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

Yu Shuen Tsai; Yao Ming Chang; Yang Mooi Lim; Soon Keng Cheong; I. Fang Chung; Chee Yin Wong

doi:10.1016/j.xpro.2022.101541

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

Yu Shuen Tsai, Yao Ming Chang, Yang Mooi Lim, Soon Keng Cheong, I. Fang Chung^*, Chee Yin Wong^*

^*Corresponding author for this work

Institute of Biomedical Informatics

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

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).

Original language	English
Article number	101541
Journal	STAR Protocols
Volume	3
Issue number	3
DOIs	https://doi.org/10.1016/j.xpro.2022.101541
State	Published - 16 Sep 2022

Keywords

Bioinformatics
Cell Differentiation
Genomics
RNAseq
Sequence analysis
Stem Cells

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10.1016/j.xpro.2022.101541

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title = "Generating transcriptional regulatory networks from time-ordered stem cell differentiation RNA sequencing data",

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).",

keywords = "Bioinformatics, Cell Differentiation, Genomics, RNAseq, Sequence analysis, Stem Cells",

author = "Tsai, {Yu Shuen} and Chang, {Yao Ming} and Lim, {Yang Mooi} and Cheong, {Soon Keng} and Chung, {I. Fang} and Wong, {Chee Yin}",

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AU - Tsai, Yu Shuen

AU - Chang, Yao Ming

AU - Lim, Yang Mooi

AU - Cheong, Soon Keng

AU - Chung, I. Fang

AU - Wong, Chee Yin

PY - 2022/9/16

Y1 - 2022/9/16

N2 - 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).

AB - 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).

KW - Bioinformatics

KW - Cell Differentiation

KW - Genomics

KW - RNAseq

KW - Sequence analysis

KW - Stem Cells

UR - http://www.scopus.com/inward/record.url?scp=85136206995&partnerID=8YFLogxK

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DO - 10.1016/j.xpro.2022.101541

M3 - Article

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VL - 3

JO - STAR Protocols

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ER -

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

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Keywords

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