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

. 2019 Aug 20;10:3407. doi: 10.1038/s41467-019-11276-9

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

© The Author(s) 2019

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

Fig. 4 — Multi-omics unsupervised analysis of lung neuroendocrine tumours. a Multi-omics factor analysis (MOFA) of transcriptomes and methylomes restricted to LNET samples (pulmonary carcinoids). Design follows that of Fig. 1a; filled coloured shapes represent the three molecular clusters (Carcinoid A1, A2, and B) identified by consensus clustering. The position of samples harbouring mutations significantly associated with a latent factor (ANOVA q-value < 0.05) are highlighted by coloured triangles on the axes. b Upper panel: boxplots of the proportion of dendritic cells in the different molecular clusters (Carcinoid A1, A2, and B) and the supra-carcinoids, estimated from transcriptomic data using quanTIseq (Methods). The permutation test q-value range is given above each comparison: q-value < 0.001 is annotated by three stars. Lower panel: boxplots of the expression levels of LAMP3 (CDLAMP) and CD1A. c DLL3 and CD1A immunohistochemistry of two typical carcinoids: case 6 (DLL3+ and CD1A+), and case 10 (DLL3- and CD1A-). Upper panels: Hematoxylin & Eosin Saffron (H&E) stain. Middle panels: staining with CD1 rabbit monoclonal antibody (cl EP3622; VENTANA), where arrows show positive stainings. Lower panels: Staining with DLL3 assay (SP347; VENTANA). d Expression levels of genes from the retinoid and xenobiotic metabolism pathway—the most significantly associated with MOFA latent factor 1—in the different molecular clusters. Upper panel: schematic representation of the phases of the pathway. Lower panel: boxplot of expression levels of CYP2C8 and CYP2C19 (both from the CYP2C gene cluster on chromosome 10), UGT2A3, and the total expression of UGT2B genes (from the UGT2 gene cluster on chromosome 4), expressed in fragments per kilobase million (FPKM) units. In all panels, boxplot centre line represents the median and box bounds represent the inter-quartile range (IQR). The whiskers span a 1.5-fold IQR or the highest and lowest observation values if they extend no further than the 1.5-fold IQR. Data necessary to reproduce the figure are provided in Supplementary Data 1, 4, 9, and in the European Genome-phenome Archive