Mouse HSC Atlas

Use

Genes:

The cluster analysis allows you to look at the expression of gene and GO terms in labled clusters If you have a gene you are interested in you can see the expression of it in the gene on the UMAP You can also look at the the differential expresssion summary statistics using the table exploration An important statistic to look at is auroc, a value >.9 tells you that this gene is a very good marker for the given cluster An AUROC=.5 means that the gene does no better than random. Statistics like fold_change and fold_change_detection serve as the signal-to-noise ratio or effect size.

Functional Annotation

For looking at functional annotations, the AUROC of the GO term selected will appear as a Star on the violin plots showing the distributino for all GO terms The AUROC is showing how well a given cluster can be identified based on expression of the genes in that GO term, using MetaNeighbor The Dotplot shows the normalized (across datasets) expression of the genes that are members of the GO term selected.

Use

Genes:

The cluster analysis allows you to look at the expression of gene and GO terms in labled clusters If you have a gene you are interested in you can see the expression of it in the gene on the UMAP You can also look at the the differential expresssion summary statistics using the table exploration An important statistic to look at is auroc, a value >.9 tells you that this gene is a very good marker for the given cluster An AUROC=.5 means that the gene does no better than random. Statistics like fold_change and fold_change_detection serve as the signal-to-noise ratio or effect size.

Functional Annotation

For looking at functional annotations, the AUROC of the GO term selected will appear as a Star on the violin plots showing the distributino for all GO terms The AUROC is showing how well a given cluster can be identified based on expression of the genes in that GO term, using MetaNeighbor The Dotplot shows the normalized (across datasets) expression of the genes that are members of the GO term selected.

Use:

The left plots show each cell, within each dataset, colored by the pseudotime. On the right side you can select a gene To see the expression of it in each individual dataset select a gene from the dropdown menu You can search through the table on the bottom left for your gene of interest to see how well is associated with pseudotime fc is the fold change (signal to noise ratio/ effect size) p_adj is the P value for testing whether a gene is associated with psuedotime ordering, irrespective of lineage while p_adj_eryth and p_adj_mono are p values from testing association with pseudotime + lineage

Use:

Here we have all of the cells from the 3 species we used, Mouse, Human, and Zebrafish. You can select a gene symbol from one of the species and it will display the expression of that gene and 1:1 orthologs if available for the other two species.