DOI: 10.7910/dvn/cdbwdp
title: Supplementary Data for "Ultimate paths of least resistance: Intrinsically disordered proteins as developmental resets in regulatory networks"

description: 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 StandardDeviarion for all cells in the grid box
Perim_StdDev StandardDeviarion for all cells in the grid box
Width_StdDev StandardDeviarion for all cells in the grid box
Height_StdDev StandardDeviarion for all cells in the grid box
Major_StdDev StandardDeviarion for all cells in the grid box
Minor_StdDev StandardDeviarion for all cells in the grid box
Angle_StdDev StandardDeviarion for all cells in the grid box
Circ_StdDev StandardDeviarion for all cells in the grid box
Feret_StdDev StandardDeviarion for all cells in the grid box
FeretAngle_StdDev StandardDeviarion for all cells in the grid box
MinFeret_StdDev StandardDeviarion for all cells in the grid box
AR_StdDev StandardDeviarion for all cells in the grid box
Shape_StdDev StandardDeviarion for all cells in the grid box
Round_StdDev StandardDeviarion for all cells in the grid box
Solidity_StdDev StandardDeviarion for all cells in the grid box
count Cell count
TotCellArea Total area occupied by cells
TotArea Total area of grid box
NestID Nest ID
Pop Population
nStage HH stage group
nPop Region
nExp Normalized expression
CellDens Cell Density

3.Supplementary Data 2 (SupplementaryData2_House_Finch_Consensus_Protein_Seqs.fasta) – Amino acid sequences for all house finch proteins under this study, including a variant of Ihh gene.

4. Supplementary Data 3 (Supplementary Data_3_Bmp4.NCBI_birds.fasta) – Bmp4 amino acid sequences for all sequenced avian species proteomes as of 17 Apr 2024

5. Supplementary Data 4 (SupplementaryData4_Calm1.NCBI_birds.fasta) – Calm1 amino acid sequences for all sequenced avian species proteomes as of 17 Apr 2024

6. Supplementary Data 5 (SupplementaryData5_CALM2.NCBI_birds.fasta) – Calm2 amino acid sequences all sequenced avian species as of 17 Apr 2024

7. Supplementary Data 6 (SupplementaryData6_CTNNB1.NCBI_birds.fasta) – CTNNB1 (β-catenin) amino acid sequences for all sequenced avian species proteomes as of 17 Apr 2024

8. Supplementary Data 7 (SupplementaryData7_Dkk3.NCBI_birds.fasta) – Dkk3 amino acid sequences for all sequenced avian species proteomes as of 17 Apr 2024

9. Supplementary Data 8 (SupplementaryData8_Fgf8.NCBI_birds.fasta) – Fgf8 amino acid sequences for all sequenced avian species proteomes as of 17 Apr 2024

10. Supplementary Data 9 (SupplementaryData9_Ihh.NCBI_birds.fasta) – Ihh amino acid sequences for all sequenced avian species proteomes as of 17 Apr 2024

11. Supplementary Data 10 (SupplementaryData10_TGFB2.NCBI_birds.fasta) – Tgfβ2 amino acid sequences for all sequenced avian species proteomes as of 17 Apr 2024

12. Supplementary Data 11 (SupplementaryData11_Wnt4.NCBI_birds.fasta) – Wnt4 amino acid sequences for all sequenced avian species proteomes as of 17 Apr 2024

13. Supplementary Table S7 (xlsx). Disorder properties, liquid-liquid phase separation propensity, connectivity and binding plasticity of proteins under this study for n=100 avian species
Tax_ID Tax ID number
Genus Genus
Species Species 
PROTEIN Name of protein
SCORE1 Liquid-liquid phase separation score for sequence 1
SCORE2 Liquid-liquid phase separation score for sequence 2
SCORE3 Liquid-liquid phase separation score for sequence 3
SCORE4 Liquid-liquid phase separation score for sequence 4
SCORE5 Liquid-liquid phase separation score for sequence 5
PERC1 Disorder score (percent disordered) for sequence 1
LONG1 Longest disordered region for sequence 1
PERC2 Disorder score (percent disordered) for sequence 2
LONG2 Longest disordered region for sequence 2
PERC3 Disorder score (percent disordered) for sequence 3
LONG3 Longest disordered region for sequence 3
PERC4 Disorder score (percent disordered) for sequence 4
LONG4 Longest disordered region for sequence 4
PERC5 Disorder score (percent disordered) for sequence 5
LONG5 Longest disordered region for sequence 5
NODES Number of nodes
EDGES Number of edges
AVGDEG Average degree
CLUSTER Clustering


14-23. Supplementary Tables S8 for all proteins (9 xlsx tables). Percent identity matrices for Bmp4 (n =120 species), Calm1 (n = 70 species), Calm2 (n = 77 species), CTNNB1 (n = 170 species), Dkk3 (n = 103 species), Fgf8 (n = 122 species), Ihh (n =72 species), Tgfβ2 (n =100 species), and Wnt4 (n = 119 species).

24-33. Supplementary Tables S9 for all proteins (9 xlsx tables). Percent identity matrices for n = 57 species with full sequence data for all nine proteins: Bmp4, Calm1, Calm2, CTNNB1, Dkk3, Fgf8, Ihh, Tgfβ2, and Wnt4.