Bifidobacteria grown on human milk oligosaccharides downregulate the expression of inflammation-related genes in Caco-2 cells

Table 2 Enriched annotation terms with significant changes in Caco-2 cells exposed to B. breve SC95 grown on different carbon sources

GLU vs HMO comparison: cluster annotation of genes downregulated by HMO
Enrichment score	Term¹	Gene count
8.8	GO:0008009 ~ chemokine activity	9
4.2	GO:0005576 ~ extracellular region	19
3.8	GO:0050900 ~ leukocyte migration	5
2.9	GO:0048514 ~ blood vessel morphogenesis	6
2.8	GO:0006915 ~ apoptosis	9
2.7	GO:0051101 ~ regulation of DNA binding	5
2.7	GO:0031328 ~ positive regulation cellular biosynthetic process	10
2.3	GO:0043066 ~ negative regulation of apoptosis	7
2.1	GO:0031349 ~ positive regulation of defense response	4
1.9	GO:0002763 ~ positive regulation myeloid leukocyte differentiation	3
HMO vs LAC comparison: cluster annotation of genes upregulated by HMO
Enrichment score	Term¹	Gene count
9.5	GO:0045449 ~ regulation of transcription	58
4.6	IPR015880:Zinc finger, C2H2-like	24
2.8	IPR012287:Homeodomain-related	10
HMO vs LAC comparison: cluster annotation of genes downregulated by HMO
Enrichment score	Term¹	Gene count
6.4	GO:0008009 ~ chemokine activity	8
5.9	GO:0042981 ~ regulation of apoptosis	21
5.0	GO:0043066 ~ negative regulation of apoptosis	13
4.2	GO:0031328 ~ positive regulation cellular biosynthetic process	18
3.3	IPR004827:Basic-leucine zipper (bZIP) transcription factor	6
3.1	GO:0051272 ~ positive regulation of cell motion	7
3.1	GO:0051674 ~ localization of cell	10
2.7	GO:0005840 ~ ribosome	8
2.7	GO:0051090 ~ regulation of transcription factor activity	6
2.6	GO:0001525 ~ angiogenesis	7
2.4	GO:0010557 ~ positive regulation macromolecule biosynthesis	14

Term¹: Annotation terms with enrichment score ≥1.3, p value (EASE score) ≤0.05 and globally corrected enrichment Benjamini p-value (to control family-wide false discovery rate) ≤0.05 were selected

ISSN: 1471-2180