Gene Pix In Situ and other pictures of gene hybridization at UCSC.

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:– 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

• 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

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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