Geographical Genomics of Human Leukocyte Gene Expression Variation in Southern Morocco
Identifieur interne : 000149 ( Pmc/Checkpoint ); précédent : 000148; suivant : 000150Geographical Genomics of Human Leukocyte Gene Expression Variation in Southern Morocco
Auteurs : Youssef Idaghdour [États-Unis] ; Wendy Czika [États-Unis] ; Kevin V. Shianna [États-Unis] ; S. Hong Lee [Australie] ; Peter M. Visscher [Australie] ; Hilary C. Martin [Australie] ; Kelci Miclaus [États-Unis] ; Sami J. Jadallah [Maroc] ; David B. Goldstein [États-Unis] ; Russell D. Wolfinger [États-Unis] ; Greg Gibson [Australie]Source :
- Nature genetics [ 1061-4036 ] ; 2009.
Abstract
Studies of the genetics of gene expression reveal expression SNPs that explain variation in transcript abundance. Here we address the robustness of eSNP associations to environmental geography and population structure in a comparison of 194 Arab and Amazigh individuals from a city and two villages in southern Morocco. Gene expression differed between pairs of locations for up to a third of all transcripts, with notable enrichment for ribosomal biosynthesis and oxidative phosphorylation. Robust associations were observed in the leukocyte samples with
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DOI: 10.1038/ng.495
PubMed: 19966804
PubMed Central: 2798927
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Geographical Genomics of Human Leukocyte Gene Expression Variation in Southern Morocco</title><author><name sortKey="Idaghdour, Youssef" sort="Idaghdour, Youssef" uniqKey="Idaghdour Y" first="Youssef" last="Idaghdour">Youssef Idaghdour</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of Genetics, North Carolina State University, Raleigh NC, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, North Carolina State University, Raleigh NC</wicri:regionArea><wicri:noRegion>Raleigh NC</wicri:noRegion></affiliation></author><author><name sortKey="Czika, Wendy" sort="Czika, Wendy" uniqKey="Czika W" first="Wendy" last="Czika">Wendy Czika</name><affiliation wicri:level="1"><nlm:aff id="A2">SAS Institute Inc., Cary NC, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>SAS Institute Inc., Cary NC</wicri:regionArea><wicri:noRegion>Cary NC</wicri:noRegion></affiliation></author><author><name sortKey="Shianna, Kevin V" sort="Shianna, Kevin V" uniqKey="Shianna K" first="Kevin V." last="Shianna">Kevin V. Shianna</name><affiliation wicri:level="1"><nlm:aff id="A3">Institute for Genome Science and Policy, Duke University, Durham NC, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Genome Science and Policy, Duke University, Durham NC</wicri:regionArea><wicri:noRegion>Durham NC</wicri:noRegion></affiliation></author><author><name sortKey="Lee, S Hong" sort="Lee, S Hong" uniqKey="Lee S" first="S. Hong" last="Lee">S. Hong Lee</name><affiliation wicri:level="1"><nlm:aff id="A4">Queensland Institute of Medical Research, Brisbane, Queensland, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Queensland Institute of Medical Research, Brisbane, Queensland</wicri:regionArea><wicri:noRegion>Queensland</wicri:noRegion></affiliation></author><author><name sortKey="Visscher, Peter M" sort="Visscher, Peter M" uniqKey="Visscher P" first="Peter M." last="Visscher">Peter M. 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Shianna</name><affiliation wicri:level="1"><nlm:aff id="A3">Institute for Genome Science and Policy, Duke University, Durham NC, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Genome Science and Policy, Duke University, Durham NC</wicri:regionArea><wicri:noRegion>Durham NC</wicri:noRegion></affiliation></author><author><name sortKey="Lee, S Hong" sort="Lee, S Hong" uniqKey="Lee S" first="S. Hong" last="Lee">S. Hong Lee</name><affiliation wicri:level="1"><nlm:aff id="A4">Queensland Institute of Medical Research, Brisbane, Queensland, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Queensland Institute of Medical Research, Brisbane, Queensland</wicri:regionArea><wicri:noRegion>Queensland</wicri:noRegion></affiliation></author><author><name sortKey="Visscher, Peter M" sort="Visscher, Peter M" uniqKey="Visscher P" first="Peter M." last="Visscher">Peter M. Visscher</name><affiliation wicri:level="1"><nlm:aff id="A4">Queensland Institute of Medical Research, Brisbane, Queensland, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Queensland Institute of Medical Research, Brisbane, Queensland</wicri:regionArea><wicri:noRegion>Queensland</wicri:noRegion></affiliation></author><author><name