MicroRNA-550a is associated with muscle system conferring poorer survival for esophageal cancer

Hong, Housong; Liu, Taisheng; Wu, Haipeng; Zhang, Jinye; Shi, Xiaoshun; Le, Xiaobing; Chen, Allen M.; Mo, Hong-ying; Huang, Qianqian; Hong-bin, Zhou; Rao, Xin

doi:10.1042/bsr20181173

Cited by 4 publications

(2 citation statements)

References 25 publications

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“…The basis for these selection criteria is that this combination represents the most common application of enrichment analysis in our previous study, which could be reproduced without the need to reanalyse the raw dataset from scratch. These articles are listed in the bibliography [32][33][34][35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50][51].…”

Section: Methodsmentioning

confidence: 99%

A recipe for extremely reproducible enrichment analysis (and why we need it)

Bora,

Ziemann

2023

Preprint

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Unreliable and irreproducible research is a significant problem that wastes resources and risks undermining the public perception of science. Previous work has highlighted that published enrichment analyses frequently suffer from statistical and reporting flaws. We sought to determine whether this translates into irreproducibility by examining whether the findings of 20 open-access articles published in 2019 describing enrichment analysis with the popular DAVID suite were reproducible. We find that only four articles exhibited a high degree of concordance, while seven exhibited major discrepancies, which we mainly ascribe to deficiencies in methodological reporting. As the tool version used is no longer available, all articles using this tool pre-2021 (~20,800 studies) including this sample of 20 articles are no longer able to be reproduced with the original tools. Based on this, we suggest that results from web-based tools without long-term preservation features should not be included in scientific publications due to the threat of link decay and short reproducibility horizon. Relying exclusively on webtools for analysis may also be in breach of institutional and funder data preservation mandates. We advocate for the adoption of extremely reproducible research workflows, and we provide a detailed protocol for how to achieve it for enrichment analysis using a combination of best practices including literate programming, version control, containerisation, documentation and persistent sharing of data and software.

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Section: Methodsmentioning

confidence: 99%

A recipe for extremely reproducible enrichment analysis (and why we need it)

Bora,

Ziemann

2023

Preprint

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“…Recently, Hu et al discovered that miR-196a had a regulatory effect on the proliferation, invasion and migration of ESCC by targeting ANXA1 [9]. In addition, microRNA-550a was found to be correlated to poor survival outcomes in patients with oesophageal cancer by affecting the muscle system [10]. Gao et al demonstrated the involvement of hsa-miR-21-3p in the maintenance of stemness through the regulation of TRAF4 [11] .…”

Section: Introductionmentioning

confidence: 99%

Identification and functional significance of MicroRNAs in esophageal squamous cell carcinoma

Zeng

et al. 2021

Preprint

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Background: Oesophageal carcinoma is one of the most frequently seen malignancies, and its incidence ranks third among men and fifth among women in China. Among all the histological categories, oesophageal squamous cell carcinoma (ESCC) accounted for the most of the cases. At present, there are few therapeutic methods applied in clinical practice for ESCC due to the limited evidence with respect to the underlying signaling pathways and the miRNAs related to the ESCC. Methods: To identify the differentially-expressed miRNAs (DE-miRNAs) in different stages of ESCC, we performed a microarray on 92 ESCC and 3 normal tissues. At the mean time, the potentially targeted genes as well as the highly-enriched signaling pathways and the relevant protein–protein interaction (PPI) network were analyzed and constructed by using a series of bioinformatic methods. Moreover, the identified DE-miRNAs in different stages of the ESCC were verified by using the TCGA dataset. Results: According to our analysis, overall 37 DE-miRNAs were identified, including 6 up-regulated miRNAs and 31 down-regulated miRNAs. 1884 genes were selected as the potentially targeted genes for the above miRNAs, most of which were found to be enriched in the PI3K-Akt signaling pathway and the Hippo signaling pathway. Based on the PPI network we constructed, PIK3R1 and NOTCH1 were considered as the potential hub genes. Conclusion: Our study provided additional explanations regarding the molecular mechanisms and prognosis of ESCC through the identification of a number of potential targeted genes of the DE-miRNAs in different stages of ESCC as well as the mostly enriched signaling pathways of the above genes, which could promote the development of the targeted treatment and improve the prognosis evaluation of ESCC.

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miR-550a-3/NFIC plays a driving role in esophageal squamous cell cancer cells proliferation and metastasis partly through EMT process

Wang

Shi

2020

Mol Cell Biochem

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MicroRNA-550a is associated with muscle system conferring poorer survival for esophageal cancer

Cited by 4 publications

References 25 publications

A recipe for extremely reproducible enrichment analysis (and why we need it)

A recipe for extremely reproducible enrichment analysis (and why we need it)

Identification and functional significance of MicroRNAs in esophageal squamous cell carcinoma

miR-550a-3/NFIC plays a driving role in esophageal squamous cell cancer cells proliferation and metastasis partly through EMT process

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