Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system
<p>Abstract</p> <p>Background</p> <p>In this study we have built and mined a gene expression database composed of 65 diverse mouse tissues for genes preferentially expressed in immune tissues and cell types. Using expression pattern criteria, we identified 360 genes wit...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2004-10-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/5/82 |
| _version_ | 1811252851967524864 |
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| author | Katz Jonathan D Williams Sarah Ebert Catherine Gupta Ashima Kong Sue Jegga Anil G Hutton John J Aronow Bruce J |
| author_facet | Katz Jonathan D Williams Sarah Ebert Catherine Gupta Ashima Kong Sue Jegga Anil G Hutton John J Aronow Bruce J |
| author_sort | Katz Jonathan D |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>In this study we have built and mined a gene expression database composed of 65 diverse mouse tissues for genes preferentially expressed in immune tissues and cell types. Using expression pattern criteria, we identified 360 genes with preferential expression in thymus, spleen, peripheral blood mononuclear cells, lymph nodes (unstimulated or stimulated), or <it>in vitro </it>activated T-cells.</p> <p>Results</p> <p>Gene clusters, formed based on similarity of expression-pattern across either all tissues or the immune tissues only, had highly significant associations both with immunological processes such as chemokine-mediated response, antigen processing, receptor-related signal transduction, and transcriptional regulation, and also with more general processes such as replication and cell cycle control. Within-cluster gene correlations implicated known associations of known genes, as well as immune process-related roles for poorly described genes. To characterize regulatory mechanisms and cis-elements of genes with similar patterns of expression, we used a new version of a comparative genomics-based <it>cis</it>-element analysis tool to identify clusters of <it>cis</it>-elements with compositional similarity among multiple genes. Several clusters contained genes that shared 5–6 <it>cis</it>-elements that included ETS and zinc-finger binding sites. <it>cis</it>-Elements AP2 EGRF ETSF MAZF SP1F ZF5F and AREB ETSF MZF1 PAX5 STAT were shared in a thymus-expressed set; AP4R E2FF EBOX ETSF MAZF SP1F ZF5F and CREB E2FF MAZF PCAT SP1F STAT cis-clusters occurred in activated T-cells; CEBP CREB NFKB SORY and GATA NKXH OCT1 RBIT occurred in stimulated lymph nodes.</p> <p>Conclusion</p> <p>This study demonstrates a series of analytic approaches that have allowed the implication of genes and regulatory elements that participate in the differentiation, maintenance, and function of the immune system. Polymorphism or mutation of these could adversely impact immune system functions.</p> |
| first_indexed | 2024-04-12T16:40:54Z |
| format | Article |
| id | doaj.art-f7e43a1cafad47f988113c9134569008 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-12T16:40:54Z |
| publishDate | 2004-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-f7e43a1cafad47f988113c91345690082022-12-22T03:24:47ZengBMCBMC Genomics1471-21642004-10-01518210.1186/1471-2164-5-82Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune systemKatz Jonathan DWilliams SarahEbert CatherineGupta AshimaKong SueJegga Anil GHutton John JAronow Bruce J<p>Abstract</p> <p>Background</p> <p>In this study we have built and mined a gene expression database composed of 65 diverse mouse tissues for genes preferentially expressed in immune tissues and cell types. Using expression pattern criteria, we identified 360 genes with preferential expression in thymus, spleen, peripheral blood mononuclear cells, lymph nodes (unstimulated or stimulated), or <it>in vitro </it>activated T-cells.</p> <p>Results</p> <p>Gene clusters, formed based on similarity of expression-pattern across either all tissues or the immune tissues only, had highly significant associations both with immunological processes such as chemokine-mediated response, antigen processing, receptor-related signal transduction, and transcriptional regulation, and also with more general processes such as replication and cell cycle control. Within-cluster gene correlations implicated known associations of known genes, as well as immune process-related roles for poorly described genes. To characterize regulatory mechanisms and cis-elements of genes with similar patterns of expression, we used a new version of a comparative genomics-based <it>cis</it>-element analysis tool to identify clusters of <it>cis</it>-elements with compositional similarity among multiple genes. Several clusters contained genes that shared 5–6 <it>cis</it>-elements that included ETS and zinc-finger binding sites. <it>cis</it>-Elements AP2 EGRF ETSF MAZF SP1F ZF5F and AREB ETSF MZF1 PAX5 STAT were shared in a thymus-expressed set; AP4R E2FF EBOX ETSF MAZF SP1F ZF5F and CREB E2FF MAZF PCAT SP1F STAT cis-clusters occurred in activated T-cells; CEBP CREB NFKB SORY and GATA NKXH OCT1 RBIT occurred in stimulated lymph nodes.</p> <p>Conclusion</p> <p>This study demonstrates a series of analytic approaches that have allowed the implication of genes and regulatory elements that participate in the differentiation, maintenance, and function of the immune system. Polymorphism or mutation of these could adversely impact immune system functions.</p>http://www.biomedcentral.com/1471-2164/5/82 |
| spellingShingle | Katz Jonathan D Williams Sarah Ebert Catherine Gupta Ashima Kong Sue Jegga Anil G Hutton John J Aronow Bruce J Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system BMC Genomics |
| title | Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system |
| title_full | Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system |
| title_fullStr | Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system |
| title_full_unstemmed | Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system |
| title_short | Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system |
| title_sort | microarray and comparative genomics based identification of genes and gene regulatory regions of the mouse immune system |
| url | http://www.biomedcentral.com/1471-2164/5/82 |
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