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| author | Bonface | 2024-02-13 23:52:26 -0600 |
|---|---|---|
| committer | Munyoki Kilyungi | 2024-08-09 13:30:43 +0300 |
| commit | b2feda451ccfbeaed02dce9088d6dd228cf15861 (patch) | |
| tree | 3dd2883524985114070a7770cd2e9f9bd7eb1848 /general/datasets/Ucla_axb_bxa_femur_0113_rsn | |
| parent | d029d5d7f8ead1f1de8d318045004a4a6f68f5fb (diff) | |
| download | gn-docs-b2feda451ccfbeaed02dce9088d6dd228cf15861.tar.gz | |
Update dataset RTF Files.
Diffstat (limited to 'general/datasets/Ucla_axb_bxa_femur_0113_rsn')
| -rw-r--r-- | general/datasets/Ucla_axb_bxa_femur_0113_rsn/experiment-type.rtf | 1 | ||||
| -rw-r--r-- | general/datasets/Ucla_axb_bxa_femur_0113_rsn/summary.rtf | 15 |
2 files changed, 16 insertions, 0 deletions
diff --git a/general/datasets/Ucla_axb_bxa_femur_0113_rsn/experiment-type.rtf b/general/datasets/Ucla_axb_bxa_femur_0113_rsn/experiment-type.rtf new file mode 100644 index 0000000..c29a175 --- /dev/null +++ b/general/datasets/Ucla_axb_bxa_femur_0113_rsn/experiment-type.rtf @@ -0,0 +1 @@ +RNA from cortical bone (femoral diaphysis free of marrow) were profiled from 99 Hybrid Mouse Diversity Panel strains were profiled. Sixteen-week old male mice were used in this study. A total of 1-3 mice per strain were arrayed.
\ No newline at end of file diff --git a/general/datasets/Ucla_axb_bxa_femur_0113_rsn/summary.rtf b/general/datasets/Ucla_axb_bxa_femur_0113_rsn/summary.rtf new file mode 100644 index 0000000..aaa3dd1 --- /dev/null +++ b/general/datasets/Ucla_axb_bxa_femur_0113_rsn/summary.rtf @@ -0,0 +1,15 @@ +<p>Summary of DatasetId 163, Name: UCLA GSE27483 AXB/BXA Bone Femur ILM Mouse WG-6 v1, v1.1 (Jan13)</p>
+
+<p><a abstractlink="yes" alsec="jour" alterm="J Bone Miner Res." aria-expanded="false" aria-haspopup="true" href="https://www.ncbi.nlm.nih.gov/pubmed/18767929#" role="menuitem" title="Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research.">J Bone Miner Res.</a> 2009 Jan;24(1):105-16. doi: 10.1359/jbmr.080908.</p>
+
+<p><b>An integrative genetics approach to identify candidate genes regulating BMD: combining linkage, gene expression, and association</b></p>
+
+<p><a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Farber%20CR%5BAuthor%5D&cauthor=true&cauthor_uid=18767929">Farber CR</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=van%20Nas%20A%5BAuthor%5D&cauthor=true&cauthor_uid=18767929">van Nas A</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Ghazalpour%20A%5BAuthor%5D&cauthor=true&cauthor_uid=18767929">Ghazalpour A</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Aten%20JE%5BAuthor%5D&cauthor=true&cauthor_uid=18767929">Aten JE</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Doss%20S%5BAuthor%5D&cauthor=true&cauthor_uid=18767929">Doss S</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Sos%20B%5BAuthor%5D&cauthor=true&cauthor_uid=18767929">Sos B</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Schadt%20EE%5BAuthor%5D&cauthor=true&cauthor_uid=18767929">Schadt EE</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Ingram-Drake%20L%5BAuthor%5D&cauthor=true&cauthor_uid=18767929">Ingram-Drake L</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Davis%20RC%5BAuthor%5D&cauthor=true&cauthor_uid=18767929">Davis RC</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Horvath%20S%5BAuthor%5D&cauthor=true&cauthor_uid=18767929">Horvath S</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Smith%20DJ%5BAuthor%5D&cauthor=true&cauthor_uid=18767929">Smith DJ</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Drake%20TA%5BAuthor%5D&cauthor=true&cauthor_uid=18767929">Drake TA</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Lusis%20AJ%5BAuthor%5D&cauthor=true&cauthor_uid=18767929">Lusis AJ</a></p>
+
+<h3>Abstract</h3>
+
+<p>Numerous quantitative trait loci (QTLs) affecting bone traits have been identified in the mouse; however, few of the underlying genes have been discovered. To improve the process of transitioning from QTL to gene, we describe an integrative genetics approach, which combines linkage analysis, expression QTL (eQTL) mapping, causality modeling, and genetic association in outbred mice. In C57BL/6J x C3H/HeJ (BXH) F(2) mice, nine QTLs regulating femoral BMD were identified. To select candidate genes from within each QTL region, microarray gene expression profiles from individual F(2) mice were used to identify 148 genes whose expression was correlated with BMD and regulated by local eQTLs. Many of the genes that were the most highly correlated with BMD have been previously shown to modulate bonemass or skeletal development. Candidates were further prioritized by determining whether their expression was predicted to underlie variation in BMD. Using network edge orienting (NEO), a causality modeling algorithm, 18 of the 148 candidates were predicted to be causally related to differences in BMD. To fine-map QTLs, markers in outbred MF1 mice were tested for association with BMD. Three chromosome 11 SNPs were identified that were associated with BMD within the Bmd11 QTL. Finally, our approach provides strong support for Wnt9a, Rasd1, or both underlying Bmd11. Integration of multiple genetic and genomic data sets can substantially improve the efficiency of QTL fine-mapping and candidate gene identification.</p>
+
+<dl>
+ <dt>PMID:18767929, PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2661539/" ref="aid_type=pmcid">PMC2661539</a>, DOI:<a href="https://dx.doi.org/10.1359/jbmr.080908" ref="aid_type=doi">10.1359/jbmr.080908</a></dt>
+</dl>
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