sortKey="Martin, Hilary C" sort="Martin, Hilary C" uniqKey="Martin H" first="Hilary C." last="Martin">Hilary C. Martin</name><affiliation wicri:level="1"><nlm:aff id="A5">School of Biological Sciences, University of Queensland, Queensland, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>School of Biological Sciences, University of Queensland, Queensland</wicri:regionArea><wicri:noRegion>Queensland</wicri:noRegion></affiliation></author><author><name sortKey="Miclaus, Kelci" sort="Miclaus, Kelci" uniqKey="Miclaus K" first="Kelci" last="Miclaus">Kelci Miclaus</name><affiliation wicri:level="1"><nlm:aff id="A2">SAS Institute Inc., Cary NC, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>SAS Institute Inc., Cary NC</wicri:regionArea><wicri:noRegion>Cary NC</wicri:noRegion></affiliation></author><author><name sortKey="Jadallah, Sami J" sort="Jadallah, Sami J" uniqKey="Jadallah S" first="Sami J." last="Jadallah">Sami J. Jadallah</name><affiliation wicri:level="1"><nlm:aff id="A6">HRH Prince Sultan International Foundation for Conservation and Development of Wildlife, Agadir, Morocco</nlm:aff><country xml:lang="fr">Maroc</country><wicri:regionArea>HRH Prince Sultan International Foundation for Conservation and Development of Wildlife, Agadir</wicri:regionArea><wicri:noRegion>Agadir</wicri:noRegion></affiliation></author><author><name sortKey="Goldstein, David B" sort="Goldstein, David B" uniqKey="Goldstein D" first="David B." last="Goldstein">David B. Goldstein</name><affiliation wicri:level="1"><nlm:aff id="A3">Institute for Genome Science and Policy, Duke University, Durham NC, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Genome Science and Policy, Duke University, Durham NC</wicri:regionArea><wicri:noRegion>Durham NC</wicri:noRegion></affiliation></author><author><name sortKey="Wolfinger, Russell D" sort="Wolfinger, Russell D" uniqKey="Wolfinger R" first="Russell D." last="Wolfinger">Russell D. Wolfinger</name><affiliation wicri:level="1"><nlm:aff id="A2">SAS Institute Inc., Cary NC, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>SAS Institute Inc., Cary NC</wicri:regionArea><wicri:noRegion>Cary NC</wicri:noRegion></affiliation></author><author><name sortKey="Gibson, Greg" sort="Gibson, Greg" uniqKey="Gibson G" first="Greg" last="Gibson">Greg Gibson</name><affiliation wicri:level="1"><nlm:aff id="A5">School of Biological Sciences, University of Queensland, Queensland, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>School of Biological Sciences, University of Queensland, Queensland</wicri:regionArea><wicri:noRegion>Queensland</wicri:noRegion></affiliation></author></analytic><series><title level="j">Nature genetics</title><idno type="ISSN">1061-4036</idno><idno type="eISSN">1546-1718</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">Studies of the genetics of gene expression reveal expression SNPs that explain variation in transcript abundance. Here we address the robustness of eSNP associations to environmental geography and population structure in a comparison of 194 Arab and Amazigh individuals from a city and two villages in southern Morocco. Gene expression differed between pairs of locations for up to a third of all transcripts, with notable enrichment for ribosomal biosynthesis and oxidative phosphorylation. Robust associations were observed in the leukocyte samples with <italic>cis</italic>-eSNPs (<italic>P</italic> < 10<sup>−08</sup>) for 346 genes, and <italic>trans</italic>-eSNPs (<italic>P</italic> < 10<sup>−11</sup>) with 10 genes. All of these were consistent across the three sample locations and after controlling for ethnicity and relatedness. No evidence for large-effect <italic>trans</italic>-acting mediators of the pervasive environmental influence was found and instead genetic and environmental factors acted in a largely additive manner.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Abegunde, Do" uniqKey="Abegunde D">DO Abegunde</name></author><author><name sortKey="Mathers, Cd" uniqKey="Mathers C">CD Mathers</name></author><author><name sortKey="Adam, T" uniqKey="Adam T">T Adam</name></author><author><name sortKey="Ortegon, M" uniqKey="Ortegon M">M Ortegon</name></author><author><name sortKey="Strong, K" uniqKey="Strong K">K Strong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cookson, W" uniqKey="Cookson W">W Cookson</name></author><author><name sortKey="Liang, L" uniqKey="Liang L">L Liang</name></author><author><name sortKey="Abecasis, G" uniqKey="Abecasis G">G Abecasis</name></author><author><name sortKey="Moffatt, M" 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<front><journal-meta><journal-id journal-id-type="nlm-journal-id">9216904</journal-id><journal-id journal-id-type="pubmed-jr-id">2419</journal-id><journal-id journal-id-type="nlm-ta">Nat Genet</journal-id><journal-id journal-id-type="iso-abbrev">Nat. Genet.