The gEAR portal - Advancing Data Sharing, Analysis and Discovery for Hearing and Balance Research

摘要 生物科学的发现已经越来越多地依赖于高通量的多组数据。这个 单细胞(Sc)转录组学的出现进一步革新了我们这个领域的研究，因为它具有复杂的结构。 由许多不同的细胞类型组成的内耳器官，这些细胞类型协同工作以正确地感觉 听力和平衡。利用现有和未来的多种体型、多形态和多物种的财富 数据因其不断增长的数据大小以及未受过培训的生物学家相对无法访问而受到挑战 在生物信息学方面。这个工具，基因表达分析资源(umgear.org)，是一个基于云的一站式- 生物学家可以在这里探索和分析与内耳相关的多组数据，而不需要 编程技能。在过去的五年里，齿轮已经成为我们领域的一项极其宝贵的资源。 渔具对现场的影响反映在其846个注册用户、440个数据集(超过70个组织在 公共领域的专题简介)，每月访问量达数千次。 这项提议的目标是在齿轮上实施必要的改进，这将显著 增强研究人员从他们自己生成的组学数据中推断生物学见解的能力 实验室和公共领域的组学数据集。我们将：(1)持续上传和策划EAR- 来自贡献实验室和公共领域的相关多组数据；(2)构建一个综合的 发育和成熟小鼠耳蜗表观遗传和转录图谱(A)作为必要的支架 用于交叉数据集整合，以及(B)作为弥合基因表达和基因表达之间差距的必要数据 基因调控；(3)在装备中实施先进的生物信息学分析工具；(4)增强用户- 界面；(5)改进可扩展性、性能和稳定性；(6)将齿轮与分析相结合 笔记本，以便只需最少的培训即可进行更复杂的分析；以及(7)继续我们的教育和外展 努力。除了用户调查外，我们还将设立用户和技术专家咨询委员会，以 提供反馈并指导发展。 齿轮生物信息学的有效运作和发展需要不同的专业知识 站台。我们的多学科团队成员包括外科科学家(PI)、生物信息学家(Co-IS)、生物学家 和工程师。我们将齿轮从一个抽象的想法转变为一个成功的平台的经验 适用于EAR领域，并成功克隆了包括Nemo Analytics(nemoanalytics.org)在内的多个克隆 大脑计划应该证明我们的经验、专业知识和交付能力。已完成的 拟议的齿轮改进将促进组学数据预期的伟大承诺的实现 生成和分析并促进现有数据的重复使用，从而催化基础科学发现和 促进听力和平衡障碍疗法的发展和翻译。

ABSTRACT Discovery in biological sciences has shifted to increasingly rely on high throughput multi-omic data. The advent of single cell (sc) transcriptomics further revolutionized research in our field, given the intricate structure of the inner ear organs consisting of numerous distinct cell types that function in concert to properly sense hearing and balance. Harnessing the wealth of existing and future multi-omic, multi-modality and multi-species data is challenged by their ever-increasing data size and relative inaccessibility to biologists that are not trained in bioinformatics. The gEAR, gene Expression Analysis Resources (umgear.org), is a cloud-based `one-stop- shop' where inner ear-related multi-omic data can be explored and analyzed by biologists without requiring programming skills. Over the past five years, the gEAR has become a critically valuable resource to our field. The impact of the gEAR on the field is reflected by its 846 registered users, 440 datasets (over 70 organized in thematic profiles in the public domain), and thousands of monthly visits. The goal of this proposal is to implement necessary improvements in the gEAR that will significantly enhance the ability of researchers to infer biological insights from the omics data generated by their own laboratories and from omics datasets in the public domain. We will: (1) continuously upload and curate ear- related multi-omic data from contributing laboratories and the public domain; (2) construct an integrated epigenetic and transcriptomic atlas of the developing and mature mouse cochlea (a) as a necessary scaffold for cross dataset integration, and (b) as necessary data for bridging the gap between gene expression and gene regulation; (3) implement advanced bioinformatic analytical tools in the gEAR; (4) enhance the user- interface; (5) make scalability, performance and stability improvements; (6) integrate the gEAR with analytical notebooks to allow more complex analyses with minimal training; and (7) continue our education and outreach efforts. In addition to user-surveys, we will establish both user and technology expertise advisory boards to provide feedback and guide development. Diverse expertise is required for the efficient operation and development of the gEAR bioinformatics platform. Our multi-disciplinary team members are a surgeon-scientist (PI), bioinformaticians (Co-Is), biologists and engineers. Our experience in turning the gEAR from an abstract idea to a successful platform, widely adapted in the ear field, and with multiple successful clones including NeMO Analytics (nemoanalytics.org) for the BRAIN initiative should attest to our experience, expertise, and ability to deliver. Completion of the proposed gEAR advancements will boost fulfillment of the great promises expected from omics data generation and analyses and foster reuse of existing data, thereby catalyzing both basic science discovery and advance development and translation of therapeutics for hearing and balance disorders.