Open Access Research article

Whole-genome microarray analysis and functional characterization reveal distinct gene expression profiles and patterns in two mouse models of ileal inflammation

Leela Rani Avula1, Dries Knapen24, Roeland Buckinx1, Lucia Vergauwen2, Dirk Adriaensen1, Luc Van Nassauw13 and Jean-Pierre Timmermans1*

Author Affiliations

1 Department of Veterinary Sciences, Laboratory of Cell Biology and Histology, University of Antwerp, Groenenborgerlaan 171, Antwerp, B-2020, Belgium

2 Department of Biology, Laboratory of Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, Antwerp, B-2020, Belgium

3 Faculty of Medicine and Health Sciences, Laboratory of Human Anatomy and Embryology, University of Antwerp, Groenenborgerlaan 171, Antwerp, B-2020, Belgium

4 Department of Veterinary Sciences, Laboratory of Physiology and Biochemistry of Domestic Animals, University of Antwerp, Universiteitsplein 1, Antwerp, B-2610, Belgium

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BMC Genomics 2012, 13:377  doi:10.1186/1471-2164-13-377

Published: 6 August 2012

Additional files

Additional file 1:

Complete list of differentially expressed genes in the S. mansoni-infected ileum. Differentially expressed genes in the S. mansoni-infected ileum are represented with their ID (Agilent probe ID), GB_ACC (gene bank accession), GENE_SYMBOL (gene symbol), GENE_NAME (gene name), log2FC (log2 fold change), p-value and adjusted p-value. Upregulated genes are shown in red; downregulated genes are shown in green; overlapping genes that changed in the same direction as in the TNBS-treated ileum are displayed in bold; overlapping genes that changed in the opposite direction to that of the TNBS-treated ileum are underlined. All genes listed in this file showed significant differential expression (p-value < 0.05, adjusted p-value < 0.1 and log2 fold change > 1 or < −1) relative to controls.

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Additional file 2:

Complete list of differentially expressed genes in the TNBS-treated ileum. Differentially expressed genes in the TNBS-treated ileum are represented with their ID (Agilent probe ID), GB_ACC (gene bank accession), GENE_SYMBOL (gene symbol), GENE_NAME (gene name), log2FC (log2 fold change), p-value and adjusted p-value. Upregulated genes are shown in red; downregulated genes are shown in green; overlapping genes that changed in the same direction as in the S. mansoni-infected ileum are displayed in bold; overlapping genes that changed in the opposite direction to that of the S. mansoni-infected ileum are underlined. All genes listed in this file showed significant differential expression (p-value < 0.05, adjusted p-value < 0.1 and log2 fold change > 1 or < −1) relative to controls.

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Additional file 3:

Complete list of differentially expressed genes that could be annotated with a KEGG pathway term and/or a GO term in the S. mansoni-infected ileum. Differentially expressed genes are listed together with their KEGG and/or GO annotations. GenID (Ensembl ID), Symbol (gene symbol), #GO-Terms Associated (number of GO terms associated), Percent GO-Terms Associated, UID-str (unique Agilent ID), GO Names (names of associated terms). Of the 207 unique genes that were differentially expressed in the S. mansoni-infected ileum, 42 genes could be linked to a KEGG pathway term and 144 genes could be linked to a GO term.

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Additional file 4:

Complete list of differentially expressed genes that could be annotated with a KEGG pathway term and/or a GO term in the TNBS-treated ileum. Differentially expressed genes are listed together with their KEGG and/or GO annotations. GenID (Ensembl ID), Symbol (gene symbol), #GO-Terms Associated (number of GO terms associated), Percent GO-Terms Associated, UID-str (unique Agilent ID), GO Names (names of associated terms). Of the 1417 unique genes that were differentially expressed in the TNBS-treated ileum, 232 genes could be linked to a KEGG pathway term and 1050 genes could be linked to a GO term.

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Additional file 5:

KEGG pathways and GO (biological process) categories that were over-represented in the S. mansoni-infected ileum. KEGG pathways and GO (biological process) categories that were over-represented in the S. mansoni-infected ileum are represented with their MAPP Name (KEGG pathway name), Z score (z-score), AdjustedP (adjusted permutation p-value calculated using the Benjamini-Hochberg method)), gene symbols, AVG-logFC (average log2FC for each enriched term calculated based on associated differential genes) and AVG-adj.P. Val (average adjusted p-value for each enriched term calculated based on associated differential genes, GOID (Gene ontology ID), GO Name (name of GO category). Threshold criteria for over-representation: z-score > 2, at least three genes from the input list in the enriched category, an adjusted permutation p-value ≤ 0.35. Top-scoring functional category groups for KEGG pathway and GO categories are shown in colour as follows: Cytokine-cytokine receptor interaction pathway and immune, defense response category group. Intestinal immune network for IgA production pathway and immune response category group. Complement and coagulation cascades pathway and protein activation cascade category group. ECM-receptor interaction pathway and cell adhesion category group. Fc epsilon RI signaling pathway and acute inflammatory response category. (Note: Although immune response category is common to more than one category group, it is coloured only once).

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Additional file 6:

KEGG pathways and GO (biological process) categories that were over-represented in the TNBS-treated ileum. KEGG pathways and GO (biological process) categories that were over-represented in the TNBS-treated ileum are represented with their MAPP Name (KEGG pathway name), Z score (z-score), AdjustedP (adjusted permutation p-value calculated using the Benjamini-Hochberg method)), gene symbols, AVG-logFC (average log2FC for each enriched term calculated based on associated differential genes) and AVG-adj.P. Val (average adjusted p-value for each enriched term calculated based on associated differential genes, GOID (Gene ontology ID), GO Name (name of GO category). Threshold criteria for over-representation: z-score > 2, at least three genes from the input list in the enriched category, an adjusted permutation p-value ≤ 0.35. Top-scoring functional category groups for KEGG pathway and GO categories are shown in colour as follows: Cytokine-cytokine receptor interaction pathway and inflammatory, immune response category group. Intestinal immune network for IgA production pathway and immune response category group. Antigen processing and presentation pathway and antigen processing and presentation category group. Cell adhesion molecules pathway and cell adhesion category group. Toll-like receptor signaling pathway and immune and inflammatory response category group. ABC transporters pathway and response to chemical stimulus category group. (Note: Although immune, inflammatory response categories are common to more than one category group, they are coloured only once).

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Additional file 7: Table S1:

High scoring functional category groups in the S. mansoni-infected ileum.

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Additional file 8: Table S2:

High scoring functional category groups in the TNBS-treated ileum.

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