</journal-id><journal-title-group><journal-title>Nature genetics</journal-title></journal-title-group><issn pub-type="ppub">1061-4036</issn><issn pub-type="epub">1546-1718</issn></journal-meta><article-meta><article-id pub-id-type="pmid">19966804</article-id><article-id pub-id-type="pmc">2798927</article-id><article-id pub-id-type="doi">10.1038/ng.495</article-id><article-id pub-id-type="manuscript">NIHMS157635</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Geographical Genomics of Human Leukocyte Gene Expression Variation in Southern Morocco</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Idaghdour</surname><given-names>Youssef</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Czika</surname><given-names>Wendy</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Shianna</surname><given-names>Kevin V.</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Lee</surname><given-names>S. Hong</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Visscher</surname><given-names>Peter M.</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Martin</surname><given-names>Hilary C.</given-names></name><xref ref-type="aff" rid="A5">5</xref></contrib><contrib contrib-type="author"><name><surname>Miclaus</surname><given-names>Kelci</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Jadallah</surname><given-names>Sami J.</given-names></name><xref ref-type="aff" rid="A6">6</xref></contrib><contrib contrib-type="author"><name><surname>Goldstein</surname><given-names>David B.</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Wolfinger</surname><given-names>Russell D.</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Gibson</surname><given-names>Greg</given-names></name><xref ref-type="aff" rid="A5">5</xref><xref ref-type="corresp" rid="cor1">*</xref></contrib></contrib-group><aff id="A1"><label>1</label>Department of Genetics, North Carolina State University, Raleigh NC, USA</aff><aff id="A2"><label>2</label>SAS Institute Inc., Cary NC, USA</aff><aff id="A3"><label>3</label>Institute for Genome Science and Policy, Duke University, Durham NC, USA</aff><aff id="A4"><label>4</label>Queensland Institute of Medical Research, Brisbane, Queensland, Australia</aff><aff id="A5"><label>5</label>School of Biological Sciences, University of Queensland, Queensland, Australia</aff><aff id="A6"><label>6</label>HRH Prince Sultan International Foundation for Conservation and Development of Wildlife, Agadir, Morocco</aff><author-notes><corresp id="cor1"><label>*</label>Corresponding author: School of Biological Sciences, Goddard Building, St Lucia Campus, University of Queensland, Brisbane, QLD 4072, Australia, <email>ggibson.uq@gmail.com</email>, Ph: +61 7 3365-2194</corresp></author-notes><pub-date pub-type="nihms-submitted"><day>17</day><month>11</month><year>2009</year></pub-date><pub-date pub-type="epub"><day>06</day><month>12</month><year>2009</year></pub-date><pub-date pub-type="ppub"><month>1</month><year>2010</year></pub-date><pub-date pub-type="pmc-release"><day>01</day><month>7</month><year>2010</year></pub-date><volume>42</volume><issue>1</issue><fpage>62</fpage><lpage>67</lpage><pmc-comment>elocation-id from pubmed: 10.1038/ng.495</pmc-comment>
<permissions><license><license-p>Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:
<ext-link ext-link-type="uri" xlink:href="http://www.nature.com/authors/editorial_policies/license.html#terms">http://www.nature.com/authors/editorial_policies/license.html#terms</ext-link></license-p></license></permissions><abstract><p id="P1">Studies of the genetics of gene expression reveal expression SNPs that explain variation in transcript abundance. Here we address the robustness of eSNP associations to environmental geography and population structure in a comparison of 194 Arab and Amazigh individuals from a city and two villages in southern Morocco. Gene expression differed between pairs of locations for up to a third of all transcripts, with notable enrichment for ribosomal biosynthesis and oxidative phosphorylation. Robust associations were observed in the leukocyte samples with <italic>cis</italic>-eSNPs (<italic>P</italic> < 10<sup>−08</sup>) for 346 genes, and <italic>trans</italic>-eSNPs (<italic>P</italic> < 10<sup>−11</sup>) with 10 genes. All of these were consistent across the three sample locations and after controlling for ethnicity and relatedness. No evidence for large-effect <italic>trans</italic>-acting mediators of the pervasive environmental influence was found and instead genetic and environmental factors acted in a largely additive manner.