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Fig. 3 | BMC Bioinformatics

Fig. 3

From: GECO: gene expression clustering optimization app for non-linear data visualization of patterns

Fig. 3

Investigation of intestinal stem genes using GECO. UMAP generated plot of colon crypt cell types with the following settings: row normalization, removal of zeros, number of neighbors = 35, minimum distance = 0.5, distance metric = Manhattan. Data points (genes) colored by a type, b average expression of assigned type, c stem expression, d stem enrichment, e stem enrichment with 500 (normalized counts) minimum expression level with box showing zoomed in region displayed in f. f Zoomed in region with stem enrichment coloring and a 1.5-fold cutoff. Highlighted in red circles are 27 genes that were previously identified as being statistically differentially expressed and enriched in stem cells in this dataset [23]. Previously published bulk RNA-seq of colon crypt cell types [23] was used to generate UMAP clustering and this dataset (.csv file) is available in Additional file 4

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