Shiny App for scRNA Analysis of L. variegatus and H. erythrogramma

Comparative Gene Expression in L. variegatus and H. erythrogramma

Welcome to our shiny app created to open our single-cell data to the world. This tab allows comparison of gene expression and cell identities between two sea urchin species with distinct developmental strategies, as described in Massri et al, 2021, Development , McDonald et al, 2024, Development and in Miranda et al, 2026, Development .

Lytechinus variegatus (indirect developer) forms a self-feeding pluteus larva with a complex skeleton, while Heliocidaris erythrogramma (direct developer) produces a non-feeding larva with accelerated development without a mouth or a skeleton. Single-cell RNA sequencing datasets cover key embryonic stages (e.g. blastula, gastrula, larva) and reveal cell clusters such as primary mesenchyme cells (PMCs), pigment cells, blastocoelar cells and others.

Instructions:
Please wait until the shiny app is fully loaded, you will see the default gene (i.e. P19) depicted below.

Then, scroll down to look into the first result and familiarize yourself with the layout.

Next, select a cell identity category (e.g. seurat_clusters, stage, or celltype), and one gene for each species to visualize cell distributions (UMAP), gene expression patterns (Feature Plots), and expression levels (Violin Plots).

Notice: No part of this document may be reproduced, distributed, or transmitted in any form or by any means, including photocopying, recording, or other electronic or mechanical methods, without the prior written permission of the author, except in the case of brief quotations embodied in critical reviews and certain other noncommercial uses permitted by copyright law. If you use any figure created using this app, please site this URL and the published articles mentioned before.

Contact: For any questions, input or issues, please contact alejo.berrio@duke.edu

Cell Identity (by cluster, cell type, or time series):

Select a category to group cells (e.g., clusters, cell types, or developmental stages) for visualization.

Choose one gene for L. variegatus:

Select a gene to visualize its expression (e.g. P19 for skeletogenesis).

Choose one gene for H. erythrogramma:

Select a gene to visualize its expression (e.g. P19 for skeletogenesis).

UMAP Plots: Cell Identity Distribution

These UMAP plots display cell distributions based on the selected cell identity category, highlighting differences in cell clustering between L. variegatus and H. erythrogramma .

L. variegatus

H. erythrogramma

Feature Plots: Gene Expression Patterns

These Feature Plots show the expression level of the selected gene in each species, with color intensity indicating expression strength (low to high).

L. variegatus

H. erythrogramma

Violin Plots: Gene Expression Levels

These Violin Plots display the distribution of expression levels for the selected gene across cell identity groups, revealing quantitative differences between L. variegatus and H. erythrogramma .

L. variegatus

H. erythrogramma

Gene Coexpression Analysis in L. variegatus and H. erythrogramma

Instructions:
Select two genes for each species to analyze coexpression patterns. The top plots show UMAP visualizations of individual gene expression. The bottom plots display coexpression, with cells colored by expression levels: gray (no expression), light green/orange (low coexpression), or dark green/firebrick (high coexpression). Metrics below summarize total cells, cells with low or high coexpression, and cells expressing only one gene.

Select Gene 1 in L. variegatus:

Select the first gene for coexpression analysis.

Select Gene 1 in H. erythrogramma:

Select the first gene for coexpression analysis.

Select Gene 2 in L. variegatus:

Select the second gene for coexpression analysis.

Select Gene 2 in H. erythrogramma:

Select the second gene for coexpression analysis.

Individual Gene Expression

L. variegatus Gene 1

H. erythrogramma Gene 1

L. variegatus Gene 2

H. erythrogramma Gene 2

Double Coexpression

L. variegatus

H. erythrogramma

Double Coexpression Metrics

L. variegatus Metrics

H. erythrogramma Metrics

Triple Gene Coexpression Analysis in L. variegatus and H. erythrogramma

Instructions:
Select three genes for each species to analyze triple coexpression patterns. The top three plot pairs show UMAP visualizations of individual gene expression. The bottom plots display triple coexpression, with cells colored by expression: gray (no expression) or dark green/firebrick (all three genes expressed). Metrics below summarize total cells and cells coexpressing all three genes.

Select Gene 1 in L. variegatus:

Select the first gene for coexpression analysis.

Select Gene 1 in H. erythrogramma:

Select the first gene for coexpression analysis.

Select Gene 2 in L. variegatus:

Select the second gene for coexpression analysis.

Select Gene 2 in H. erythrogramma:

Select the second gene for coexpression analysis.

Select Gene 3 in L. variegatus:

Select the third gene for coexpression analysis.

Select Gene 3 in H. erythrogramma:

Select the third gene for coexpression analysis.

Individual Gene Expression

L. variegatus Gene 1

H. erythrogramma Gene 1

L. variegatus Gene 2

H. erythrogramma Gene 2

L. variegatus Gene 3

H. erythrogramma Gene 3

Triple Coexpression

L. variegatus

H. erythrogramma

Coexpression Metrics

L. variegatus Metrics

H. erythrogramma Metrics

Gene Expression in L. variegatus & H. erythrogramma

Instructions: Select a clustering category and genes to view expression patterns. Dot plots show average expression across clusters, with dot size indicating the percentage of cells expressing each gene and color showing expression level.

Clustering Category:

Select a category to group cells (e.g., seurat_clusters, cell type, stage).

Genes for L. variegatus:

Choose up to 10 genes to visualize expression patterns.

Genes for H. erythrogramma:

Dot Plots

Dot size shows the percentage of cells expressing each gene; color intensity reflects average expression.

L. variegatus

H. erythrogramma

Differentially Expressed Genes and Sequence Search in L. variegatus

Instructions:
Select a gene to analyze its differential expression and sequence in Lytechinus variegatus . View protein and coding sequences, submit to AlphaFold or forge.evolutionaryscale.ai, or perform a BLAST search. Tables below display differentially expressed genes (DEGs) by cluster and cell type.

Choose one gene for L. variegatus:

Select a gene to analyze its sequence and differential expression.

Differentially Expressed Genes and Sequence Search in H. erythrogramma

Instructions:
Select a gene to analyze its differential expression and sequence in Heliocidaris erythrogramma . View protein and coding sequences, submit to AlphaFold or forge.evolutionaryscale.ai, or perform a BLAST search. Tables below display differentially expressed genes (DEGs) by cluster and cell type.

Choose one gene for H. erythrogramma:

Select a gene to analyze its sequence and differential expression.

WOT Trajectory Analysis in L. variegatus

Instructions:
Select multiple genes and a cell type to visualize gene expression trajectories in Lytechinus variegatus using Waddington-OT (WOT) analysis.
Click 'Add Plot' to generate a plot for the selected genes and cell type.
Plots are displayed below, showing expression trends over time or developmental stages.

WOT Trajectory Analysis in H. erythrogramma

Instructions:
Select multiple genes and a cell type to visualize gene expression trajectories in Heliocidaris erythrogramma using Waddington-OT (WOT) analysis.
Click 'Add Plot' to generate a plot for the selected genes and cell type.
Plots are displayed below, showing expression trends over time or developmental stages.