Academic Journal
COTAN : ScRNA-seq data analysis based on gene co-expression
| العنوان: | COTAN : ScRNA-seq data analysis based on gene co-expression |
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| المؤلفون: | Galfre S. G., Morandin F., Pietrosanto M., Cremisi F., Helmer-Citterich M. |
| المساهمون: | Galfre, S. G., Morandin, F., Pietrosanto, M., Cremisi, F., Helmer-Citterich, M. |
| سنة النشر: | 2021 |
| المجموعة: | Scuola Normale Superiore: CINECA IRIS |
| مصطلحات موضوعية: | Rna-seq, cell level, cell population, contingency table, gene expression, gene interaction, genetic marker, genetic transcription, nervous system development, network analysi, single cell RNA seq, Settore BIO/06 - Anatomia Comparata e Citologia |
| الوصف: | Estimating the co-expression of cell identity factors in single-cell is crucial. Due to the low efficiency of scRNA-seq methodologies, sensitive computational approaches are critical to accurately infer transcription profiles in a cell population. We introduce COTAN, a statistical and computational method, to analyze the co-expression of gene pairs at single cell level, providing the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts' distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can assess the correlated or anti-correlated expression of gene pairs, providing a new correlation index with an approximate p-value for the associated test of independence. COTAN can evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Similarly to correlation network analysis, it provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions, becoming a new tool to identify cell-identity markers. We assayed COTAN on two neural development datasets with very promising results. COTAN is an R package that complements the traditional single cell RNA-seq analysis and it is available at https://github.com/seriph78/COTAN. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| Relation: | info:eu-repo/semantics/altIdentifier/pmid/34396096; info:eu-repo/semantics/altIdentifier/wos/WOS:000745279200016; volume:3; issue:3; firstpage:1; lastpage:11; numberofpages:11; journal:NAR GENOMICS AND BIOINFORMATICS; https://hdl.handle.net/11384/125063; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85117107330 |
| DOI: | 10.1093/nargab/lqab072 |
| الاتاحة: | https://hdl.handle.net/11384/125063 https://doi.org/10.1093/nargab/lqab072 |
| Rights: | info:eu-repo/semantics/openAccess |
| رقم الانضمام: | edsbas.ECCE1642 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1093/nargab/lqab072 |
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