The Inflammatory Bowel Disease Transcriptome and Metatranscriptome Meta-Analysis (IBD TaMMA) framework

Abstract

Inflammatory bowel disease (IBD) is a class of chronic disorders whose etiogenesis is still unknown. Despite the high number of IBD-related omics studies, the RNA-sequencing data produced results that are hard to compare because of the experimental variability and different data analysis approaches. We here introduce the IBD Transcriptome and Metatranscriptome Meta-Analysis (TaMMA) framework, a comprehensive survey of publicly available IBD RNA-sequencing datasets. IBD TaMMA is an open-source platform where scientists can explore simultaneously the freely available IBD-associated transcriptomics and microbial profiles thanks to its interactive interface, resulting in a useful tool to the IBD community.

Fig. 1. IBD TaMMA overview.

a,b, Multidimensional scaling of the human whole transcriptome by UMAP from patients with UC and CD, as well as healthy (control) participants. c, MA plots showing the differential gene expression results, expressed as log₂(fold change) between the indicated comparisons (M) as a function of log₂(average gene expression) (A). Red dots represent genes being differentially expressed with high statistical significance (false discovery rate (FDR) < 1 × 10⁻¹⁰). The number of differentially expressed genes and their trends are indicated in red. d, Box plots showing differential tumor necrosis factor (TNF) normalized expression among UC and CD, as well as healthy ileum, colon and rectum. e,f, Box plots showing differential calprotectin (S100A8 and S100A9) (e) and S100A12 (f) encoding gene normalized expression among UC and CD, as well as healthy (control) ileum, colon and rectum. g, Bar plots showing the relative abundance of the indicated bacterial phyla in stools, ileum and colon from patients with UC and CD, and healthy participants (control). h–j, Violin plots showing Shannon diversity indices among CD, healthy (control) and UC in stools (h), colon (i) and ileum (j). k, Box plots showing relative Caudovirales order abundance in colon, ileum and stools from healthy participants (control) and patients with CD, and UC. All box plots represent the sample distribution with median, minimum, maximum, first and third quartiles. An interquartile range of 1.5 is used to define outliers. Statistical differences between groups were calculated by analysis of variance with Tukey’s honestly significant difference post hoc test for multiple comparisons. Differences with adjusted P ≤ 0.05 were considered significant. For complete statistics, see Supplementary Table 2. Source data