DOI: 10.5061/dryad.5fb633t
title: Data from: The architecture of an empirical genotype-phenotype map

description: Recent advances in high-throughput technologies are bringing the study of
 empirical genotype-phenotype (GP) maps to the fore. Here, we use data from
 protein binding microarrays to study an empirical GP map of transcription
 factor (TF) binding preferences. In this map, each genotype is a DNA
 sequence. The phenotype of this DNA sequence is its ability to bind one or
 more TFs. We study this GP map using genotype networks, in which nodes
 represent genotypes with the same phenotype, and edges connect nodes if
 their genotypes differ by a single small mutation. We describe the
 structure and arrangement of genotype networks within the space of all
 possible binding sites for 525 TFs from three eukaryotic species
 encompassing three kingdoms of life (animal, plant, and fungi). We thus
 provide a high-resolution depiction of the architecture of an empirical GP
 map. Among a number of findings, we show that these genotype networks are
 “small-world” and assortative, and that they ubiquitously overlap and
 interface with one another. We also use polymorphism data from Arabidopsis
 thaliana to show how genotype network structure influences the evolution
 of TF binding sites in vivo. We discuss our findings in the context of
 regulatory evolution.
description: The architecture of an
 empirical genotype-phenotype mapThis DRYAD package
 contains files from: Aguilar-Rodríguez, J., Peel, L., Stella, M., Wagner,
 A., and Payne, J. L. The architecture of an empirical genotype-phenotype
 map. This package contains the network files in GML format for the
 genotype space of transcription factor (TF) binding sites
 ('genotype_space.gml'), 525 genotype networks of TF binding
 sites, and 66 genotype networks of DNA binding domains. The genotype
 networks of TF binding sites are classified in three directories according
 to their species provenance ('Arabidopsis_thaliana',
 'Mus_musculus,' and 'Neurospora_crassa'). Each network
 file is named with the TF name. More information about these networks can
 be found in Table S1. The genotype networks of DNA binding domains are
 within a 'domains' sub-folder that can be found inside each of
 the three species folders. Each file is named with the DNA binding domain
 class. Each network file has the following vertex attributes: - id: vertex
 identification number. - sequence: the nucleotide sequence of the binding
 site. - reversecomplement: the reverse complement of 'sequence.'
 Genotype network of TF binding sites have the following additional vertex
 attributes: - Escore: the enrichment score in protein binding microarrays
 of the sequence. - PartitionSBM: Information about the stochastic block
 model partition group where the vertex is found: '0',
 '1', or 'None'. 'None' is for vertices not
 found in the dominant genotype network. - PartitionBA: Information about
 the binding affinity partition group where the vertex is found:
 '0', '1', or 'None'. 'None' is for
 vertices not found in the dominant genotype network. For questions
 regarding these data, contact Joshua Payne at joshua.payne@env.ethz.ch or
 Andreas Wagner at andreas.wagner@ieu.uzh.ch.dryad.zip