</p></abstract><kwd-group><kwd>Peripheral blood</kwd><kwd>eSNP</kwd><kwd>GWAS</kwd><kwd>ethnicity</kwd><kwd>relatedness</kwd><kwd>environmental geography</kwd></kwd-group></article-meta></front><floats-group><fig id="F1" position="float"><label>Figure 1</label><caption><title>Map of the Souss region of southern Morocco</title><p id="P32">showing the location of the two rural villages, Boutroch and Ighrem, near the town of Tiznit, relative to the urban locations Anza and Dchiera north and south of the city of Agadir, respectively.</p></caption><graphic xlink:href="nihms157635f1"></graphic></fig><fig id="F2" position="float"><label>Figure 2</label><caption><title>Population structure in southern Morocco</title><p id="P33">(<bold>a</bold>)Eigenstrat principal component analysis of 579,144 SNPs reveals 7 significant eigenvectors, the first two of which, explaining just 1.3 and 0.8 % of the genotypic variance respectively, are plotted here. By self-report, Boutroch Amazigh are blue squares, Agadir Amazigh green triangles, Agadir Arabs green plus symbols, Ighrem Arabsred circles, and Ighrem Amazigh red triangles. 3 individuals with uncertain ethnicity possibly including sub-Saharan heritage, are indicated as gray spots, and have high values of PC1, which is characteristic of Yoruban ancestry as shown in <xref ref-type="supplementary-material" rid="SD1">Supplementary Figure 1b online</xref>. (<bold>b</bold>) Structure analysis of 16,000 autosomal SNPs, with k=3 and employing the admixture model with correlated allele frequencies, highlights the same individuals with large PC1 values (brown bars) and shows that Boutroch Amazigh are predominantly derived from one population group (pale blue) while all other samples are a mixture of the two populations represented by pale red and blue bars.</p></caption><graphic xlink:href="nihms157635f2"></graphic></fig><fig id="F3" position="float"><label>Figure 3</label><caption><title>Location impacts gene expression transcriptome-wide</title><p id="P34">(<bold>a</bold>) Venn diagram of the number of genes significant at 1% FDR for ANOVA of the three pair-wise comparisons indicated. Variance components of expression variation (<bold>b</bold>) just in the 118 residents of Agadir (excluding 9 individuals with strongly positive gPC1 scores, and including reassignment of ethnicity according to gPC2 for just 11 individuals relative to self-report, <xref ref-type="supplementary-material" rid="SD6">Supplementary Table 5</xref>),where Ethnicity is modeled as the PC2 of the genotype variation as shown in <xref ref-type="fig" rid="F1">Figure 1a</xref>, or (<bold>c</bold>) for all 22,300 probes in the full sample of 208 individuals.</p></caption><graphic xlink:href="nihms157635f3"></graphic></fig><fig id="F4" position="float"><label>Figure 4</label><caption><title>Principal component plot for the most differentially expressed genes</title><p id="P35">The two major principal components of the expression of the 1,500 most significant genes shows significant separation of individuals by location (PC1 and PC2) and gender (PC2) (all <italic>P</italic> < 0.0001) as described in the text. Individuals from Boutroch are blue, Ighrem red, and Agadir green. Arabs are indicated with solid spots, Amazigh open circles, and males are lighter symbols for each color. Boutroch and Arab women from Ighrem (clusters 1 and 2) separate from Amazigh women and Arab men from Ighrem (clusters 3 and 4) who are closer to Agadir residents. If Boutroch residents and Ighrem Arab women are grouped and contrasted with Agadir residents, Ighrem Amazigh women, and Ighrem men, 8,239 genes are significantly differentially expressed at the 1% FDR rate, more than any pair-wise comparison of locations. A similar plot for all genes is shown in <xref ref-type="supplementary-material" rid="SD1">Supplementary Figure 11</xref>.