Related Experiment Video
Updated: Mar 9, 2026
09:35
A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research
Published on: August 16, 2017
18.4K
SemanticSCo: A platform to support the semantic composition of services for gene expression analysis
Gabriela D A Guardia1, Luís Ferreira Pires2, Eduardo G da Silva2
1Department of Computer Science and Mathematics - Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP) - University of São Paulo (USP), Ribeirão Preto, Brazil.
Journal of Biomedical Informatics
|January 7, 2017
Summary
This study introduces SemanticSCo, a novel platform for automating gene expression analysis. It simplifies the integration of diverse bioinformatics tools, enabling researchers to focus on biological insights rather than technical complexities.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Gene expression analysis involves multiple tools, often leading to manual integration challenges.
- Existing semantic web service composition environments lack automation and user-friendliness for complex biological workflows.
Purpose of the Study:
- To develop a novel approach for semantic composition of gene expression analysis services.
- To address limitations in existing tools by providing a more automated and user-centric solution.
Main Methods:
- Proposed a new architecture for gene expression analysis service composition.
- Developed a flexible strategy for semi-automatic composition of semantic web services.
- Implemented the SemanticSCo platform supporting RESTful web services annotated with SAWSDL and complex workflow definitions.
Main Results:
- Successfully reproduced a documented microarray study using the SemanticSCo platform.
- Demonstrated the platform's ability to handle complex service behaviors through defined constraints and conditions.
- Validated the high-level abstraction for defining analysis workflows.
Conclusions:
- The SemanticSCo platform offers a robust solution for semantic web service composition in gene expression analysis.
- The approach enables researchers to focus on biological questions by abstracting technical complexities.
- The platform supports diverse stakeholder needs throughout the service composition process.
Related Concept Videos
01:42What is Gene Expression?
198.2K
Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
198.2K
01:36What is Gene Expression?
11.9K
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then...
11.9K
03:21RNA-seq
12.3K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
12.3K
03:36Genome Annotation and Assembly
21.3K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
21.3K
02:51mRNA Stability and Gene Expression
3.6K
3.6K
02:51mRNA Stability and Gene Expression
6.8K
The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity.
Cis-acting Elements involved in mRNA stability
Cis-acting Elements involved in mRNA stability
6.8K