Supplementary Data for "Ultimate paths of least resistance: Intrinsically disordered proteins as developmental resets in regulatory networks"

DATA FILES OVERVIEW This repository features the data for the paper "Ultimate paths of least resistance: Intrinsically disordered proteins as developmental resets in regulatory networks", which can be found TBD. The manuscript examines how IDP links act as developmental resets in development and evolution This data repository consists of 33 data files described below: Data files and variables: 1. Supplementary Data 1a.txt: Morphology and protein expression data for n=2,792362 pre-condensation mesenchymal cells from which the main dataset is selected. TF - IHC protein assay Name - EmbryoID Stage- Developmental Stage (HH) Section - Slide section Run - IHC run GridID - Image Grid ID CellID -- Cell ID Area -- cell Area X,Y -- coordinates of cell centroid Perim -- Cell perimeter BX,BY -- the coordinates of the upper left corner of the rectangle enclodsing cell Width,Height - dimensions of rectangle enclosing cell Major,Minor -- major and minor axes of epipsoid enclosing cell Angle -- angle between elipsoid axes Circ - circularity Feret - feret length FeretX,FeretY - feret coordinates FeretAngle - feret angle (major axis) MinFeret -- feret angle (minor axis) AR - aspect ratio Round - roundness Solidity-solidity 2. Supplementary Data 1b.xlsx: Summary of cell morphology and protein expression for n =5,886 grid boxes with pre-condensation mesenchymal cells and associated data on developmental stage, population, IHC run and section ID GridID GridID (10x10) TF Protein Name EmbryoID Stage HH Developmental Stage Section Section ID Run Run ID Exp For all: UMES-undifferentiated mesenchyme Area_Mean Mean values for all cells in the grid box Perim_Mean Mean values for all cells in the grid box Width_Mean Mean values for all cells in the grid box Height_Mean Mean values for all cells in the grid box Major_Mean Mean values for all cells in the grid box Minor_Mean Mean values for all cells in the grid box Angle_Mean Mean values for all cells in the grid box Circ_Mean Mean values for all cells in the grid box Feret_Mean Mean values for all cells in the grid box FeretAngle_Mean Mean values for all cells in the grid box MinFeret_Mean Mean values for all cells in the grid box AR_Mean Mean values for all cells in the grid box Shape_Mean Mean values for all cells in the grid box Round_Mean Mean values for all cells in the grid box Solidity_Mean Mean values for all cells in the grid box Area_Var Variance for all cells in the grid box Perim_Var Variance for all cells in the grid box Width_Var Variance for all cells in the grid box Height_Var Variance for all cells in the grid box Major_Var Variance for all cells in the grid box Minor_Var Variance for all cells in the grid box Angle_Var Variance for all cells in the grid box Circ_Var Variance for all cells in the grid box Feret_Var Variance for all cells in the grid box FeretAngle_Var Variance for all cells in the grid box MinFeret_Var Variance for all cells in the grid box AR_Var Variance for all cells in the grid box Shape_Var Variance for all cells in the grid box Round_Var Variance for all cells in the grid box Solidity_Var Variance for all cells in the grid box Area_CV Coefficient of variation for all cells in the grid box Perim_CV Coefficient of variation for all cells in the grid box Width_CV Coefficient of variation for all cells in the grid box Height_CV Coefficient of variation for all cells in the grid box Major_CV Coefficient of variation for all cells in the grid box Minor_CV Coefficient of variation for all cells in the grid box Angle_CV Coefficient of variation for all cells in the grid box Circ_CV Coefficient of variation for all cells in the grid box Feret_CV Coefficient of variation for all cells in the grid box FeretAngle_CV Coefficient of variation for all cells in the grid box MinFeret_CV Coefficient of variation for all cells in the grid box AR_CV Coefficient of variation for all cells in the grid box Shape_CV Coefficient of variation for all cells in the grid box Round_CV Coefficient of variation for all cells in the grid box Solidity_CV Coefficient of variation for all cells in the grid box Area_StdErr StandardError for all cells in the grid box Perim_StdErr StandardError for all cells in the grid box Width_StdErr StandardError for all cells in the grid box Height_StdErr StandardError for all cells in the grid box Major_StdErr StandardError for all cells in the grid box Minor_StdErr StandardError for all cells in the grid box Angle_StdErr StandardError for all cells in the grid box Circ_StdErr StandardError for all cells in the grid box Feret_StdErr StandardError for all cells in the grid box FeretAngle_StdErr StandardError for all cells in the grid box MinFeret_StdErr StandardError for all cells in the grid box AR_StdErr StandardError for all cells in the grid box Shape_StdErr StandardError for all cells in the grid box Round_StdErr StandardError for all cells in the grid box Solidity_StdErr StandardError for all cells in the grid box Area_StdDev...

