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Uniform approach for pathway and gene-set based analysis of heterogeneity in single-cell epigenome and transcriptome profiles

ABSTRACT: Representation of single cells in biologically meaningfull terms has potential to improve classical analysis steps as well as give rise to multiple new applications. We have developed UniPath for representation of single-cell expression and open-chromatin profile using pathway enrichment scores. UniPath can also perform pseudo-temporal ordering of single-cells using their pathway enrichment-scores. We analysed several datasets using UniPath. Analysis of atlas of mouse single-cell RNAseq profiles with UniPath revealed surprising but biologically-meaningful convergence of different cell-types from distant organs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE156138 | GEO | 2020/11/06

REPOSITORIES: GEO

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Project description:OBJECTIVE: To investigate the differentially expressed genes related to the chemosensitivity of laryngeal squamous cell carcinoma ï¼LSCCï¼by microarrays arrays. METHODS: 1. A total number of 11 patients who underwent induction chemotherapy for primary hypopharyngeal squamous cell carcinoma (7 patients are sensitive to chemotherapy ,and others are not) were recruited for microarray and miRNA array gene expression analysis 2. Bioinformatics analysis of differentially expressed genes screened by microarrays : The differential gene cluster analysis was applied in biological processes, cellular components and molecular functions by GO database; The differential gene enrichment analysis was applied in signaling pathways by KEGG database, and the differentially expressed and biologically meaningful core genes would be screened. RESULTS: 1. Analyzed by microarrays, there were 1554 genes significantly related to the sensitivity to chemotherapy; Among these 1554genes, 777 showed a higher expression in the tissue from patients who are sensitive to chemotherapy , while 785 presented the contrasting pattern. CONCLUSIONS: The research revealed a gene expression signature of chemosensitivity in laryngeal squamous cell carcinoma by microarrays arrays. The result will contribute to the understanding of the molecular basis of laryngeal squamous cell carcinoma and help to improve diagnosis and treatment. 1. A total number of 11 patients who underwent induction chemotherapy for primary hypopharyngeal squamous cell carcinoma (7 patients are sensitive to chemotherapy ,and others are not) were recruited for microarray and miRNA array gene expression analysis 2. Bioinformatics analysis of differentially expressed genes screened by microarrays : The differential gene cluster analysis was applied in biological processes, cellular components and molecular functions by GO database; The differential gene enrichment analysis was applied in signaling pathways by KEGG database, and the differentially expressed and biologically meaningful core genes would be screened.

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Uniform approach for pathway and gene-set based analysis of heterogeneity in single-cell epigenome and transcriptome profiles

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