</p></caption><graphic xlink:href="nihms157635f4"></graphic></fig><fig id="F5" position="float"><label>Figure 5</label><caption><title>Genome-wide association with transcript abundance</title><p id="P36">(<bold>a</bold>)Manhattan plot of all 1,636 genome-wide associations at <italic>P</italic> < 10<sup>−8</sup>(NLP > 8) for model 3, which includes control for genotype-determined ethnicity, location, relatedness, and gender. Each chromosome is indicated by a different color. The horizontal red line indicates the genome-wide significance threshold (NLP > 11.4) for <italic>trans</italic> associations. Note the excess of peaks at the MHC complex on chromosome 6 due to multiple cis-eSNPs. (<bold>b</bold>) Cis-<italic>Trans</italic> plot showing target transcript location against eSNP location indicating that most eSNPs are in <italic>cis</italic> to the regulated transcript, while just 13 <italic>trans</italic> associations at NLP > 11.4are visible. (<bold>c</bold>) High correlation of significance measures for all eSNPs detected by simple correlation of genotype with expression (model 1) or robust control for ethnicity, gender and location (model 3). (<bold>d</bold>) Absence of genome-wide significance for the Genotype-by-Location interaction effect, which is not correlated with the Genotype effect.</p></caption><graphic xlink:href="nihms157635f5"></graphic></fig><fig id="F6" position="float"><label>Figure 6</label><caption><title>The relationship between genotype, expression, and phenotype</title><p id="P37">(<bold>a</bold>) A typical example of a transcript (encoding C21ORF57, a putative metallo-proteinase) that shows both a significant difference between locations (<italic>P</italic> < 10<sup>−5</sup>) and a <italic>cis</italic>-eSNP association, with rs1556337 (<italic>P</italic> < 10<sup>−13</sup>) but no interaction effect in an additive model on the log scale. Expression is lower in Boutroch (blue points and line), while genotype has a consistent effect across all three locations (Ighrem, red; Agadir, green). (<bold>b</bold>) The Actual vs Predicted plot separates the genotypes by location for clarity. Suppose that a disease or phenotype is only seen in individuals with transcript abundance less than 1.0 (on a relative log2 scale), indicated by the gray area. Then in Agadir and Ighrem (green and red respectively) almost all affected are AA homozygotes, whereas in Boutroch (blue) heterozygotes and some GG homozygotes are also affected. There is thus a G×E interaction for the phenotype in the absence of a G×E interaction for transcription, because the environment shifts more individuals into the susceptible zone. Similar arguments would apply for phenotypes with high expression values, and for graded rather than threshold-dependent traits.</p></caption><graphic xlink:href="nihms157635f6"></graphic></fig><table-wrap id="T1" position="float" orientation="landscape"><label>Table 1</label><caption><p id="P38">Number of transcripts significant at 1% FDR</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">Location</th><th align="right" rowspan="1" colspan="1"></th><th align="right" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1">Gender</th><th align="right" rowspan="1" colspan="1"></th><th align="right" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1">Interaction</th><th align="right" rowspan="1" colspan="1"></th><th align="right" rowspan="1" colspan="1"></th></tr><tr><th align="left" rowspan="1" colspan="1">ANOVA</th><th align="right" colspan="2" rowspan="1">ANCOVA</th><th align="left" rowspan="1" colspan="1"></th><th align="right" rowspan="1" colspan="1">ANOVA</th><th align="right" rowspan="1" colspan="1">ANCOVA</th><th align="left" rowspan="1" colspan="1"></th><th align="right" rowspan="1" colspan="1">ANOVA</th><th align="right" rowspan="1" colspan="1">ANCOVA</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">3-way</td><td align="right" rowspan="1" colspan="1">8459</td><td align="right" rowspan="1" colspan="1">7057</td><td align="left" rowspan="1" colspan="1">Male : Female</td><td align="right" rowspan="1" colspan="1">151</td><td align="right" rowspan="1" colspan="1">233</td><td align="left" rowspan="1" colspan="1">Location*Gender</td><td align="right" rowspan="1" colspan="1">133</td><td align="right" rowspan="1" colspan="1">203</td></tr><tr><td align="left" rowspan="1" colspan="1">Aga : Bou</td><td align="right" rowspan="1" colspan="1">6744</td><td align="right" rowspan="1" colspan="1">4974</td><td align="left" rowspan="1" colspan="1">In Agadir</td><td align="right" rowspan="1" colspan="1">24</td><td