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| author | zsloan | 2015-03-27 20:28:51 +0000 |
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| committer | zsloan | 2015-03-27 20:28:51 +0000 |
| commit | d0911a04958a04042da02a334ccc528dae79cc17 (patch) | |
| tree | 3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/dbdoc/HLC_0311_F.html | |
| parent | a840ad18e1fe3db98a359a159e9b9b72367a2839 (diff) | |
| download | genenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz | |
Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'
Diffstat (limited to 'web/dbdoc/HLC_0311_F.html')
| -rwxr-xr-x | web/dbdoc/HLC_0311_F.html | 112 |
1 files changed, 0 insertions, 112 deletions
diff --git a/web/dbdoc/HLC_0311_F.html b/web/dbdoc/HLC_0311_F.html deleted file mode 100755 index 9fc18edd..00000000 --- a/web/dbdoc/HLC_0311_F.html +++ /dev/null @@ -1,112 +0,0 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> -<HTML><HEAD><TITLE>GSE9588 Human Liver Normal (Mar11) Females</TITLE> -<META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> - -<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'> -<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'> -<link rel="stylesheet" media="all" type="text/css" href="/css/tabbed_pages.css" /> -<script type="text/javascript" src="/javascript/jquery.js"></script> -<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT> -<SCRIPT SRC="/javascript/dhtml.js"></SCRIPT> -<SCRIPT SRC="/javascript/jqueryFunction.js"></SCRIPT> -<script src="/javascript/tabbed_pages.js" type="text/javascript"></script> - -</HEAD> -<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff > - -<TABLE cellSpacing=5 cellPadding=4 width="100%" border=0> - <TBODY> - <TR> - <script language="JavaScript" src="/javascript/header.js"></script> - </TR> - <TR> - <TD bgColor=#eeeeee class="solidBorder"> - <Table width= "100%" cellSpacing=0 cellPadding=5> - <TR> - - <!-- split from Here --> - <!-- Body Start from Here --> - - <P class="title">GSE9588 Human Liver Normal (Mar11) Females<A HREF="/webqtl/main.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A><BR><BR> - - Accession number: <A HREF="/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=322">GN322</A></P> - <blockquote> -<p class="subtitle">Summary:</p> -<p>The Human Liver Cohort (HLC) study aimed to characterize the genetic -architecture of gene expression in human liver using genotyping, gene expression -profiling, and enzyme activity measurements of Cytochrom P450. The HLC was -assembled from a total of 780 liver samples screened. These liver samples -were acquired from caucasian individuals from three independant tissue -collection centers. DNA samples were genotyped on the Affymetrix 500K SNP -and Illumina 650Y SNP genotyping arrays representing a total of 782,476 unique -single nucleotide polymorphisms (SNPs). Only the genotype data from those -samples which were collected postmortem are accessible in dbGap. These 228 -samples represent a subset of the 427 samples included in the Human Liver -Cohort Publication (Schadt, Molony et al. 2008). RNA samples were profiled on -a custom Agilent 44,000 feature microarray composed of 39,280 oligonucleotide -probes targeting transcripts representing 34,266 known and predicted genes, -including high-confidence, noncoding RNA sequences. Each of the liver samples -was processed into cytosol and microsomes using a standard differential -centrifugation method. The activities of nine P450 enzymes (CYP1A2, 2A6, 2B6, -2C8, 2C9, 2C19, 2D6, 2E1, and 3A4) in isolated microsomes from 398 HLC liver -samples were measured in the microsome preparations using probe substrate -metabolism assays expressed as nmol/min/mg protein. Each was measured with a -single substrate except for the CYP3A4 activity that was measured using two -substrates, midazolam and testosterone.</p> -<p>To uncover the genetic determinants affecting expression in a metabolically active tissue relevant to the study of obesity, diabetes, atherosclerosis, and other common human diseases, we profiled 427 human liver samples on a comprehensive gene expression microarray targeting greater than 40,000 transcripts and genotyped DNA from each of these samples at greater than 1,000,000 SNPs. The relatively large sample size of this study and the large number of SNPs genotyped provided the means to assess the relationship between genetic variants and gene expression and it provided this look for the first time in a non-blood derived, metabolically active tissue. A comprehensive analysis of the liver gene expression traits revealed that thousands of these traits are under the control of well defined genetic loci, with many of the genes having already been implicated in a number of human diseases.</p> -<p class="subtitle">Overall Design:</p> -<p>Liver samples (1-2 g) were acquired from Caucasian individuals from three independent liver collections at tissue resource centers at Vanderbilt University, University of Pittsburg, and Merck Research Laboratories. All individuals were compared to a common pool created from equal portions of RNA from 191 (111 from Vanderbilt University and 80 from University of Pittsburg) samples.</p> -<p class="subtitle">Platforms:</p> -<p><a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL4372" target="_blank">Rosetta/Merck Human 44k 1.1 microarray</a></p> -<p class="subtitle">Data Source Acknowledgements:</p> -<p> -<p><a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Schadt EE[Author]">Schadt EE</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Molony C[Author]">Molony C</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Chudin E[Author]">Chudin E</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Hao K[Author]">Hao K</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Yang X[Author]">Yang X</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Lum P[Author]">Lum P</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Kasarskis A[Author]">Kasarskis A</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Zhang B[Author]">Zhang B</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Wang S[Author]">Wang S</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Suver C[Author]">Suver C</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Zhu J[Author]">Zhu J</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Millstein J[Author]">Millstein J</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Sieberts S[Author]">Sieberts S</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Lamb J[Author]">Lamb J</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Guhathakurta D[Author]">Guhathakurta D</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Derry J[Author]">Derry J</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Storey J[Author]">Storey J</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Mehrabian M[Author]">Mehrabian M</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Drake TA[Author]">Drake TA</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Lusis AJ[Author]">Lusis AJ</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Smith R[Author]">Smith R</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Guengerich P[Author]">Guengerich P</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Strom SC[Author]">Strom SC</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Schuetz E[Author]">Schuetz E</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Rushmore T[Author]">Rushmore T</a>, <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&term=Ulrich R[Author]">Ulrich R</a></p> -<p class="subtitle">Source:</p> -<p><a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9588" target="_blank">GEO Series GSE9588</a><br> -Genotype data for 228 individuals who satisfy privacy policy have been submitted to the NCBI dbGaP (<a href="http://www.ncbi.nlm.nih.gov/gap/" target="_blank">http://www.ncbi.nlm.nih.gov/gap/</a>) under accession no. phs000253.v1.p1.] -</blockquote> - - </TR></TABLE> - </TD> - </TR> - <TR> - <TD align=center bgColor=#ddddff class="solidBorder"> - <!--Start of footer--> - <TABLE width="100%"> - <script language='JavaScript' src='/javascript/footer.js'></script> - <TR> - <TD colspan=4 id="smallsize" align="left"> - - </TD> - </TR> - </TABLE> - <!--End of footer--> - </TD> - </TR> -</TABLE> -<!-- /Footer --> -<!-- menu script itself. you should not modify this file --> -<script language="JavaScript" src="/javascript/menu_new.js"></script> -<!-- items structure. menu hierarchy and links are stored there --> -<script language="JavaScript" src="/javascript/menu_items.js"></script> -<!-- files with geometry and styles structures --> -<script language="JavaScript" src="/javascript/menu_tpl.js"></script> -<script language="JavaScript"> - <!--// - // Note where menu initialization block is located in HTML document. - // Don't try to position menu locating menu initialization block in - // some table cell or other HTML element. 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