An unbiased Boolean analysis of public gene expression data for core cell cycle gene classification
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ABSTRACT:
PROVIDER: PRJNA488232 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below.
2018-08-29 | GSE119128 | GEO
Project description:Numerous gene expression datasets from diverse human tissue samples have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions. We propose here a new large scale meta-analysis of all of the publicly available human datasets to identify Boolean logical relationships between genes. Boolean logic is a branch of mathematics that deals with two possible values. In the context of gene expression datasets we use qualitative high and low expression values. A strong logical relationship between genes emerges if at least one of the quadrants is sparsely populated.
2018-08-29 | GSE119087 | GEO
Project description:Numerous gene expression datasets from diverse mouse tissue samples have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions. We propose here a new large scale meta-analysis of all of the publicly available mouse datasets to identify Boolean logical relationships between genes. Boolean logic is a branch of mathematics that deals with two possible values. In the context of gene expression datasets we use qualitative high and low expression values. A strong logical relationship between genes emerges if at least one of the quadrants is sparsely populated.
2018-08-29 | GSE119085 | GEO
Project description:Numerous gene expression datasets from diverse fly tissue samples have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions. We propose here a new large scale meta-analysis of all of the publicly available fly datasets to identify Boolean logical relationships between genes. Boolean logic is a branch of mathematics that deals with two possible values. In the context of gene expression datasets we use qualitative high and low expression values. A strong logical relationship between genes emerges if at least one of the quadrants is sparsely populated.
2018-08-29 | GSE119084 | GEO
Project description:Numerous gene expression datasets from diverse plant tissue samples have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions. We propose here a new large scale meta-analysis of all of the publicly available plant datasets to identify Boolean logical relationships between genes. Boolean logic is a branch of mathematics that deals with two possible values. In the context of gene expression datasets we use qualitative high and low expression values. A strong logical relationship between genes emerges if at least one of the quadrants is sparsely populated.
2018-08-29 | GSE119083 | GEO
Project description:Cell proliferation is essential for the development and maintenance of all organisms and is dysregulated in cancer. Using synchronized cells progressing through the cell cycle, pioneering microarray studies defined cell cycle genes based on cyclic variation in their expression. However, the concordance of the small number of synchronized cell studies has been limited, leading to discrepancies in definition of the transcriptionally regulated set of cell cycle genes within and between species. Here we present an informatics approach based on Boolean logic to identify cell cycle genes. This approach used the vast array of publicly available gene expression data sets to query similarity to CCNB1, which encodes the cyclin subunit of the Cdk1-cyclin B complex that triggers the G2-to-M transition. In addition to highlighting conservation of cell cycle genes across large evolutionary distances, this approach identified contexts where well-studied genes known to act during the cell cycle are expressed and potentially acting in nondivision contexts. An accessible web platform enables a detailed exploration of the cell cycle gene lists generated using the Boolean logic approach. The methods employed are straightforward to extend to processes other than the cell cycle.
| S-EPMC6727750 | biostudies-literature
Project description:Understanding the structure and interplay of cellular signalling pathways is one of the great challenges in molecular biology. Boolean Networks can infer signalling networks from observations of protein activation. In situations where it is difficult to assess protein activation directly, Nested Effect Models are an alternative. They derive the network structure indirectly from downstream effects of pathway perturbations. To date, Nested Effect Models cannot resolve signalling details like the formation of signalling complexes or the activation of proteins by multiple alternative input signals. Here we introduce Boolean Nested Effect Models (B-NEM). B-NEMs combine the use of downstream effects with the higher resolution of signalling pathway structures in Boolean Networks. We show that B-NEMs accurately reconstruct signal flows in simulated data. Using B-NEM we then resolve BCR signalling via PI3K and TAK1 kinases in BL2 lymphoma cell lines. 84 BL2 cell-line samples were hybridized to HGU133+2 Affymetrix GeneChips.
2015-12-10 | E-GEOD-68761 | biostudies-arrayexpress
Project description:In this dataset, we report the analysis by RNA-sequencing (RNA-seq) of the transcriptional profile of neuroblastoma cell lines at baseline and after treatment with 13-cis-retinoic acid. Data from this study validated Boolean Implication Network derived differentiation signature in neuroblastoma. Our differentiation signature included a cluster of genes involved in intracellular signaling and growth factor receptor trafficking pathways that is strongly associated with neuroblastoma differentiation, and we validated the associations of UBE4B, a gene within this cluster, with neuroblastoma cell and tumor differentiation. Our findings demonstrate that Boolean network analyses of symmetric and asymmetric gene expression relationships can identify novel genes and pathways relevant for neuroblastoma tumor differentiation that could represent potential therapeutic targets.
2023-04-24 | GSE226935 | GEO
Project description:Understanding the structure and interplay of cellular signalling pathways is one of the great challenges in molecular biology. Boolean Networks can infer signalling networks from observations of protein activation. In situations where it is difficult to assess protein activation directly, Nested Effect Models are an alternative. They derive the network structure indirectly from downstream effects of pathway perturbations. To date, Nested Effect Models cannot resolve signalling details like the formation of signalling complexes or the activation of proteins by multiple alternative input signals. Here we introduce Boolean Nested Effect Models (B-NEM). B-NEMs combine the use of downstream effects with the higher resolution of signalling pathway structures in Boolean Networks. We show that B-NEMs accurately reconstruct signal flows in simulated data. Using B-NEM we then resolve BCR signalling via PI3K and TAK1 kinases in BL2 lymphoma cell lines.
2015-12-10 | GSE68761 | GEO
Project description:Background Rheumatoid arthritis (RA) is a chronic inflammatory disease, characterized by joint destruction and perpetuated by the synovial membrane (SM). In the inflamed SM, activated synovial fibroblasts (SFB) form the major cell type promoting development and progression of the disease by an abnormal expression/secretion of pro-inflammatory cytokines, tissue-degrading enzymes resulting in a predominant degradation of the extra-cellular matrix (ECM), and collagens causing joint fibrosis. We developed a new procedure, based on human knowledge and formal concept analysis (FCA), to simulate and analyze the temporal behaviour of regulatory and signaling networks. It was applied to a regulatory network (containing 18 genes from 5 functional groups) representing ECM formation and destruction in TGFβ - and TNFα -stimulated SFB. Results For the modelling of SFB-controlled ECM turnover in rheumatic diseases, Boolean network architecture was used as well as extensive literature information and revision by experimental gene expression data from stimulated SFB. In course of revision, the additional experimental information resulted in different biologically reasonable changes, yielding two Boolean networks that describe TGFβ and TNFα effects, respectively. The final simulations were further analyzed by the attribute exploration algorithm of FCA, integrating again the observed time series in a more fine-grained and automated manner. The generated temporal rules clearly reveal subtle regulatory relationships between different genes, co-expression patterns and converse gene expression regulation in rheumatic diseases. Conclusion The developed Boolean network based method for the dynamical analysis of regulatory and signaling networks represents a reliable systems biological solution for the improved understanding of complex regulatory pathways and the interactions among different genes in disease. The resulting knowledge base can be used for further analysis of the ECM system in human fibroblasts and may be queried to predict the functional consequences of observed (e.g. in diseases as RA) or hypothetical (e.g. for therapeutic purposes) gene expression disturbances.
2009-07-20 | GSE13837 | GEO