Transcript genePix

Gene Pix
In Situ and other pictures of gene
hybridization at UCSC
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Data Sets
• Paul Gray - ~1000 mouse transcription factor
genes - whole embryo & sections. These are in the
database now.
• Other potential sources:
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German AxelDB frog in situs
Japanese NIBB frog in situs (have nice browser)
Genepaint.org - mouse stuff
EMAGE and Jackson Lab mouse images
• From development and other journals, copyright issues.
– Nathaniel Heintz BAC expression constructs
– Eddy Rubin lab mouse embryos
– UCSF cell-localization stuff?
Types of images
• Whole animal vs.
sectioned tissues, vs.
single cell.
• Single vs. multiple
probes within same
image.
• Single image vs. image
series (movies even).
• RNA, Antibody, Fusion
protein.
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Mitotic cell 3 stains
Gene Pix Programs
• genePixLoad - loads SQL database from a well
defined format involving a .ra file and a tab
separated file. See genePixLoad.doc
• loadMahoney - converts Paul Gray (Mahoney
center) spreadsheet and image directory into
genePixLoad format
• Hg/lib/genePix.c - interface with SQL database.
• hgGenePix - cgi script to display images
• knownToGenePix - makes table in mm5 (or other)
genome database to connect known genes to
genePix Ids.
Gene Pix Database
• Just a single database for all assemblies of
all organisms.
• A knownToGenePix table in the assembly
database.
GenePix tables
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fileLocation - directory
bodyPart - whole, brain etc.
sliceType - transverse, sagital
treatment - tech details
contributor - who done it
Journal - scientific journal
submissionSet - info about a
whole set of images from one
author
• sectionSet - links together
separate sections of same
specimen.
• Gene - gene info
• geneSynonym
• Antibody - info on an
antibody
• probeType - antibody, RNA,
fusion protein
• Probe - links gene, primers,
sequence Ab.
• probeColor - color probe is
• imageFile - file containing
image
• Image - a single image.
• imageProbe links image and
probe
Some Anatomy Required
QuickTime™ and a
TIFF (LZW) decompressor
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QuickTime™ and a
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are needed to see this picture.
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
Especially with slices
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Edinburgh mouse atlas
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Theiler Stages
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Later Stages
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NIBB Japanese Frog Site
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Earlier Stages
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GenePix software demo time