Fig 1.
IRIS-EDA integrated functions.
Comparison of IRIS-EDA and six other DGE analyses and visualization tools regarding available features, integrated tools, visualizations, and analyses.
Fig 2.
(A) Interactive correlation heatmap generated from single-cell gene expression data; (B) Scatterplot generated by selected a cell in the interactive correlation heatmap; (C) Sample distance matrix showing Euclidean distances between samples, along with hierarchical clustering.
Fig 3.
Principal component analysis, multidimensional scaling, and t-distributed Stochastic Neighbor Embedding.
(A) PCA plot showing the first two principal components; (B) MDS plot showing the first two MDS coordinates; and (C) t-SNE plot showing the first two t-SNE coordinates.
Fig 4.
(A) Sample dendrogram and color bar representing optimized identified clusters for the WGCNA method of clustering on the scRNA-Seq example data. The dendrogram shows the 2- and 4-cell samples clustering together, with the Late Blastocysts forming a unique cluster. (B) The first three biclusters were generated using QUBIC on the IRIS-EDA server. The first two biclusters (69 and 49 genes) show the grouping of Oocyte, Zygote, and 2- and 4-cell samples and Oocytes, Zygote, and 2-, 4-, and 8-cell samples, respectively. The third bicluster (52 genes) separates the Late Blastocysts from the other samples. These three biclusters demonstrate the expression similarity between the Oocyte, Zygote, and multi-cell samples relative to the Late Blastocyst samples over numerous gene sets.
Fig 5.
An overview of the number of DEGs determined using DESeq2 on the IRIS-EDA server. Cell-type Seven is compared against the other six cell types based on the number of up- and down-regulated genes. The Seven and Four comparison shows the highest number of DEGs of all comparisons, followed by Seven and Five comparison. The other four comparisons show similar numbers of DEGs, with all comparisons showing at least as many down-regulated genes as up.
Fig 6.
(A) MA plot for the Seven and Four cluster comparison with particular genes highlighted in the results table and corresponding location in the figure; (B) Volcano plot for the Seven and Four cluster comparison with particular genes highlighted in the results table and corresponding location in the figure; (C) The searchable, interactive table corresponding to both the MA plot and Volcano plot, showing results of the DGE analysis from the user-selected DGE tool.