Evidence map›Paper›PMID 25171496›Full record

ArticlePloS one2014

Synergistic transcriptional and post-transcriptional regulation of ESC characteristics by core pluripotency transcription factors in protein-protein interaction networks.

Leijie Li, Liangcai Zhang, Guiyou Liu, Rennan Feng, Yongshuai Jiang, Lei Yang, Shihua Zhang, Mingzhi Liao, Jinlian Hua

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.6field-weighted citation impact, top 33% of its field
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

4 citing papers in PubMed, 7 citations in OpenAlex.

  1. Article
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  4. Review
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

9 authors at 4 institutions in 2 countries.

Leijie LiCollege of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
Liangcai ZhangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China; Department of Statistics, Rice University, Houston, TX, United States of America.
Guiyou LiuCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China; Genome Analysis Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
Rennan FengCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China; Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, China.
Yongshuai JiangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Lei YangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Shihua ZhangDepartment of Biostatistics, School of Science, Anhui Agricultural University, Hefei, China.
Mingzhi LiaoCollege of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
Jinlian HuaCollege of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, China.
Harbin Medical University · CNNorthwest A&F University · CNAnhui Agricultural University · CNChinese Academy of Sciences · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The molecular mechanism that maintains the pluripotency of embryonic stem cells (ESCs) is not well understood but may be reflected in complex biological networks. However, there have been few studies on the effects of transcriptional and post-transcriptional regulation during the development of ESCs from the perspective of computational systems biology. In this study, we analyzed the topological properties of the "core" pluripotency transcription factors (TFs) OCT4, SOX2 and NANOG in protein-protein interaction networks (PPINs). Further, we identified synergistic interactions between these TFs and microRNAs (miRNAs) in PPINs during ESC development. Results show that there were significant differences in centrality characters between TF-targets and non-TF-targets in PPINs. We also found that there was consistent regulation of multiple "core" pluripotency TFs. Based on the analysis of shortest path length, we found that the module properties were not only within the targets regulated by common or multiple "core" pluripotency TFs but also between the groups of targets regulated by different TFs. Finally, we identified synergistic regulation of these TFs and miRNAs. In summary, the synergistic effects of "core" pluripotency TFs and miRNAs were analyzed using computational methods in both human and mouse PPINs.

Indexed as

Gene Expression RegulationProtein Interaction MapsAnimalsEmbryonic Stem CellsGene Regulatory NetworksHomeodomain ProteinsHumansMiceMicroRNAsNanog Homeobox ProteinOctamer Transcription Factor-3SOXB1 Transcription FactorsTranscriptional ActivationTranscription FactorsHomeodomain ProteinsMicroRNAsNanog Homeobox ProteinNANOG protein, humanNanog protein, mouseOctamer Transcription Factor-3SOXB1 Transcription FactorsTranscription Factors

Identifiers

PMID25171496
PMCPMC4149371
OpenAlexW2064559242

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.