Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2022 Jun 20;54(7):985–995. doi: 10.1038/s41588-022-01088-x

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Extended Data Fig. 6 — (a) Upper 8 panels: UMAP projection of normal colon epithelial cells colored by scATAC gene activity scores of the epithelial marker genes RETNLB (immature goblet), MUC2 (goblet), FEV (enteroendocrine), RAB6B (enterocyte), SOX9 (stem), BEST4 (Best4+ enterocyte), LGR5 (stem), and ASCL2 (stem). Lower 4 panels: UMAP projection of normal colon epithelial cells colored by expression of marker genes EPCAM (general epithelial), SMOC2 (stem), BEST4, and MUC2. (b) Violin and boxplot representation of gene expression of stem marker genes by epithelial cell type. Asterisks indicate that gene expression is significantly upregulated when compared to all other cell types. Boxplots represent the median, 25th percentile, and 75th percentile of the data and whiskers represent the highest and lowest values within 1.5 times the interquartile range of the boxplots. (c) Labeling of scATAC-seq epithelial cells by nearest snRNA-seq cells following integration of the datasets with CCA. (d) Confusion matrix comparing annotation of scATAC cells using marker genes and labeling of scATAC cells with the nearest snRNA-seq cell following integration of scATAC and snRNA-seq datasets. (e) UMAP representation of snRNA-seq epithelial cells colored by disease state. (f) Results of computing the continuum on plasma cells and TA2 cells using the same method performed for stem cells. (g) Log₂FC in expression of ASCL2, HNF4A, and GPX2 in stem-like cells from each sample relative to stem-like cells in unaffected samples plotted against the malignancy continuum defined in 4D. Samples are colored based on the patient the sample was collected from. (H) Log₂FC in expression of NR3C2, NORAD, SLC4A4, LRIG3, NR5A2, and RPL13 as a function of malignancy continuum. Samples are colored based on if they are derived from polyps or CRCs. (i) Relationship between the malignancy continuum and percent of sample with any degree of dysplasia as determined by microscopic pathology. Samples are colored based on gross classification as a polyp (purple) or unaffected (green) tissue. Note that some samples classified as unaffected had dysplasia while some samples classified as polyps did not have dysplasia. (i) Relationship between the malignancy continuums defined from the scATAC and snRNA-seq datasets. Samples are colored based on gross classification as unaffected, polyp, or CRC. (k) Enrichment of gene ontology terms in clusters of differential RNA genes in Fig. 4.