Automated pipeline for atlas-based annotation of gene expression patterns: application to postnatal day 7 mouse brain.
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.
Carson
James
J
Biological Monitoring and Modeling Group, Pacific Northwest National Laboratory, Richland, WA, USA.
Ju
Tao
T
Bello
Musodiq
M
Thaller
Christina
C
Warren
Joe
J
Kakadiaris
Ioannis A
IA
Chiu
Wah
W
Eichele
Gregor
G
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
IEEE Trans Med Imaging. 2002 Nov;21(11):1421-39
12575879
J Histochem Cytochem. 1995 Apr;43(4):347-52
7897179
Am J Physiol Gastrointest Liver Physiol. 2006 Dec;291(6):G1041-50
16825705
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D637-41
16381949
Symp Geom Process. 2003;2003:166-176
20631855
Genome Biol. 2008 Jan 30;9(1):R23
18234097
Med Image Anal. 2008 Oct;12(5):616-25
18640069
IEEE/ACM Trans Comput Biol Bioinform. 2007 Jul-Sep;4(3):382-393
17666758
Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18267-72
17108082
Nat Neurosci. 2004 May;7(5):483
15114362
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D552-6
14681479
Proc Natl Acad Sci U S A. 2008 Jan 29;105(4):1291-6
18216249
Bioinformatics. 2004 Jun 12;20(9):1453-4
14871861
Conf Proc IEEE Eng Med Biol Soc. 2004;2004:2917-20
17270888
Nature. 2007 Jan 11;445(7124):168-76
17151600
Mech Dev. 2000 Nov;98(1-2):77-94
11044609
J Am Med Inform Assoc. 2001 Sep-Oct;8(5):401-30
11522763
J Immunol Methods. 1989 Dec 20;125(1-2):279-85
2558138
Radiographics. 2001 May-Jun;21(3):789-98
11353125
J Digit Imaging. 2009 Oct;22(5):492-502
18478296
Nat Neurosci. 2004 May;7(5):429-33
15114353
J Neurosci Methods. 2006 Sep 30;156(1-2):84-100
16580732
PLoS Comput Biol. 2005 Sep;1(4):e41
16184189
PLoS Genet. 2007 Oct;3(10):1867-83
17953485
IEEE Trans Med Imaging. 2007 May;26(5):728-44
17518066
Curr Opin Neurobiol. 2002 Oct;12(5):562-5
12367636
Novartis Found Symp. 2001;239:129-46; discussion 146-59
11529308
Nature. 2003 Oct 30;425(6961):917-25
14586460
Nucleic Acids Res. 2001 Jan 1;29(1):98-101
11125060
J Anat. 2004 Feb;204(2):93-102
15032916
J Microsc. 2005 Mar;217(Pt 3):275-81
15725131
PLoS Biol. 2006 Apr;4(4):e86
16602821