CluGene: A Bioinformatics Framework for the Identification of Co-Localized, Co-Expressed and Co-Regulated Genes Aimed at the Investigation of Transcriptional Regulatory Networks from High-Throughput Expression Data
نویسندگان
چکیده
The full understanding of the mechanisms underlying transcriptional regulatory networks requires unravelling of complex causal relationships. Genome high-throughput technologies produce a huge amount of information pertaining gene expression and regulation; however, the complexity of the available data is often overwhelming and tools are needed to extract and organize the relevant information. This work starts from the assumption that the observation of co-occurrent events (in particular co-localization, co-expression and co-regulation) may provide a powerful starting point to begin unravelling transcriptional regulatory networks. Co-expressed genes often imply shared functional pathways; co-expressed and functionally related genes are often co-localized, too; moreover, co-expressed and co-localized genes are also potential targets for co-regulation; finally, co-regulation seems more frequent for genes mapped to proximal chromosome regions. Despite the recognized importance of analysing co-occurrent events, no bioinformatics solution allowing the simultaneous analysis of co-expression, co-localization and co-regulation is currently available. Our work resulted in developing and valuating CluGene, a software providing tools to analyze multiple types of co-occurrences within a single interactive environment allowing the interactive investigation of combined co-expression, co-localization and co-regulation of genes. The use of CluGene will enhance the power of testing hypothesis and experimental approaches aimed at unravelling transcriptional regulatory networks. The software is freely available at http://bioinfolab.unipg.it/.
منابع مشابه
In silico identification of miRNAs and their target genes and analysis of gene co-expression network in saffron (Crocus sativus L.) stigma
As an aromatic and colorful plant of substantive taste, saffron (Crocus sativus L.) owes such properties of matter to growing class of the secondary metabolites derived from the carotenoids, apocarotenoids. Regarding the critical role of microRNAs in secondary metabolic synthesis and the limited number of identified miRNAs in C. sativus, on the other hand, one may see the point how the characte...
متن کاملI-13: Transcriptome Dynamics of Human and Mouse Preimplantation Embryos Revealed by Single Cell RNA-Sequencing
Background: Mammalian preimplantation development is a complex process involving dramatic changes in the transcriptional architecture. However, it is still unclear about the crucial transcriptional network and key hub genes that regulate the proceeding of preimplantation embryos. Materials and Methods: Through single-cell RNAsequencing (RNA-seq) of both human and mouse preimplantation embryos, ...
متن کاملBioinformatics identification of miRNA-mRNA regulatory network contributing to lung cancer invasion
Background: Over the past 15 years, significant insights have been gained into the roles of miRNAs in cancer. In various cancers, miRNAs can act as oncogenes, tumor suppressors, or control the metastasis process by modulating the expression of numerous target genes. This study is aimed at determining molecular network of miRNA-mRNA regulating lung cancer invasion, by bioinformatics approaches. ...
متن کاملBioinformatics Identification of miRNA-mRNA Regulatory Network Contributing Primary Lung Cancer
Introduction: In clinical practice, distinguishing invasive lung tumors from primary tumors remains a challenge. With recent advances in understanding biological alterations of tumorigenesis and molecular analytic technologies, using these molecular alterations can be sensitive and tumor-specific as biomarker for the stratification of patients. In this study, the molecular network of miRNA-mRNA...
متن کاملCo-expression networks: graph properties and topological comparisons
MOTIVATION Microarray-based gene expression data have been generated widely to study different biological processes and systems. Gene co-expression networks are often used to extract information about groups of genes that are 'functionally' related or co-regulated. However, the structural properties of such co-expression networks have not been rigorously studied and fully compared with known bi...
متن کامل