regulated by that motif. The ranking is conducted via motif enrichment or motif position bias analysis. Our results indicate that motif position bias analysis is an effective tool for genome-wide motif analysis. Sub-networks containing the top ranked genes are extracted and analyzed for inherent gene expression modules. This approach identified novel expression modules for the G-box, W-box, site II, and MYB motifs from an Arabidopsis thaliana gene co-expression network based on the graphical Gaussian model. The novel expression modules include those involved in house-keeping functions, primary and secondary metabolism, and abiotic and biotic stress responses. In addition to confirmation of previously described modules, we identified modules that include new signaling pathways. To associate transcription factors that regulate genes in these co-expression modules, we developed a novel reporter system. Using this approach, we evaluated MYB transcription factor-promoter interactions within MYB motif modules.
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