数据文件概览
本仓库配套论文《Ultimate paths of least resistance: Intrinsically disordered proteins as developmental resets in regulatory networks》，论文原文待公开（TBD）。该论文探讨了固有无序蛋白（intrinsically disordered proteins, IDP）连接元件如何在发育与演化过程中充当发育重置节点。本数据集仓库共包含33份数据文件，下文将逐一说明：

## 数据文件与变量
1. 补充数据1a.txt：包含n=2,792,362个凝前间质细胞的形态与蛋白表达数据，主数据集即从中筛选得到。各变量说明如下：
- TF：转录因子（Transcription Factor, TF），对应免疫组化（Immunohistochemistry, IHC）蛋白检测结果
- Name：样本名称
- EmbryoID：胚胎编号
- Stage：发育阶段（HH分期）
- Section：玻片切片编号
- Run：免疫组化实验批次
- GridID：图像网格编号
- CellID：细胞编号
- Area：细胞面积
- X,Y：细胞质心坐标
- Perim：细胞周长
- BX,BY：包裹细胞的矩形左上角坐标
- Width,Height：包裹细胞的矩形尺寸（宽、高）
- Major,Minor：包裹细胞的椭圆长、短轴长度
- Angle：椭圆主轴夹角
- Circ：细胞圆度
- Feret：费雷特直径（Feret diameter）
- FeretX,FeretY：费雷特直径端点坐标
- FeretAngle：费雷特直径夹角（对应椭圆主轴）
- MinFeret：最小费雷特直径
- AR：细胞长宽比
- Round：细胞圆整度
- Solidity：细胞固体度（轮廓紧致度）

2. 补充数据1b.xlsx：包含n=5,886个含凝前间质细胞的网格区块的细胞形态与蛋白表达汇总数据，同时附带发育阶段、细胞群、免疫组化实验批次及切片编号相关数据。各变量说明如下：
- GridID：（10×10）网格区块编号
- TF：转录因子（Transcription Factor, TF）
- Protein：蛋白名称
- Name：样本名称
- EmbryoID：胚胎编号
- Stage HH：HH发育分期
- Section：切片编号
- Section ID：切片编号
- Run：实验批次
- Run ID：实验批次编号
- Exp：实验相关信息
- 通用标注：UMES=未分化间质细胞（undifferentiated mesenchyme, UMES）
以下为各类统计量变量：
- Area_Mean：网格区块内所有细胞的面积均值
- Perim_Mean：网格区块内所有细胞的周长均值
- Width_Mean：网格区块内所有细胞的包裹矩形宽度均值
- Height_Mean：网格区块内所有细胞的包裹矩形高度均值
- Major_Mean：网格区块内所有细胞的椭圆长轴均值
- Minor_Mean：网格区块内所有细胞的椭圆短轴均值
- Angle_Mean：网格区块内所有细胞的椭圆主轴夹角均值
- Circ_Mean：网格区块内所有细胞的圆度均值
- Feret_Mean：网格区块内所有细胞的费雷特直径均值
- FeretAngle_Mean：网格区块内所有细胞的费雷特直径夹角均值
- MinFeret_Mean：网格区块内所有细胞的最小费雷特直径均值
- AR_Mean：网格区块内所有细胞的长宽比均值
- Shape_Mean：网格区块内所有细胞的形态均值
- Round_Mean：网格区块内所有细胞的圆整度均值
