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Meta-analysis of gene expression signatures reveals hidden links among diverse biological processes in Arabidopsis.

Lai L, Ge SX - PLoS ONE (2014)

Bottom Line: The network highlights the correlation across the gene expression signatures of the diverse biological processes.We also partitioned the main network into 20 sub-networks, representing groups of highly similar expression signatures.Overall, our result suggests that diverse gene expression signatures are highly interconnected in a modular fashion.

View Article: PubMed Central - PubMed

Affiliation: Department of Mathematics and Statistics, South Dakota State University, Brookings, South Dakota, United States of America.

ABSTRACT
The model plant Arabidopsis has been well-studied using high-throughput genomics technologies, which usually generate lists of differentially expressed genes under various conditions. Our group recently collected 1065 gene lists from 397 gene expression studies as a knowledgebase for pathway analysis. Here we systematically analyzed these gene lists by computing overlaps in all-vs.-all comparisons. We identified 16,261 statistically significant overlaps, represented by an undirected network in which nodes correspond to gene lists and edges indicate significant overlaps. The network highlights the correlation across the gene expression signatures of the diverse biological processes. We also partitioned the main network into 20 sub-networks, representing groups of highly similar expression signatures. These are common sets of genes that were co-regulated under different treatments or conditions and are often related to specific biological themes. Overall, our result suggests that diverse gene expression signatures are highly interconnected in a modular fashion.

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Related in: MedlinePlus

Sub-network 3 corresponding to the module 3/cluster 3 (see note in Figure 2 for meanings of node and edge and their color.edge label  =  number of overlapping genes between two nodes).
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pone-0108567-g005: Sub-network 3 corresponding to the module 3/cluster 3 (see note in Figure 2 for meanings of node and edge and their color.edge label  =  number of overlapping genes between two nodes).

Mentions: The sub-network 3 includes 33 nodes (gene lists) and 124 most frequently shared genes (Figure 5 and Table S3 in File S1). There are 28 nodes to be up-regulated, four to be down-regulated, and one to be differently regulated. Most gene lists (84.85%) involving up-regulated nodes are related to nine biological themes and 20 treatments or conditions. By contrast to sub-networks 1 and 2, sub-network 3 is smaller in size, has a lower cluster density score, and less treatments or conditions for gene lists. Sub-network 3 are regulated by 25 treatments or conditions from 25 publications associated with 11 biological themes. Nine themes in sub-network 3 are common with sub-network 1: development, disease, energy, function, immune, mechanism, metabolism, photosynthesis, and virus. There are seven common themes (development, disease, function, mechanism, metabolism, photosynthesis, and virus) between sub-networks 3 and 2. These indicate sub-networks 3 and 1 or 2 have relationships linked by the same themes.


Meta-analysis of gene expression signatures reveals hidden links among diverse biological processes in Arabidopsis.

Lai L, Ge SX - PLoS ONE (2014)

Sub-network 3 corresponding to the module 3/cluster 3 (see note in Figure 2 for meanings of node and edge and their color.edge label  =  number of overlapping genes between two nodes).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4232243&req=5

pone-0108567-g005: Sub-network 3 corresponding to the module 3/cluster 3 (see note in Figure 2 for meanings of node and edge and their color.edge label  =  number of overlapping genes between two nodes).
Mentions: The sub-network 3 includes 33 nodes (gene lists) and 124 most frequently shared genes (Figure 5 and Table S3 in File S1). There are 28 nodes to be up-regulated, four to be down-regulated, and one to be differently regulated. Most gene lists (84.85%) involving up-regulated nodes are related to nine biological themes and 20 treatments or conditions. By contrast to sub-networks 1 and 2, sub-network 3 is smaller in size, has a lower cluster density score, and less treatments or conditions for gene lists. Sub-network 3 are regulated by 25 treatments or conditions from 25 publications associated with 11 biological themes. Nine themes in sub-network 3 are common with sub-network 1: development, disease, energy, function, immune, mechanism, metabolism, photosynthesis, and virus. There are seven common themes (development, disease, function, mechanism, metabolism, photosynthesis, and virus) between sub-networks 3 and 2. These indicate sub-networks 3 and 1 or 2 have relationships linked by the same themes.

Bottom Line: The network highlights the correlation across the gene expression signatures of the diverse biological processes.We also partitioned the main network into 20 sub-networks, representing groups of highly similar expression signatures.Overall, our result suggests that diverse gene expression signatures are highly interconnected in a modular fashion.

View Article: PubMed Central - PubMed

Affiliation: Department of Mathematics and Statistics, South Dakota State University, Brookings, South Dakota, United States of America.

ABSTRACT
The model plant Arabidopsis has been well-studied using high-throughput genomics technologies, which usually generate lists of differentially expressed genes under various conditions. Our group recently collected 1065 gene lists from 397 gene expression studies as a knowledgebase for pathway analysis. Here we systematically analyzed these gene lists by computing overlaps in all-vs.-all comparisons. We identified 16,261 statistically significant overlaps, represented by an undirected network in which nodes correspond to gene lists and edges indicate significant overlaps. The network highlights the correlation across the gene expression signatures of the diverse biological processes. We also partitioned the main network into 20 sub-networks, representing groups of highly similar expression signatures. These are common sets of genes that were co-regulated under different treatments or conditions and are often related to specific biological themes. Overall, our result suggests that diverse gene expression signatures are highly interconnected in a modular fashion.

Show MeSH
Related in: MedlinePlus