What is a transcript cluster?
What is a transcript cluster?
Transcript Cluster – A group of one or more exon clusters (on Exon Arrays) or probes (on Gene Arrays) covering a region of the genome reflecting all the exonic transcription evidence known for the region and corresponding to a known or putative gene.
What is Affymetrix probe id?
Probe Set Summary Probe Set ID – The identifier that refers to a set of probe pairs selected to represent expressed sequences on an array. The probe set names never change, but they can give you an idea of what was known about the sequence at the time of design. _at = all the probes hit one known transcript.
What is Affymetrix array?
The Affymetrix GeneChip Tiling Array Sets contain probes that cover virtually every base pair of the genome and are designed for identifying novel transcripts, mapping sites of protein/DNA interaction in chromatin immunoprecipitation (ChIP) experiments, and other experiments.
How do you convert Affymetrix to gene symbol?
If nothing works out,… you can use DAVID to convert Affymetrix probe ID to Gene Symbol. Step 1: Paste the Affy Probe ID in the “enter gene list” box. Step : Select Official gene symbol as identifier and Submit. DAVID will automatically recognize the probes and helps in converting them to Gene Symbol.
Who developed gene chips for Affymetrix?
Stephen Fodor
was founded by Stephen Fodor and his group, based on their earlier development of methods to fabricate DNA microarrays using semiconductor manufacturing techniques. In 1994, the company’s first product under the “GeneChip” Affymetrix trademark, an HIV genotyping chip was introduced, and the company went public in 1996.
What is probe in microarray?
What are probes and probesets? In expression arrays a probe (or oligoprobe) is a short DNA sequence targeting a short region of a transcript. They are used to detect the presence of nucleotide sequences through hybridisation to single-stranded nucleic acid due to complementarity between the probe and the target.
What is Affymetrix microarray data?
Affymetrix microarray data are normalized in three steps: background correction, to adjust for hybridization effects unrelated to the interaction between probes and target DNA; normalization, to remove systematic errors and biases thereby allowing data to be compared from one array to another; summarization, combining …
What happened to Affymetrix?
In 1994, the company’s first product under the “GeneChip” Affymetrix trademark, an HIV genotyping chip was introduced, and the company went public in 1996. On January 8, 2016, Thermo Fisher Scientific announced its acquisition of Affymetrix for approximately $1.3 billion, which closed on March 31, 2016.
How do you cite Metascape?
How to cite Metascape? Please cite the following paper: Zhou et al., Nature Communications 2019, 10(1):1523.. We will really appreciate if you also show our URL [https://metascape.org] in your text. Please avoid citing [https://metascape.org/gp/index.html#/main/step1], as that URL may be changed in the future.
How do I find my Ensembl ID?
Click “Attributes” (left menu) and expand GENE. Check Ensembl Gene ID, Transcript ID and Protein ID. Click “Results” (top left menu)
How does Affymetrix microarray work?
Affymetrix GeneChip System uses arrays fabricated by direct synthesis of oligonucleotides (probes) on the glass surface using the photolithographic technology employed in the semiconductor industry. Hybridization to Affymetrix chips is DNA:RNA. Control and experimental samples are hybridized to separate chips.
What is Rnaseq data?
RNA-seq involves conversion of a sample of RNA to a cDNA library, which is then sequenced and mapped against a reference genome. In addition to the ability to measure the level of gene expression, it provides further information on alternative splicing and non-coding RNA (such as microRNA) (Chaussabel et al., 2010).
What is the Affymetrix identifier for UniGene clusters?
The identifier is a number assigned by Affymetrix and does not refer to any external database. For HG-U133, HG-Focus, and newer arrays, the number of UniGene clusters detected by the probe set is also provided.
Transcript Cluster – A group of one or more exon clusters (on Exon Arrays) or probes (on Gene Arrays) covering a region of the genome reflecting all the exonic transcription evidence known for the region and corresponding to a known or putative gene.
Where does Affymetrix data come from?
Affymetrix data comes from the UniGene record for UniGene based arrays such as human, mouse, and rat. For arrays that are not based on the UniGene database, Affymetrix obtains the gene symbol from various sources including: FlyBase, WormBase, and Saccharomyses Genome Database.
What is a probe group in netaffx?
On Exon Arrays, a probe group can be a probe set, exon cluster, or transcript cluster .� On Gene Arrays, the only kind of probe group is the transcript cluster. NetAffx detail pages are provided for all probe groups of each type for Exon and Gene Arrays.
