Research article
The landscape of human genes involved in the immune response to parasitic worms
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* Corresponding author: Manuela Sironi manuela.sironi@bp.lnf.it
- † Equal contributors
1 Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Via don L. Monza 20, 23842 Bosisio Parini (LC), Italy
2 Bioengineering Department, Politecnico di Milano, P.zza L. da Vinci, 32, 20133 Milan, Italy
3 Dino Ferrari Centre, Department of Neurological Sciences, University of Milan, IRCCS Ospedale Maggiore Policlinico, Mangiagalli and Regina Elena Foundation, Via F. Sforza 35, 20100 Milan, Italy
4 Department of Biomedical Sciences and Technologies LITA Segrate, University of Milan, Via F.lli Cervi 93, 20090 Milan, Italy
5 Don C. Gnocchi ONLUS Foundation IRCCS, Via Capecelatro 66, 20148 Milan, Italy
BMC Evolutionary Biology 2010, 10:264 doi:10.1186/1471-2148-10-264
Published: 31 August 2010Additional files
Additional file 1:
Table S1. Populations in the HGDP-CEPH panel and helminth diversity estimates.
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Additional file 2:
Table S2. Genes in the ImmPort list that display at least one SNP significantly associated with helminth diversity. For each gene the SNP showing the strongest correlation is reported. SNPs are ranked according to the value of τ.
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Additional file 3:
Table S3. SNPs significantly associated with helminth diversity. The table reports all SNPs that withstood Bonferroni correction at the genome-wide level (with alpha = 0.5) and displayed a tau percentile rank higher than the 95th among MAF-matched SNPs, as described in the main text. SNPs are ranked according to the value of τ. If the SNP is located within a genic region (or in the 500 upstream nucleotides) the gene symbol is reported. Alternatively, the gene closest to the SNP and its distance (in bp) are indicated.
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Additional file 4:
Figure S1. In addition to the two merged networks in the main text, IPA identified three additional networks (A-C) with p < 10-9. Genes are represented as nodes, edges indicate known interactions between proteins (sold lines depicts direct and dashed lines depict indirect interaction). Genes are color coded as follows: green, genes with at least one SNP significantly associated with helminth diversity; gray, genes covered by at least one SNP in the HGDP-CEPH panel; white, genes with no SNPs in the panel.
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Additional file 5:
Figure S2. Analysis of LD in the genomic region encompassing CD28 and CTLA4. SNPs significantly associated with helminth diversity are shown in red while the region covered by CD28 and CTLA4 are shown in blue. The location of DNAse hypersensitive sites in CD4+ T cells is shown in gray while recombination hot-spots are in black. LD plots (r2) are shown for Yoruba (YRI), Europeans (CEU) and Asians (JPT+CHB). The image was generated by using the "add custom track" utility available through the UCSC Genome Browser.
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Additional file 6:
Table S4. Helminth species/genera transmitted in at least one country and that are common in at least one country.
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Additional file 7:
Table S5. Gene subdivision on the basis of SNP number. Genes were divided in 24 intervals according to the number of SNPs typed in the HGDP-CEPH panel.
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