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元研究:在全基因组检测与结果报告之间存在渗漏的管道,从而导致一些研究较少的基因丢失。

Meta-Research: Understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results.

机构信息

Interdisciplinary Biological Sciences, Northwestern University, Evanston, United States.

Department of Chemical and Biological Engineering, Northwestern University, Evanston, United States.

出版信息

Elife. 2024 Mar 28;12:RP93429. doi: 10.7554/eLife.93429.

Abstract

Present-day publications on human genes primarily feature genes that already appeared in many publications prior to completion of the Human Genome Project in 2003. These patterns persist despite the subsequent adoption of high-throughput technologies, which routinely identify novel genes associated with biological processes and disease. Although several hypotheses for bias in the selection of genes as research targets have been proposed, their explanatory powers have not yet been compared. Our analysis suggests that understudied genes are systematically abandoned in favor of better-studied genes between the completion of -omics experiments and the reporting of results. Understudied genes remain abandoned by studies that cite these -omics experiments. Conversely, we find that publications on understudied genes may even accrue a greater number of citations. Among 45 biological and experimental factors previously proposed to affect which genes are being studied, we find that 33 are significantly associated with the choice of hit genes presented in titles and abstracts of -omics studies. To promote the investigation of understudied genes, we condense our insights into a tool, (FMUG), that allows scientists to engage with potential bias during the selection of hits. We demonstrate the utility of FMUG through the identification of genes that remain understudied in vertebrate aging. FMUG is developed in Flutter and is available for download at fmug.amaral.northwestern.edu as a MacOS/Windows app.

摘要

目前关于人类基因的出版物主要集中在 2003 年人类基因组计划完成之前已经在许多出版物中出现的基因上。尽管随后采用了高通量技术,这些技术通常可以识别与生物过程和疾病相关的新基因,但这些模式仍然存在。尽管已经提出了几个关于作为研究目标的基因选择存在偏差的假设,但它们的解释力尚未得到比较。我们的分析表明,在完成组学实验和报告结果之间,未被充分研究的基因被系统地放弃,而更受关注的基因则被优先选择。引用这些组学实验的研究仍然放弃了未被充分研究的基因。相反,我们发现,关于未被充分研究的基因的出版物甚至可能获得更多的引用。在先前提出的 45 个可能影响正在研究的基因的生物学和实验因素中,我们发现其中 33 个因素与组学研究标题和摘要中呈现的命中基因的选择显著相关。为了促进对未被充分研究的基因的研究,我们将我们的见解浓缩到一个工具中,即(FMUG),该工具允许科学家在选择命中基因时参与潜在的偏差。我们通过识别脊椎动物衰老中仍然未被充分研究的基因来展示 FMUG 的实用性。FMUG 是用 Flutter 开发的,可以在 fmug.amaral.northwestern.edu 上下载,作为 MacOS/Windows 应用程序。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2a48/10977968/3478b5a6ff1f/elife-93429-fig1.jpg

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