Kafatos:Microarray annotations: Difference between revisions
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{{Kafatos/Christophides Lab}} | |||
==MMC2 annotation== | ==MMC2 annotation== | ||
'''EMBL A. gambiae MMC2 12k v1''' | '''EMBL A. gambiae MMC2 12k v1''' | ||
Download [[Media:EMBL MMC2 12k v1 ANNOT single line.txt|this tab-delimited file of annotations]] based on the mapping of MMC2 reporters to the AgamP3.3 assembly/gene build using the VectorBase pipeline | Download [[Media:EMBL MMC2 12k v1 ANNOT single line.txt|this tab-delimited file of annotations]] based on the mapping of MMC2 reporters to the AgamP3.3 assembly/gene build using the VectorBase pipeline. All annotations are derived from the corresponding Ensembl gene(s) and transcript(s). When a microarray reporter (probe) corresponds to more than one gene, the corresponding annotations are joined with a vertical bar ("|"). Duplicate annotations (e.g. where two different transcipts contain the same domains) are removed. | ||
If your existing data files contain ENSANGTnnnnnnnnnn reporter IDs, you will have to convert them to "gene-neutral" IDs (e.g. 123.4.5) using the [[Media:MMC2 grid1 150205.gal|this GAL file]], before using the annotation file. | If your existing data files contain ENSANGTnnnnnnnnnn reporter IDs, you will have to convert them to "gene-neutral" IDs (e.g. 123.4.5) using the [[Media:MMC2 grid1 150205.gal|this GAL file]], before using the annotation file. | ||
'''Warning:''' error found for reporter 64.1.1 (it is not spotted many times as the GAL file suggests) [[User:Maccallum|Maccallum]] 12:37, 6 March 2007 (EST) | |||
To look up the current genome mapping of an MMC2 reporter, use a URL in the following style: | |||
http://agambiae.vectorbase.org/Genome/FeatureView/?type=OligoProbe;id=1.2.3 | |||
replacing the "1.2.3" with your reporter ID. | |||
Latest revision as of 05:13, 20 April 2007
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MMC2 annotation
EMBL A. gambiae MMC2 12k v1
Download this tab-delimited file of annotations based on the mapping of MMC2 reporters to the AgamP3.3 assembly/gene build using the VectorBase pipeline. All annotations are derived from the corresponding Ensembl gene(s) and transcript(s). When a microarray reporter (probe) corresponds to more than one gene, the corresponding annotations are joined with a vertical bar ("|"). Duplicate annotations (e.g. where two different transcipts contain the same domains) are removed.
If your existing data files contain ENSANGTnnnnnnnnnn reporter IDs, you will have to convert them to "gene-neutral" IDs (e.g. 123.4.5) using the this GAL file, before using the annotation file.
Warning: error found for reporter 64.1.1 (it is not spotted many times as the GAL file suggests) Maccallum 12:37, 6 March 2007 (EST)
To look up the current genome mapping of an MMC2 reporter, use a URL in the following style:
http://agambiae.vectorbase.org/Genome/FeatureView/?type=OligoProbe;id=1.2.3
replacing the "1.2.3" with your reporter ID.