- Solidity_Mean：网格区块内所有细胞的固体度均值
- Area_Var：网格区块内所有细胞的面积方差
- Perim_Var：网格区块内所有细胞的周长方差
- Width_Var：网格区块内所有细胞的包裹矩形宽度方差
- Height_Var：网格区块内所有细胞的包裹矩形高度方差
- Major_Var：网格区块内所有细胞的椭圆长轴方差
- Minor_Var：网格区块内所有细胞的椭圆短轴方差
- Angle_Var：网格区块内所有细胞的椭圆主轴夹角方差
- Circ_Var：网格区块内所有细胞的圆度方差
- Feret_Var：网格区块内所有细胞的费雷特直径方差
- FeretAngle_Var：网格区块内所有细胞的费雷特直径夹角方差
- MinFeret_Var：网格区块内所有细胞的最小费雷特直径方差
- AR_Var：网格区块内所有细胞的长宽比方差
- Shape_Var：网格区块内所有细胞的形态方差
- Round_Var：网格区块内所有细胞的圆整度方差
- Solidity_Var：网格区块内所有细胞的固体度方差
- Area_CV：变异系数（Coefficient of variation, CV），网格区块内所有细胞的面积变异系数
- Perim_CV：网格区块内所有细胞的周长变异系数
- Width_CV：网格区块内所有细胞的包裹矩形宽度变异系数
- Height_CV：网格区块内所有细胞的包裹矩形高度变异系数
- Major_CV：网格区块内所有细胞的椭圆长轴变异系数
- Minor_CV：网格区块内所有细胞的椭圆短轴变异系数
- Angle_CV：网格区块内所有细胞的椭圆主轴夹角变异系数
- Circ_CV：网格区块内所有细胞的圆度变异系数
- Feret_CV：网格区块内所有细胞的费雷特直径变异系数
- FeretAngle_CV：网格区块内所有细胞的费雷特直径夹角变异系数
- MinFeret_CV：网格区块内所有细胞的最小费雷特直径变异系数
- AR_CV：网格区块内所有细胞的长宽比变异系数
- Shape_CV：网格区块内所有细胞的形态变异系数
- Round_CV：网格区块内所有细胞的圆整度变异系数
- Solidity_CV：网格区块内所有细胞的固体度变异系数
- Area_StdErr：标准误（Standard Error, StdErr），网格区块内所有细胞的面积标准误
- Perim_StdErr：网格区块内所有细胞的周长标准误
- Width_StdErr：网格区块内所有细胞的包裹矩形宽度标准误
- Height_StdErr：网格区块内所有细胞的包裹矩形高度标准误
- Major_StdErr：网格区块内所有细胞的椭圆长轴标准误
- Minor_StdErr：网格区块内所有细胞的椭圆短轴标准误
- Angle_StdErr：网格区块内所有细胞的椭圆主轴夹角标准误
- Circ_StdErr：网格区块内所有细胞的圆度标准误
- Feret_StdErr：网格区块内所有细胞的费雷特直径标准误
- FeretAngle_StdErr：网格区块内所有细胞的费雷特直径夹角标准误
- MinFeret_StdErr：网格区块内所有细胞的最小费雷特直径标准误
- AR_StdErr：网格区块内所有细胞的长宽比标准误
- Shape_StdErr：网格区块内所有细胞的形态标准误
- Round_StdErr：网格区块内所有细胞的圆整度标准误
- Solidity_StdErr：网格区块内所有细胞的固体度标准误
- Area_StdDev：标准差（Standard Deviation, StdDev），网格区块内所有细胞的面积标准差（原文未完整收尾）