align="right" rowspan="1" colspan="1">24</td><td align="left" rowspan="1" colspan="1">Fem (Aga : Bou)</td><td align="right" rowspan="1" colspan="1">4830</td><td align="right" rowspan="1" colspan="1">3791</td></tr><tr><td align="left" rowspan="1" colspan="1">Aga : Igh</td><td align="right" rowspan="1" colspan="1">635</td><td align="right" rowspan="1" colspan="1">651</td><td align="left" rowspan="1" colspan="1">In Boutroch</td><td align="right" rowspan="1" colspan="1">13</td><td align="right" rowspan="1" colspan="1">14</td><td align="left" rowspan="1" colspan="1">Fem (Aga : Igh)</td><td align="right" rowspan="1" colspan="1">1451</td><td align="right" rowspan="1" colspan="1">1467</td></tr><tr><td align="left" rowspan="1" colspan="1">Bou : Igh</td><td align="right" rowspan="1" colspan="1">7339</td><td align="right" rowspan="1" colspan="1">6286</td><td align="left" rowspan="1" colspan="1">In Ighrem</td><td align="right" rowspan="1" colspan="1">589</td><td align="right" rowspan="1" colspan="1">890</td><td align="left" rowspan="1" colspan="1">Mal (Aga : Bou)<xref ref-type="table-fn" rid="TFN2">†</xref></td><td align="right" rowspan="1" colspan="1">407</td><td align="right" rowspan="1" colspan="1">806</td></tr><tr><td align="left" rowspan="1" colspan="1">Aga : Rural</td><td align="right" rowspan="1" colspan="1">1521</td><td align="right" rowspan="1" colspan="1">607</td><td align="left" rowspan="1" colspan="1"></td><td align="right" rowspan="1" colspan="1"></td><td align="right" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1">Mal (Aga : Igh)</td><td align="right" rowspan="1" colspan="1">8</td><td align="right" rowspan="1" colspan="1">8</td></tr></tbody></table><table-wrap-foot><fn id="TFN1"><p id="P39">ANOVA includes terms for Location, Gender, and Location*Gender interaction. The False Discovery Rate was evaluated using the conservative Benjamin and Hochberg method. The left hand columns show the number of genes significant at the 1% FDR threshold for Location effects (either in the 3-way comparison of Agadir (Aga), Boutroch (Bou) and Ighrem (Igh); between pairs of locations, or between Agadir (Aga) and the two rural sites combined). The central columns contrast gender (male versus female) effects, either in the total sample or each location individually. The right hand columns show interaction effects, either in the total sample or showing the indicated contrast between Agadir and either village, for females or males separately. ANCOVA is the same model with an additional continuous covariate for ethnicity, genotypic PC2.</p></fn><fn id="TFN2"><label>†</label><p id="P40">Significance of this contrast was reduced by the small sample of Boutroch males (12, cf 26 females).</p></fn></table-wrap-foot></table-wrap></floats-group></pmc><affiliations><list><country><li>Australie</li><li>Maroc</li><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Idaghdour, Youssef" sort="Idaghdour, Youssef" uniqKey="Idaghdour Y" first="Youssef" last="Idaghdour">Youssef Idaghdour</name></noRegion><name sortKey="Czika, Wendy" sort="Czika, Wendy" uniqKey="Czika W" first="Wendy" last="Czika">Wendy Czika</name><name sortKey="Goldstein, David B" sort="Goldstein, David B" uniqKey="Goldstein D" first="David B." last="Goldstein">David B. Goldstein</name><name sortKey="Miclaus, Kelci" sort="Miclaus, Kelci" uniqKey="Miclaus K" first="Kelci" last="Miclaus">Kelci Miclaus</name><name sortKey="Shianna, Kevin V" sort="Shianna, Kevin V" uniqKey="Shianna K" first="Kevin V." last="Shianna">Kevin V. Shianna</name><name sortKey="Wolfinger, Russell D" sort="Wolfinger, Russell D" uniqKey="Wolfinger R" first="Russell D." last="Wolfinger">Russell D. Wolfinger</name></country><country name="Australie"><noRegion><name sortKey="Lee, S Hong" sort="Lee, S Hong" uniqKey="Lee S" first="S. Hong" last="Lee">S. Hong Lee</name></noRegion><name sortKey="Gibson, Greg" sort="Gibson, Greg" uniqKey="Gibson G" first="Greg" last="Gibson">Greg Gibson</name><name sortKey="Martin, Hilary C" sort="Martin, Hilary C" uniqKey="Martin H" first="Hilary C." last="Martin">Hilary C. Martin</name><name sortKey="Visscher, Peter M" sort="Visscher, Peter M" uniqKey="Visscher P" first="Peter M." last="Visscher">Peter M. Visscher</name></country><country name="Maroc"><noRegion><name sortKey="Jadallah, Sami J" sort="Jadallah, Sami J" uniqKey="Jadallah S" first="Sami J." last="Jadallah">Sami J. Jadallah</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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