gene expression profilling

[dayana42200]

Hello everyone.

I have a questions on gene expression profiling.

1. Does the end product of gene expression profiling is in a DNA sequence? If so, does the sequence is in normal DNA sequence or mutated DNA sequence?
2. What are the method use to develop the expression profile?
3. Please share any related article of the method. Ive have search a lot on the method, but i cant understand since im not from bioinformatic background.
4. If anyone familiar with BRCA1 gene expression profiling, can anyone share with me the development of the profile?

Thank you for your time and reply.

[GenoMax]

1. If you are doing RNAseq then yes you would sequence DNA that is derived from RNA. Unless you know beforehand the DNA being sequenced may be normal or mutated.
2. DESeq2 , edgeR and LIMMA are some of the popular methods used for differential gene expression. They can also generate normalized data giving you a profile of gene expression.
3. Original concept came from microarrays. This link contains a basic introduction.
4. I am not sure what you referring to when you say profile. You can refer to this publication for a set of 50 genes that was identified to predict risk/classify breast cancers.

[dayana42200]

@GenoMax

Ive read the introduction of microarray. I dont really understand this statement.

"Both sets of labeled DNA are then inserted into the chip and allowed to hybridize - or bind - to the synthetic DNA on the chip.

If the individual does not have a mutation for the gene, both the red and green samples will bind to the sequences on the chip that represent the sequence without the mutation (the "normal" sequence).

If the individual does possess a mutation, the individual's DNA will not bind properly to the DNA sequences on the chip that represent the "normal" sequence but instead will bind to the sequence on the chip that represents the mutated DNA"

1. Synthetic DNA in the microarray, is the synthetic DNA is normal or mutated DNA or both?
2. Also for BRCA1 profile, I mean is a strand of DNA in a certain length that is able to detect BRCA1 gene.

[dayana42200]

@GenoMax

If read the introduction of microarray. I dont really understand this statement.

"Both sets of labeled DNA are then inserted into the chip and allowed to hybridize - or bind - to the synthetic DNA on the chip.

If the individual does not have a mutation for the gene, both the red and green samples will bind to the sequences on the chip that represent the sequence without the mutation (the "normal" sequence).

If the individual does possess a mutation, the individual's DNA will not bind properly to the DNA sequences on the chip that represent the "normal" sequence but instead will bind to the sequence on the chip that represents the mutated DNA"

1. Synthetic DNA in the microarray, is the synthetic DNA is normal or mutated DNA or both?
2. Also for BRCA1 profile, I mean is a strand of DNA in a certain length that is able to detect BRCA1 gene.