Additional file 1: of Web-TCGA: an online platform for integrated analysis of molecular cancer data sets

The supplemental material includes additional examples and an introduction to the Web-TCGA user interface. (DOCX 1522 kb

Additional file 16: of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

Venn diagram of differentially expressed genes (CONV-R versus GF) that also contain DMPs within a 5-kb window. (PDF 377 kb

Additional file 6: of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

Gene ontology (GO) analysis of the microbially regulated genes from each developmental stage. (XLSX 39 kb

Additional file 5: of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

MA transcriptome plot for CONV-R versus GF comparison. Every dot represents one transcript. The x-axis denotes the mean expression value and the y-axis denotes the log2 fold change of CONV-R versus GF. Red dots indicate statistically significant transcripts (CONV-R versus GF, adjusted p value < 0.05). The ceiling/floor of two on log2 fold change (y-axis) is set because of better visualization. (PDF 632 kb

Additional file 10: of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

Gene ontology (GO) analysis of the co-expressed genes in different selected groups from Fig. 3. (XLSX 53 kb

Additional file 2: of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

R code used for the integrated analysis shown in Fig. 5a. (R 1 kb

Additional file 9: of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

Heatmap of developmentally regulated genes (n = 553 genes). (PDF 818 kb

Additional file 15: of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

Heatmap of methylation levels for developmentally related methylation sites. (PDF 658 kb

Additional file 4: of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

Gene expression data of small intestinal epithelial cells from germ-free (GF) and conventionally raised (CONV-R) mice at the three developmental stages W1, W4, and W12/16 determined by RNA sequencing. (XLSX 9442 kb

Additional file 12: of Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

Genomic location of DMPs (CONV-R versus GF) in the three developmental stages. (PDF 384 kb