Affymetrix Human Genome U133 Plus 2.0 Array sequence analysis

Question

[sujasubramanian]

Hello i am working with Affymetrix Human Genome U133 Plus 2.0 gene expression dataset, i want to analyse each gene sequence wise, is there any option to collect the sequences corresponding to each probe id .

[sujasubramanian]

can anybody help me to find a good journal for publishing my research work, i am running out of time .Bioinformatics (SCI indexed) journal is preferable.

[Kevin Blighe]

How is this related to this thread, which is about the Affymetrix Human Genome U133 Plus 2.0 Array probe sequences?

Answer 1

[Kevin Blighe]

You can get the sequence of each probe in tabular or FASTA format from the Affymetrix support site: Human Genome U133 Plus 2.0 Array - Support Materials.

I give a previous example for another Affymetrix array, here: Sequence corresponding to each probe id of affymetrix gene chip

You can also get the coding / mRNA sequence of the gene targeted by the probe in R via biomaRt. I give an example of this, here: A: getting gene sequence from probeset id

I believe there are other ways to do this, too.

Kevin

[sujasubramanian]

sorry by mistake i post this here

[sujasubramanian]

hello, i have used the support materials from affymetrix support site, instead of using refseq/ensembl i am using alignment column vales for my studies , so i can get multiple probeid for each gene i considered each differently with this alignment infn, but i come across a problem related with some genes for eg gene DDX11L2 residing in chr2, according to alignment it is in both chr1 and chr2, how can i interpret the change, please help me :

223777_at   **DDX11L2** chr1:13680-14407 (+) // 91.71 // p36.33 /// chr16:63361-64088 (+) // 91.84 // p13.3 /// chr9:13793-14520 (+) // 91.58 // p24.3 /// chr15:102516762-102517489 (-) // 91.71 // q26.3 /// chr2:114356610-114357337 (-) // 92.73 // q13

[Kevin Blighe]

These 'DDX11L' genes are pseudogenes, so, the probes will map to multiple regions of the genome. Normally, you will have absolutely no interest in data from these genes.

[sujasubramanian]

from where i get the infn about pseudogenes, is that ok i reject them from my analysis

[Kevin Blighe]

I just knew from experience that the 'DDX' genes have known pseudogenes. I would expect that information on gene biotype (i.e., lincRNA, protinc coding, pseudogene, etc) is stored within the other Affymetrix annotation files, no? If not, you could generate a list of genes and their biotypes using the data from GENCODE: https://www.gencodegenes.org/human/ (you will need the Comprehensive gene annotation).

I would not exclude these from the initial data processing of your microarray. Which commands have you used? Have you used oligo package?

Does that help?

[sujasubramanian]

biocLite('affy')
library(affy)
ensembl=useMart("ensembl")
ensembl=useDataset("hsapiens_gene_ensembl",mart=ensembl) 
MyBioinfData<-ReadAffy()
eset.rma<-rma(MyBioinfData)

affy package is used for normalisation, and get the eset (expression set data ), i directly link this expression values corresponding to each probe id with there gene name from affymetrix support site, no filtering at all

[Kevin Blighe]

That generally looks fine. I presume that you are using ensembl for a good reason? How was the box-and-whisker plot of the normalised, transformed data?

[sujasubramanian]

IS THERE IS ANY WAY TO PRODUCE MAS5 S/W RESULT WITH BOOLEAN LOGIC, PRESENCE 'p', ABSENCE 'A', LIKE. I AM USING TWO DATA SET ONE IS .CEL FILES I NORMALIZED WITH RMA, ANOTHER ONE GIVE EXPRESSION VALUES FROM MAS5 S/W INTENSITY VALUES, WITH BOOLEAN VALUES

[Kevin Blighe]

You left Caps Lock on.

[Kevin Blighe]

Where have you seen this: MAS5 S/W RESULT WITH BOOLEAN LOGIC ?