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Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules.

Okamura Y, Obayashi T, Kinoshita K - PLoS ONE (2015)

Bottom Line: For this purpose, the similarities of gene expression patterns and gene sequences have been separately utilized, although the combined information will provide a better solution.Some of the tightly coupled genes (modules) showed clear functional enrichment, such as immune system and cell cycle, indicating that our method could identify functionally related genes without any prior knowledge.We also found a few functional modules without any annotations, which may be good candidates for novel functional modules.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan.

ABSTRACT

Background: Computational approaches toward gene annotation are a formidable challenge, now that many genome sequences have been determined. Each gene has its own function, but complicated cellular functions are achieved by sets of genes. Therefore, sets of genes with strong functional relationships must be identified. For this purpose, the similarities of gene expression patterns and gene sequences have been separately utilized, although the combined information will provide a better solution.

Result & discussion: We propose a new method to find functional modules, by comparing gene coexpression profiles among species. A coexpression pattern is represented as a list of coexpressed genes with each guide gene. We compared two coexpression lists, one from a human guide gene and the other from a homologous mouse gene, and defined a measure to evaluate the similarity between the lists. Based on this coexpression similarity, we detected the highly conserved genes, and constructed human gene networks with conserved coexpression between human and mouse. Some of the tightly coupled genes (modules) showed clear functional enrichment, such as immune system and cell cycle, indicating that our method could identify functionally related genes without any prior knowledge. We also found a few functional modules without any annotations, which may be good candidates for novel functional modules. All of the comparisons are available at the http://v1.coxsimdb.info web database.

No MeSH data available.


How to use COXSIMdb.(A) First, search for a gene by its symbol or entrez gene ID. (B) Second, select a gene of interest. (C) View of the coexpression conservation results. This view provides a summary of the genes, a list of CC genes, the detected gene modules, and a comparison of coexpression.
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pone.0132039.g005: How to use COXSIMdb.(A) First, search for a gene by its symbol or entrez gene ID. (B) Second, select a gene of interest. (C) View of the coexpression conservation results. This view provides a summary of the genes, a list of CC genes, the detected gene modules, and a comparison of coexpression.

Mentions: All results of coexpression conservation, CC genes, and module detection are available through the web database named COeXpression SIMilarity DataBase (COXSIMdb, http://v1.coxsimdb.info). The overview of the database is shown in Fig 5. To use this web database, insert the gene symbol or entrez gene ID into the search field at the top of the COXSIMdb page (shown in Fig 5A). This web service provides a list of genes related to the query, with a view of the results of the coexpression conservation of a gene (Fig 5B). Fig 5C illustrates an example of a COXSIMdb main result view. The result view has up to 4 sections. The first section is a summary of the human and mouse genes and a conservation chart. The second section is a list of CC genes and any associated KEGG pathway. The third section is a list of detected gene modules that include the gene if it is involved in the modules. The gene modules detected with SCS = 4 are shown in the default mode, but links to the modules detected with SCS = 3 and SCS = 5 are also provided. The last section is a table view of the comparison of coexpressed genes between human and mouse. Each gene is colored by the gene type and whether it is a CC gene, and homologous genes are shown in a pop-up window when the cursor moves over the genes.


Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules.

Okamura Y, Obayashi T, Kinoshita K - PLoS ONE (2015)

How to use COXSIMdb.(A) First, search for a gene by its symbol or entrez gene ID. (B) Second, select a gene of interest. (C) View of the coexpression conservation results. This view provides a summary of the genes, a list of CC genes, the detected gene modules, and a comparison of coexpression.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493118&req=5

pone.0132039.g005: How to use COXSIMdb.(A) First, search for a gene by its symbol or entrez gene ID. (B) Second, select a gene of interest. (C) View of the coexpression conservation results. This view provides a summary of the genes, a list of CC genes, the detected gene modules, and a comparison of coexpression.
Mentions: All results of coexpression conservation, CC genes, and module detection are available through the web database named COeXpression SIMilarity DataBase (COXSIMdb, http://v1.coxsimdb.info). The overview of the database is shown in Fig 5. To use this web database, insert the gene symbol or entrez gene ID into the search field at the top of the COXSIMdb page (shown in Fig 5A). This web service provides a list of genes related to the query, with a view of the results of the coexpression conservation of a gene (Fig 5B). Fig 5C illustrates an example of a COXSIMdb main result view. The result view has up to 4 sections. The first section is a summary of the human and mouse genes and a conservation chart. The second section is a list of CC genes and any associated KEGG pathway. The third section is a list of detected gene modules that include the gene if it is involved in the modules. The gene modules detected with SCS = 4 are shown in the default mode, but links to the modules detected with SCS = 3 and SCS = 5 are also provided. The last section is a table view of the comparison of coexpressed genes between human and mouse. Each gene is colored by the gene type and whether it is a CC gene, and homologous genes are shown in a pop-up window when the cursor moves over the genes.

Bottom Line: For this purpose, the similarities of gene expression patterns and gene sequences have been separately utilized, although the combined information will provide a better solution.Some of the tightly coupled genes (modules) showed clear functional enrichment, such as immune system and cell cycle, indicating that our method could identify functionally related genes without any prior knowledge.We also found a few functional modules without any annotations, which may be good candidates for novel functional modules.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan.

ABSTRACT

Background: Computational approaches toward gene annotation are a formidable challenge, now that many genome sequences have been determined. Each gene has its own function, but complicated cellular functions are achieved by sets of genes. Therefore, sets of genes with strong functional relationships must be identified. For this purpose, the similarities of gene expression patterns and gene sequences have been separately utilized, although the combined information will provide a better solution.

Result & discussion: We propose a new method to find functional modules, by comparing gene coexpression profiles among species. A coexpression pattern is represented as a list of coexpressed genes with each guide gene. We compared two coexpression lists, one from a human guide gene and the other from a homologous mouse gene, and defined a measure to evaluate the similarity between the lists. Based on this coexpression similarity, we detected the highly conserved genes, and constructed human gene networks with conserved coexpression between human and mouse. Some of the tightly coupled genes (modules) showed clear functional enrichment, such as immune system and cell cycle, indicating that our method could identify functionally related genes without any prior knowledge. We also found a few functional modules without any annotations, which may be good candidates for novel functional modules. All of the comparisons are available at the http://v1.coxsimdb.info web database.

No MeSH data available.