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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 2 corresponding to the module 2/cluster 2 (see note in Figure 2 for meanings of node and edge and their color).
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pone-0108567-g004: Sub-network 2 corresponding to the module 2/cluster 2 (see note in Figure 2 for meanings of node and edge and their color).

Mentions: Sub-network 2 is shown in Figure 4 and Table S2 in File S1. It includes 54 nodes (gene lists) and 168 frequently shared genes, which are regulated under 38 different treatments or conditions from 38 publications related to 10 biological themes. The score of cluster density is 9.907. There are 17 nodes to be up-regulated, 34 to be down-regulated, and three to be differently regulated. Most gene lists (62.96%) involving down-regulated nodes are related to nine biological themes and 23 treatments or conditions. Compared to sub-network 1, sub-network 2 has a lower cluster density score with even more treatments or conditions. Nine themes in sub-network 2 are common with sub-network 1: development, disease, function, genome analysis, mechanism, metabolism, photosynthesis, virus, and yield. This indicates the two sub-networks have relationships linked by same themes. No gene is common between the 256 frequently shared genes in sub-network 1 and the 168 frequently shared genes in sub-network 2. The two sub-networks have relatively independent functions. The most significant function of sub-network 2 is biological process of plastid thylakoid membrane based on results of DAVID (Table 1), suggesting that sub-network 2 is specifically associated with plastid thylakoid membrane, i.e. the lipid bilayer membrane of any thylakoid within a plastid. The other significant functions of sub-network 2 are response to chloroplast thylakoid membrane, thylakoid membrane, plastid thylakoid, and chloroplast thylakoid based on DAVID with cut-off p-value of 6.8×10−58. The top 10 most frequently shared genes with their gene descriptions corresponding to gene lists, biological themes, and treatments or conditions were specifically listed in Table S2 in File S1. Gene AT4G27030 (fatty acid desaturase A), for example, has the highest frequency of 20, indicating it is the most active gene in sub-network 2.


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

Lai L, Ge SX - PLoS ONE (2014)

Sub-network 2 corresponding to the module 2/cluster 2 (see note in Figure 2 for meanings of node and edge and their color).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0108567-g004: Sub-network 2 corresponding to the module 2/cluster 2 (see note in Figure 2 for meanings of node and edge and their color).
Mentions: Sub-network 2 is shown in Figure 4 and Table S2 in File S1. It includes 54 nodes (gene lists) and 168 frequently shared genes, which are regulated under 38 different treatments or conditions from 38 publications related to 10 biological themes. The score of cluster density is 9.907. There are 17 nodes to be up-regulated, 34 to be down-regulated, and three to be differently regulated. Most gene lists (62.96%) involving down-regulated nodes are related to nine biological themes and 23 treatments or conditions. Compared to sub-network 1, sub-network 2 has a lower cluster density score with even more treatments or conditions. Nine themes in sub-network 2 are common with sub-network 1: development, disease, function, genome analysis, mechanism, metabolism, photosynthesis, virus, and yield. This indicates the two sub-networks have relationships linked by same themes. No gene is common between the 256 frequently shared genes in sub-network 1 and the 168 frequently shared genes in sub-network 2. The two sub-networks have relatively independent functions. The most significant function of sub-network 2 is biological process of plastid thylakoid membrane based on results of DAVID (Table 1), suggesting that sub-network 2 is specifically associated with plastid thylakoid membrane, i.e. the lipid bilayer membrane of any thylakoid within a plastid. The other significant functions of sub-network 2 are response to chloroplast thylakoid membrane, thylakoid membrane, plastid thylakoid, and chloroplast thylakoid based on DAVID with cut-off p-value of 6.8×10−58. The top 10 most frequently shared genes with their gene descriptions corresponding to gene lists, biological themes, and treatments or conditions were specifically listed in Table S2 in File S1. Gene AT4G27030 (fatty acid desaturase A), for example, has the highest frequency of 20, indicating it is the most active gene in sub-network 2.

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