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Literature DB >> 36042881

Generating transcriptional regulatory networks from time-ordered stem cell differentiation RNA sequencing data.

Yu-Shuen Tsai¹, Yao-Ming Chang², Yang-Mooi Lim³, Soon-Keng Cheong³, I-Fang Chung⁴, Chee-Yin Wong⁵.

Abstract

We describe steps to 1) identify ascending and descending monotonic key genes from time-ordered stem cell differentiation expression data, 2) construct time-ordered transcriptional regulatory networks, and 3) infer the involvement of transcription factors along the differentiation process. For complete details on the use and execution of this protocol, please refer to Wong et al. (2020).

Entities: Chemical

Keywords: Bioinformatics; Cell Differentiation; Genomics; RNAseq; Sequence analysis; Stem Cells

Mesh：

Substances：
RNA

Year: 2022 PMID： 36042881 PMCID： PMC9420390 DOI： 10.1016/j.xpro.2022.101541

Source DB: PubMed Journal: STAR Protoc ISSN： 2666-1667

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References

7 in total

1. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.

Authors: Steffen Durinck; Yves Moreau; Arek Kasprzyk; Sean Davis; Bart De Moor; Alvis Brazma; Wolfgang Huber
Journal: Bioinformatics Date: 2005-08-15 Impact factor: 6.937

2. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor.

Authors: Sean Davis; Paul S Meltzer
Journal: Bioinformatics Date: 2007-05-12 Impact factor: 6.937

3. Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes.

Authors: Yao-Ming Chang; Hsin-Hung Lin; Wen-Yu Liu; Chun-Ping Yu; Hsiang-June Chen; Putu Puja Wartini; Yi-Ying Kao; Yeh-Hua Wu; Jinn-Jy Lin; Mei-Yeh Jade Lu; Shih-Long Tu; Shu-Hsing Wu; Shin-Han Shiu; Maurice S B Ku; Wen-Hsiung Li
Journal: Proc Natl Acad Sci U S A Date: 2019-02-04 Impact factor: 11.205

Generating transcriptional regulatory networks from time-ordered stem cell differentiation RNA sequencing data.

1. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.

2. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor.

3. Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes.

4. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.

5. Discovering monotonic stemness marker genes from time-series stem cell microarray data.

6. Decoding the differentiation of mesenchymal stem cells into mesangial cells at the transcriptomic level.

7. AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors.