Open Access Research article

Expression QTL mapping in regulatory and helper T cells from the BXD family of strains reveals novel cell-specific genes, gene-gene interactions and candidate genes for auto-immune disease

Rudi Alberts1, Hairong Chen1, Claudia Pommerenke1, August B Smit3, Sabine Spijker3, Robert W Williams4, Robert Geffers5, Dunja Bruder2 and Klaus Schughart1*

Author Affiliations

1 Department of Infection Genetics, Helmholtz Centre for Infection Research & University of Veterinary Medicine Hannover, Inhoffenstr. 7, D-38124 Braunschweig, Germany

2 Research Group Immune Regulation, Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany and Research Group Infection Immunology, Department of Medical Microbiology, Otto-von-Guericke-University Magdeburg, Leipziger Straße 44, D-39120 Magdeburg, Germany

3 Department of Molecular and Cellular Neurobiology, Center for Neuroscience and Cognitive Research, Neuroscience Campus Amsterdam, VU University, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands

4 Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, USA

5 Research Group Genome Analytics, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany

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BMC Genomics 2011, 12:610  doi:10.1186/1471-2164-12-610

Published: 19 December 2011

Additional files

Additional file 1:

Table S1. Treg specific genes. The table lists genes that exhibited a differential expression in Treg compared to Th cells. Probeset: probeset ID of microarray hybridization probe, logFC: fold changes of expression level in Treg versus Th as difference of log2 values, pFDR: FDR-corrected p-value, Treg: expression level in Treg cells as log2 value, Th: expression level in Th cells as log2 value.

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Additional file 2:

Table S2 Th specific genes. The table lists genes that exhibited a differential expression in Th compared to Treg cells. Probeset: probeset ID of microarray hybridization probe, logFC: fold changes of expression level in Treg versus Th as difference of log2 values (a negative value represents higher expression in Th compared to Treg cells), pFDR: FDR-corrected p-value, tr: expression level in Treg cells as log2 value, th: expression level in Th cells as log2 value.

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Additional file 3:

Table S3 Genes with known functions in Treg cells. The table lists genes that have been described in the literature to exhibit a functional role in Treg cells. Table S4: Treg functional genes with a higher expression in Tregs. The table lists probesets of genes that were expressed at a higher level in Treg compared to Th cells and which exhibit known Treg functions. Table S5. Genes regulated by cis-eQTL in Treg cells. The table lists probesets from genes that exhibited a cis-eQTL larger or equal to an LRS of 18 in Treg but not in Th cells and which were expressed at least 2-fold higher in Treg cells. Table S6. Genes regulated by cis-eQTL (LRS > = 18) in Th. The table lists probesets from genes that exhibited a cis-eQTL larger or equal to an LRS of 18 in Th but not in Treg cells and which were expressed at least 2-fold higher in Th cells. Table S7. Treg specific genes regulated by trans-eQTL in Treg cells. The table lists probesets from genes that exhibited a trans-eQTL larger or equal to an LRS of 18 in Treg but not in Th cells and which were expressed at least 2-fold higher in Treg cells. Table S8. Th specific genes regulated by trans-eQTL in Th cells. The table lists probesets from genes that exhibited a trans-eQTL larger or equal to an LRS of 18 in Th but not in Treg cells and which were expressed at least 2-fold higher in Th cells. Table S9. Treg functional genes regulated and highly expressed in Treg cells. The table lists probesets of differentially expressed genes in Treg cells with a known Treg function, a high expression signal in Tregs (expression signal > 8) and which are regulated by a trans-eQTL with an LRS > = 14. Table S10: Intervals selected for further QTL analysis. The table lists the QTL intervals from selected Treg and Th cis- and trans-eQTLs that were further analyzed for the presence of candidate regulatory genes. Table S11 Candidate genes located in the F2rl1-QTL interval on chromosome 4. The table lists probesets of possible candidate genes that are located in the QTL interval on chromosome 4 which regulates the expression of F2rl1. Only genes with an expression signal larger than 8 were selected. Table S12 Candidate genes located in the QTL interval on chromosome 2 (autoimmunity to DNA). The table lists probesets of possible candidate genes that are located in the QTL interval on chromosome 2 which regulates autoimmunity to DNA. Only genes expressed in Treg cells (signal > 8 on log2 scale) and exhibiting a cis-eQTL of LRS > = 15 were selected.

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Additional file 4:

Figure S1. Genome-wide graph of cis- and trans-eQTLs in Treg and Th cells. The file shows the genome-wide mapping graphs for Treg cells and the same graph for Th cells overlaid in grey. Figure S2. Genome-wide graph of cis- and trans-eQTLs in Th and Treg cells. The file shows the genome-wide mapping graphs for Th cells and the same graph for Treg cells overlaid in grey. Figure S3, Genome wide eQTL mapping of Lycat transcript in Treg and Th cells. The file contains a graph showing the result of a genome-wide mapping of eQTLs for the Lycat transcript in Treg and Th cells. Figure S4, Genome wide eQTL mapping of Prpf3 transcript in Treg and Th cells. The file contains a graph showing the result of a genome-wide mapping of eQTLs for the Prpf3 transcript in Treg and Th cells. Figure S5, Genome wide eQTL mapping of Nrp1 transcript in Treg and Th cells. The file contains a graph showing the result of a genome-wide mapping of eQTLs for the Nrp1 transcript in Treg and Th cells. Figure S6, Genome wide eQTL mapping of F2rl1 transcript in Treg and Th cells. The file contains a graph showing the result of a genome-wide mapping of eQTLs for the F2rl1 transcript in Treg and Th cells. Figure S7, Genome wide eQTL mapping of Ctla4 transcript in Treg and Th cells. The file contains a graph showing the result of a genome-wide mapping of eQTLs for the Ctla4 transcript in Treg and Th cells.

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Additional file 5:

'Additional Results and Discussion': This file contains additional results on: Trans-eQTLs mapping in Treg and Th cells, the analysis of candidate genes in trans-eQTL intervals, and the analysis of autoimmune traits. Also, the file contains additional discussion points on Treg-specifc genes, the analysis of the interval on chromosome 2 found to regulate expression of Nrp1, analysis of an interval on chromosome × regulating expression of Klrb1f/A630024B12Rik (killer cell lectin-like receptor subfamily B member 1F) and Ctla4 (cytotoxic T-lymphocyte-associated protein 4), the analysis of known Treg functional genes for possible cis- or trans-eQTLs, and the analysis of the QTLs interval chromosome 4 associated with autoimmune traits.

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