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Hi Ensembl people,<div><br></div><div>We've recently begun using the "Codelink" microarray platform to analyze whole genome gene expression in rat. This product was developed by Amersham/GE_Healthcare, and is still being manufactured to this day by a spin-off company named Applied Microarrays (Tempe, AZ, USA). I have no affiliation with the company. The Rat Whole Genome platform file is GPL2896. We chose this platform as a 'first pass' to check gene expression levels relative to certain treatment regimes, with an eye towards KEGG or GO style pathway analysis.</div><div><br></div><div>Because of the age of the chipset relative to the Rat Genome sequencing efforts at the time (~2005), many thousands of the probes were solely identified by EST identifiers. Now many years later, thousands of the probes are still solely identified by EST identifiers.</div><div><br></div><div>My question is whether there is an Ensembl effort underway to update these whole-genome platform files (human, mouse, rat), specifically GPL2896??? The computational resources required to BLAST identify unknown genes for tens of thousands of EST sequences seems far beyond the capabilities of a simple end user. Furthermore the lack of a full per-gene information record ('hole-y data') makes it very difficult if not impossible to do pathway analysis.</div><div><br></div><div>Any advice appreciated,</div><div><br></div><div>Best Regards, Bill.</div><div><div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 11px; "><div>William Michels, Ph.D.</div><div>Assistant Research Biochemist</div><div>Department of Anesthesia</div><div>University of California, San Francisco</div><div>513 Parnassus Avenue S-261, Box 0542</div><div>San Francisco, CA 94143</div><div>phone: (415) 476-6231</div><div>fax (415) 476-8841</div><div>email: <a href="mailto:michelsw@anesthesia.ucsf.edu">michelsw@anesthesia.ucsf.edu</a></div></div></div><div><br class="webkit-block-placeholder"></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></span></span></span> </div><br></div></div></body></html>