Hello Shraddha, The track description and following the data links from the track will likely address most of these questions. Start by going into the mm8 assembly and clicking on the track name "Allen Brain".
Allen Brain Atlas Probes Description This track provides a link into the Allen Brain Atlas (ABA) images for this probe. The ABA is an extensive database of high resolution in-situ hybridization images of adult male mouse brains covering the majority of genes. As stated, the track contains the probes. Expression information is available from the data source. Click on a probe name to view the detailed information for that data point and a link to the Allen Brain Atlas: http://www.brain-map.org/ Searching in mm8 with RP_050628_02_E04, and using the link from the probe's detail page (click on probe name), the resulting Allen Brain Atlas's web page is just the default page. http://mouse.brain-map.org/search.do?queryText=egeneid=237360 (this is not expected - I will run this by the development team) Since the search did not work correctly from the link, I did an independent search with the term RP_050628_02_E04 using the upper right search box to find: http://www.brain-map.org/search/index.html?query=RP_050628_02_E04 Clicking into the resulting link finds: http://mouse.brain-map.org/brain/gene/71489809.html Where the NCBI accession is noted as being: XM_137117 Using XM_137117 as a search term in UCSC's VisiGene finds one image with the following annotation: source: Allen Brain Atlas (ABA) Reference: n/a Year: 2006 Contributors: Boe A.,Dang C.,Jeung D.,Luong L.,Sunkin S.,Sutram M.,Youngstrom B.,Lein E.,Jones A.,ABA ABA,ABI ABI,Allen Institute for Brain Science,Allen Brain Atlas, Gene: LOC237360 Probe: RNA sequenced GenBank: Organism: Mus musculus Sex: male Strain: C57BL/6 Genotype: wild type Stage: 5.3 week old pup (Theiler 28) Body Part: brain Expression: n/a Section Type: sagittal Copyright: © 2004-2006 Allen Institute for Brain Science Acknowledgements: Thanks to the Allen Institute for Brain Science, particularly to Andrew Boe, Chinh Dang, Darren Jeung, Lon Luong, Susan Sunkin, Madhavi Sutram, and Brian Youngstrom for helping make these images available in VisiGene.contributor Allen Institute for Brain Science Hopefully this is helpful. Thank you for asking your question since it may have uncovered a problem link (likely something changed since the track was first constructed). Very sorry for any confusion this may have caused, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/21/10 12:41 PM, Shraddha Pai wrote: > Hi, > > I'm unclear as to what it means when a gene is shown in the Allen Brain Atlas > mouse track. > Does it only mean that the probe was used for the FISH or does it mean that > the FISH did detect some non-zero level of expression in some part of the > mouse brain? > > (e.g. I'm looking at RP_050628_02_E04 in mouse build mm8 and am not sure what > that represents.) > > Moreover, when I enter this ID in the VisiGene search engine I don't get any > records in my result. > > Thanks in advance, > Shraddha > > ______________________________________________________________________ > This email has been scanned by the CAMH Email Security System. > ______________________________________________________________________ > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
