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

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

PROVIDER: PRJNA656828 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12440400.fastq.gz	Fastqsanger.gz
	SRR12440500.fastq.gz	Fastqsanger.gz
	SRR12440401.fastq.gz	Fastqsanger.gz
	SRR12440501.fastq.gz	Fastqsanger.gz
	SRR12440402.fastq.gz	Fastqsanger.gz

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UniPath: a uniform approach for pathway and gene-set based analysis of heterogeneity in single-cell epigenome and transcriptome profiles.

Project description:Recent advances in single-cell open-chromatin and transcriptome profiling have created a challenge of exploring novel applications with a meaningful transformation of read-counts, which often have high variability in noise and drop-out among cells. Here, we introduce UniPath, for representing single-cells using pathway and gene-set enrichment scores by a transformation of their open-chromatin or gene-expression profiles. The robust statistical approach of UniPath provides high accuracy, consistency and scalability in estimating gene-set enrichment scores for every cell. Its framework provides an easy solution for handling variability in drop-out rate, which can sometimes create artefact due to systematic patterns. UniPath provides an alternative approach of dimension reduction of single-cell open-chromatin profiles. UniPath's approach of predicting temporal-order of single-cells using their pathway enrichment scores enables suppression of covariates to achieve correct order of cells. Analysis of mouse cell atlas using our approach yielded surprising, albeit biologically-meaningful co-clustering of cell-types from distant organs. By enabling an unconventional method of exploiting pathway co-occurrence to compare two groups of cells, our approach also proves to be useful in inferring context-specific regulations in cancer cells. Available at https://reggenlab.github.io/UniPathWeb/.

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