Evidence map›Paper›PMID 36042881›Full record

ArticleSTAR protocols2022

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

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Yu-Shuen TsaiCenter for Systems and Synthetic Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan.
Yao-Ming ChangInstitute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
Yang-Mooi LimFaculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Selangor, Malaysia.
Soon-Keng CheongFaculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Selangor, Malaysia.
I-Fang ChungCenter for Systems and Synthetic Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan; Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan; Preventive Medicine Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan. Electronic address: ifchung@nycu.edu.tw.
Chee-Yin WongFaculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Selangor, Malaysia. Electronic address: wongcy@1utar.my.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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).

Indexed as

Gene Regulatory NetworksRNACell DifferentiationExome SequencingSequence Analysis, RNARNABioinformaticsCell DifferentiationGenomicsRNAseqSequence analysisStem Cells

Identifiers

PMID36042881
PMCPMC9420390

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.