Gene Expression Data from a Genetically Diverse Mouse Lung Cohort Used to Construct Ptpn14 Co-expression Networks

This dataset contains whole-transcriptome normalized Affymetrix Mouse Gene 1.1 ST microarray expression data generated from lung tissue collected from 69 genetically diverse mice derived from an inter-species backcross between Mus musculus (FVB/N) and Mus spretus (SPRET/Ei). The diversity panel was designed to maximize naturally occurring genetic and transcriptional variation and was used to investigate molecular pathways associated with endothelial homeostasis and pulmonary vascular biology. This dataset is published both to reproduce figures found in Mamai et al (see complete reference below) and to serve as a data-mining resource to investigate co-expression networks in lung tissue of genes of interest. The dataset was used to generate a Ptpn14-centered gene co-expression network. Spearman correlations were calculated between Ptpn14 expression and all other genes across the cohort. The 150 genes most strongly correlated with Ptpn14 expression were selected to define the Ptpn14 metagene. Pairwise correlations among these genes were subsequently used for hierarchical clustering, network construction, and Gene Ontology enrichment analyses. These analyses identified enrichment for angiogenesis, lymphangiogenesis, cardiovascular development, TGF-β/BMP signaling, endothelial biology, and related processes, leading to the hypothesis that PTPN14 functions as a regulator of endothelial BMP/SMAD signaling. The data deposited here represent the normalized expression values used for all correlation, network, clustering, and functional enrichment analyses presented in the manuscript. File 1: expr.txt This file contains normalized Affymetrix Mouse Gene 1.1 ST microarray expression values for all measured probes across 69 mouse lung samples. Rows correspond to microarray probe sets and columns correspond to individual biological samples. Values represent normalized expression intensities used for downstream co-expression and network analyses. File 2: sample_attributes.txt This file contains metadata describing each mouse lung sample included in the expression matrix. File 3: gene_attributes_MoGene-1_1-st-v1.na30.txt This file provides annotation information for the Affymetrix Mouse Gene 1.1 ST microarray platform. File 4: Ptpn14_network_zenodo.R This R script reproduces the transcriptomic analyses described in Figure 1 and related supplementary analyses. The pipeline imports normalized mouse lung microarray expression data, sample metadata, and probe annotations; constructs a Ptpn14-centered metagene using genome-wide Spearman correlation analysis; generates gene-gene co-expression networks and hierarchical clustering heatmaps; performs Gene Ontology enrichment analyses of network-derived gene modules using topGO; and produces associated figures and output tables. Original publication: Mamai, O. et al, ..., Akhurst, R. PTPN14 stabilizes nuclear SMAD4 to promote endothelial integrity and suppress arteriovenous malformations (2026). in revision.