Datasets for YaliFunTome database

All the data and the metadata are also presented in the form of a searchable database YaliFunTome, to be found via the link: https://sparrow.up.poznan.pl/tsdatabase/
General:
The aim of this project was to examine the potential implications of transcription factors (TFs) identified in Yarrowia lipolytica genome in stress resistance and/or in the synthesis of heterologous proteins (recombinant proteins: r-Prots). The amount and potential of the data we gathered from completing experimental design inspired us to present them in the form of a searchable catalog.
This database can be used to characterize functional behavior of a specific TF across an array of conditions or to screen for TFs that were responsive to a specific combination of environmental factors in our studies.

Experimental setup:
In short: A collection of 125 Y. lipolytica strains over-expressing (OE) individually TFs was subjected to extensive phenotype screening under different environmental conditions, and the data processing was assisted by mathematical modeling. It was presumed that apart from genetic engineering of the TFs-encoding genes by their OE, implementation of the environmental perturbations will further manipulate the activation status of the TFs.

The search of the TFs within the Y. lipolytica genome and construction of the strains co-over-expressing (co-OE) individually one of 125 identified TFs and a reporter protein (RedStar2) was done previously, by our Colleagues: doi:10.1093/femsyr/foy037. Both genes were cloned under a constitutive promoter pTEF (more details can be found here: doi:10.1093/femsyr/fov052).
The TF co-OE strains were cultured under a combination of enviromental conditions. The experimental setup was designed using DoE (Design of Experiments; DesignExpert software; StatSoft)

Data presentation
Each strain overexpressing an individual TF (TF-OE strain) was tested under an array of conditions, and so was the reference strain. Raw data for:
optical density at 600 nm wavelength as a proxy of growth,
fluorescence intensity from a reporter protein as a proxy of r-Prot synthesis,
are presented in a form of heat-maps of fold change (FC) of a given measure response in the TF-OE strain over the control strain (file RAW DATA YaliFunTome.xlsx).
The data were also processed according to the Response Surface Methodology to acquire models describing a behavior of a given read parameter within the range of investigated variables (Model Factor's Contributions.xlsx). The adopted data processing strategy enabled the evaluation of each specific variable's contribution to the response's variability (growth, amount of r-Prot) elicited by a given TF-OE strain. This evaluation is presented in Factor's Contribution tables indicating the dominant level of a variable (color-coded and as +1 or -1, according to the adopted coding system) and a percentage contribution of the variable to the response.

所有数据与元数据均以可搜索数据库YaliFunTome的形式呈现，可通过以下链接获取：https://sparrow.up.poznan.pl/tsdatabase/
概述：
本项目旨在探究解脂耶氏酵母（Yarrowia lipolytica）基因组中鉴定得到的转录因子（transcription factors, TFs）在抗逆性及异源蛋白（重组蛋白，r-Prots）合成方面的潜在调控作用。我们通过完成实验设计所收集的数据体量与应用价值，促使我们将其整理为可搜索的目录数据库。
该数据库可用于表征特定转录因子在多种培养条件下的功能特性，也可用于筛选本研究中对特定环境因子组合产生响应的转录因子。

实验设计：
简言之：我们构建了125株分别过表达（over-expressing, OE）单个转录因子的解脂耶氏酵母菌株，并在多种环境条件下开展了全面的表型筛选，实验数据处理辅以数学建模。我们推测，除了通过过表达转录因子编码基因完成基因工程改造外，施加环境扰动可进一步调控转录因子的激活状态。
解脂耶氏酵母基因组内转录因子的筛选、以及分别共过表达（co-over-expressing, co-OE）125个鉴定得到的转录因子与报告蛋白RedStar2的菌株构建工作，均由我们的合作者此前完成（相关文献DOI：10.1093/femsyr/foy037）。两个基因均克隆于组成型启动子pTEF下游（详细信息可参阅文献DOI：10.1093/femsyr/fov052）。
共过表达转录因子的菌株在多种环境条件组合下进行培养，实验设计通过DoE（实验设计，Design of Experiments；使用DesignExpert软件；StatSoft开发）完成。

数据呈现：
每一株单独过表达转录因子的菌株（TF-OE菌株）均在多种培养条件下进行检测，同时设置参考菌株作为对照。原始数据包括：以600纳米光密度表征的菌体生长情况、以及以报告蛋白荧光强度表征的重组蛋白合成量，以上数据均以TF-OE菌株相对于对照菌株的响应指标倍数变化（fold change, FC）热图形式呈现（文件：RAW DATA YaliFunTome.xlsx）。
此外，我们依据响应面法（Response Surface Methodology）对数据进行处理，以构建能够描述目标响应参数在所研究变量范围内变化规律的模型（文件：Model Factor's Contributions.xlsx）。本研究采用的数据处理策略可用于评估各特定变量对目标TF-OE菌株所引发的响应变异（包括菌体生长情况与重组蛋白产量）的贡献程度。该评估结果以因子贡献表格形式呈现，表格中通过颜色编码以及采用+1或-1的编码体系标注变量的主导水平，并给出该变量对响应指标的贡献百分比。