Can Affymetrix HG-U133 Plus 2.0 test LncRNA?

Question

[ybling2008]

Can Affymetrix HG-U133 Plus 2.0 test LncRNA?

The information is from Affymetrix website First and most comprehensive whole human genome expression array Convenient one-array view. Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts. Use the Power of the Probe Set and get multiple independent measurements for each transcript that deliver the greatest accuracy and reproducibility of any microarray platform. GeneChip® System: Richer data, sharper insights, better decisions Array Profile All probe sets represented on the GeneChip® Human Genome U133 Set are identically replicated on the GeneChip® Human Genome U133 Plus 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz Golden-Path human genome database (April 2001 release). In addition, there are 9,921 new probe sets representing approximately 6,500 new genes. These gene sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from the UniGene database (Build 159, January 25, 2003) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the NCBI human genome assembly (Build 31).

Answer 1

[karl.stamm]

That marketing material claims they have a lot of coverage in a lot of places.

To know if the chip will assay the things you want it to, you will have to find the technical details of the platform, and search for your desired sequences. It's the only certain way.

Read over this one for a more technical description: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570

The GEO website includes a table of all the probe IDs and what they map to. Now you just have to define your desired sequences and search for them.

Answer 2

[Denise CS]

If you check with Ensembl BioMart, you will see that this array seems to be used to monitor the expression of just over 2k lincRNA genes. Some of the probes are 1561398_at and 237540_at. If you know R, use biomaRt in bioconductor. You can check the alternatives to go about Extracting data with BioMart. This is an example of perl code that will give you the ENSG ID, ENST ID, associated gene name and probeset:

An example script demonstrating the use of BioMart API. This perl API representation is only available for configuration versions >= 0.5 use strict; use BioMart::Initializer; use BioMart::Query; use BioMart::QueryRunner;

my $confFile = "PATH TO YOUR REGISTRY FILE UNDER biomart-perl/conf/. For Biomart Central Registry navigate to http://www.biomart.org/biomart/martservice?type=registry"; NB: change action to 'clean' if you wish to start a fresh configuration
and to 'cached' if you want to skip configuration step on subsequent runs from the same registry

my $action='cached'; my $initializer = BioMart::Initializer->new('registryFile'=>$confFile, 'action'=>$action); my $registry = $initializer->getRegistry;

my $query = BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');

$query->setDataset("hsapiens_gene_ensembl");
$query->addFilter("biotype", ["lincRNA"]); 
$query->addFilter("with_affy_hg_u133_plus_2", ["Only"]);
$query->addAttribute("ensembl_gene_id");
$query->addAttribute("ensembl_transcript_id");
$query->addAttribute("external_gene_name");
$query->addAttribute("affy_hg_u133_plus_2");

$query->formatter("TSV");

my $query_runner = BioMart::QueryRunner->new(); GET COUNT $query->count(1); $query_runner->execute($query); print $query_runner->getCount();

<h6>#</h6>

GET RESULTS to obtain unique rows only $query_runner->uniqueRowsOnly(1);

query_runner->execute($query); query_runner->printHeader(); query_runner->printResults(); query_runner->printFooter();

<h6>#</h6>