This web application allows users to browse the t-SNE-transformed microarray data from the above paper.
The dataset is comprised of genomic expression data obtained using mouse 430A genome arrays (Affymetrix). Expression data were obtained from four replicates per sample of early passage retinal progenitor cells (RPCs), whole postnatal day 1 and day 5 mouse retinas, and FACS derived Rho-eGFP positive and negative cells from postnatal day 5 Rho-eGFP retinas. Positive Rho-eGFP cells are developing rod photoreceptors, Rho-eGFP negative cells represent the remaining non-rod portion of the neural retina.
Inputting the Entrez Gene name of your gene of interest (e.g. Rho for rhodopsin) will show a region of the t-SNE plot centered on that gene. The t-SNE plot preserves both local and global structure from the high-dimensional microarray data during the conversion to a 2-D plot, and so the nearest neighbours to your gene of interest will be those genes whose normalized expression patterns are very similar across the different conditions studied. If multiple probes target your gene of interest, one plot will be generated per probe.
We hope that this web app will be useful in identifying clusters of co-regulated genes, or genes implicated in the same developmental processes.Please input name of gene to plot: