title: Automated pipeline for atlas-based annotation of gene expression patterns: application to postnatal day 7 mouse brain.
abstract: Massive amounts of image data have been collected and continue to be generated for representing cellular gene expression throughout the mouse brain. Critical to exploiting this key effort of the post-genomic era is the ability to place these data into a common spatial reference that enables rapid interactive queries, analysis, data sharing, and visualization. In this paper, we present a set of automated protocols for generating and annotating gene expression patterns suitable for the establishment of a database. The steps include imaging tissue slices, detecting cellular gene expression levels, spatial registration with an atlas, and textual annotation. Using high-throughput in situ hybridization to generate serial sets of tissues displaying gene expression, this process was applied toward the establishment of a database representing over 200 genes in the postnatal day 7 mouse brain. These data using this protocol are now well-suited for interactive comparisons, analysis, queries, and visualization.
authors.affiliation: Biological Monitoring and Modeling Group, Pacific Northwest National Laboratory, Richland, WA, USA.
authors.forename: James
authors.initials: J
authors.lastname: Carson
authors.forename: Tao
authors.initials: T
authors.lastname: Ju
authors.forename: Musodiq
authors.initials: M
authors.lastname: Bello
authors.forename: Christina
authors.initials: C
authors.lastname: Thaller
authors.forename: Joe
authors.initials: J
authors.lastname: Warren
authors.forename: Ioannis A
authors.initials: IA
authors.lastname: Kakadiaris
authors.forename: Wah
authors.initials: W
authors.lastname: Chiu
authors.forename: Gregor
authors.initials: G
authors.lastname: Eichele
mesh_terms: D000818:Animals; D001331:Automation; D001921:Brain / Q000378:metabolism*; D001931:Brain Mapping / Q000379:methods*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D017403:In Situ Hybridization; D051379:Mice; D015233:Models, Statistical; D005810:Multigene Family
references.citation: IEEE Trans Med Imaging. 2002 Nov;21(11):1421-39
references.pmid: 12575879
references.citation: J Histochem Cytochem. 1995 Apr;43(4):347-52
references.pmid: 7897179
references.citation: Am J Physiol Gastrointest Liver Physiol. 2006 Dec;291(6):G1041-50
references.pmid: 16825705
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D637-41
references.pmid: 16381949
references.citation: Symp Geom Process. 2003;2003:166-176
references.pmid: 20631855
references.citation: Genome Biol. 2008 Jan 30;9(1):R23
references.pmid: 18234097
references.citation: Med Image Anal. 2008 Oct;12(5):616-25
references.pmid: 18640069
references.citation: IEEE/ACM Trans Comput Biol Bioinform. 2007 Jul-Sep;4(3):382-393
references.pmid: 17666758
references.citation: Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18267-72
references.pmid: 17108082
references.citation: Nat Neurosci. 2004 May;7(5):483
references.pmid: 15114362
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D552-6
references.pmid: 14681479
references.citation: Proc Natl Acad Sci U S A. 2008 Jan 29;105(4):1291-6
references.pmid: 18216249
references.citation: Bioinformatics. 2004 Jun 12;20(9):1453-4
references.pmid: 14871861
references.citation: Conf Proc IEEE Eng Med Biol Soc. 2004;2004:2917-20
references.pmid: 17270888
references.citation: Nature. 2007 Jan 11;445(7124):168-76
references.pmid: 17151600
references.citation: Mech Dev. 2000 Nov;98(1-2):77-94
references.pmid: 11044609
references.citation: J Am Med Inform Assoc. 2001 Sep-Oct;8(5):401-30
references.pmid: 11522763
references.citation: J Immunol Methods. 1989 Dec 20;125(1-2):279-85
references.pmid: 2558138
references.citation: Radiographics. 2001 May-Jun;21(3):789-98
references.pmid: 11353125
references.citation: J Digit Imaging. 2009 Oct;22(5):492-502
references.pmid: 18478296
references.citation: Nat Neurosci. 2004 May;7(5):429-33
references.pmid: 15114353
references.citation: J Neurosci Methods. 2006 Sep 30;156(1-2):84-100
references.pmid: 16580732
references.citation: PLoS Comput Biol. 2005 Sep;1(4):e41
references.pmid: 16184189
references.citation: PLoS Genet. 2007 Oct;3(10):1867-83
references.pmid: 17953485
references.citation: IEEE Trans Med Imaging. 2007 May;26(5):728-44
references.pmid: 17518066
references.citation: Curr Opin Neurobiol. 2002 Oct;12(5):562-5
references.pmid: 12367636
references.citation: Novartis Found Symp. 2001;239:129-46; discussion 146-59
references.pmid: 11529308
references.citation: Nature. 2003 Oct 30;425(6961):917-25
references.pmid: 14586460
references.citation: Nucleic Acids Res. 2001 Jan 1;29(1):98-101
references.pmid: 11125060
references.citation: J Anat. 2004 Feb;204(2):93-102
references.pmid: 15032916
references.citation: J Microsc. 2005 Mar;217(Pt 3):275-81
references.pmid: 15725131
references.citation: PLoS Biol. 2006 Apr;4(4):e86
references.pmid: 16602821