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CorrelaGenes: a new tool for the interpretation of the human transcriptome.

Cremaschi P, Rovida S, Sacchi L, Lisa A, Calvi F, Montecucco A, Biamonti G, Bione S, Sacchi G - BMC Bioinformatics (2014)

Bottom Line: The significance of the correlation is measured coupling the Lift, a well-known standard ARM index, and the χ(2) p value.The manually curated selection of the comparisons and the developed algorithm constitute a new approach in the field of gene expression profiling studies.The preliminary results of the simulation showed how CorrelaGenes could contribute to the characterization of molecular pathways and biological processes integrating data obtained from other applications and available in public repositories.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: The amount of gene expression data available in public repositories has grown exponentially in the last years, now requiring new data mining tools to transform them in information easily accessible to biologists.

Results: By exploiting expression data publicly available in the Gene Expression Omnibus (GEO) database, we developed a new bioinformatics tool aimed at the identification of genes whose expression appeared simultaneously altered in different experimental conditions, thus suggesting co-regulation or coordinated action in the same biological process. To accomplish this task, we used the 978 human GEO Curated DataSets and we manually performed the selection of 2,109 pair-wise comparisons based on their biological rationale. The lists of differentially expressed genes, obtained from the selected comparisons, were stored in a PostgreSQL database and used as data source for the CorrelaGenes tool. Our application uses a customized Association Rule Mining (ARM) algorithm to identify sets of genes showing expression profiles correlated with a gene of interest. The significance of the correlation is measured coupling the Lift, a well-known standard ARM index, and the χ(2) p value. The manually curated selection of the comparisons and the developed algorithm constitute a new approach in the field of gene expression profiling studies. Simulation performed on 100 randomly selected target genes allowed us to evaluate the efficiency of the procedure and to obtain preliminary data demonstrating the consistency of the results.

Conclusions: The preliminary results of the simulation showed how CorrelaGenes could contribute to the characterization of molecular pathways and biological processes integrating data obtained from other applications and available in public repositories.

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Related in: MedlinePlus

Schematic representation of the CorrelaGenes workflow.
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Figure 1: Schematic representation of the CorrelaGenes workflow.

Mentions: CorrelaGenes was conceived to explore the biological role of a gene of interest selected by the user identifying a set of genes whose expression appeared altered in the same experimental or physiological state. The tool exploits GEO expression data and uses a customized Association Rule Mining algorithm for a cross-sectional analysis aimed at identifying those genes showing a coordinated modulation of their transcriptional profiles in different conditions. A schematic representation of the CorrelaGenes workflow is shown in Figure 1.


CorrelaGenes: a new tool for the interpretation of the human transcriptome.

Cremaschi P, Rovida S, Sacchi L, Lisa A, Calvi F, Montecucco A, Biamonti G, Bione S, Sacchi G - BMC Bioinformatics (2014)

Schematic representation of the CorrelaGenes workflow.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4016313&req=5

Figure 1: Schematic representation of the CorrelaGenes workflow.
Mentions: CorrelaGenes was conceived to explore the biological role of a gene of interest selected by the user identifying a set of genes whose expression appeared altered in the same experimental or physiological state. The tool exploits GEO expression data and uses a customized Association Rule Mining algorithm for a cross-sectional analysis aimed at identifying those genes showing a coordinated modulation of their transcriptional profiles in different conditions. A schematic representation of the CorrelaGenes workflow is shown in Figure 1.

Bottom Line: The significance of the correlation is measured coupling the Lift, a well-known standard ARM index, and the χ(2) p value.The manually curated selection of the comparisons and the developed algorithm constitute a new approach in the field of gene expression profiling studies.The preliminary results of the simulation showed how CorrelaGenes could contribute to the characterization of molecular pathways and biological processes integrating data obtained from other applications and available in public repositories.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

Background: The amount of gene expression data available in public repositories has grown exponentially in the last years, now requiring new data mining tools to transform them in information easily accessible to biologists.

Results: By exploiting expression data publicly available in the Gene Expression Omnibus (GEO) database, we developed a new bioinformatics tool aimed at the identification of genes whose expression appeared simultaneously altered in different experimental conditions, thus suggesting co-regulation or coordinated action in the same biological process. To accomplish this task, we used the 978 human GEO Curated DataSets and we manually performed the selection of 2,109 pair-wise comparisons based on their biological rationale. The lists of differentially expressed genes, obtained from the selected comparisons, were stored in a PostgreSQL database and used as data source for the CorrelaGenes tool. Our application uses a customized Association Rule Mining (ARM) algorithm to identify sets of genes showing expression profiles correlated with a gene of interest. The significance of the correlation is measured coupling the Lift, a well-known standard ARM index, and the χ(2) p value. The manually curated selection of the comparisons and the developed algorithm constitute a new approach in the field of gene expression profiling studies. Simulation performed on 100 randomly selected target genes allowed us to evaluate the efficiency of the procedure and to obtain preliminary data demonstrating the consistency of the results.

Conclusions: The preliminary results of the simulation showed how CorrelaGenes could contribute to the characterization of molecular pathways and biological processes integrating data obtained from other applications and available in public repositories.

Show MeSH
Related in: MedlinePlus