Gene Expression Between Different Organisms

Question

[milady81]

Hi everybody,

I need your help regarding the gene expression analysis.

I am working on genes from 9 Amoeba species. My Prof. said that next step of my analysis should be to do the gene expression of the genes I have. I did annotation before, assembly of transcriptome, and all analysis which should be done after sequencing. I am using the RNA-Seq data.

I thought the gene expression analysis could be done only within one species. Example I would have three the same genes "AB" but from different Yeast growth stage. I could check the gene expressions between them and find example: that on log stage the gene AB is overexpressed compared with the same gene but from the dying phase. Is that correct? Hope I explained simply.

I am working on 12 proteins (genes) but in 9 species of Amoeba. Some distance between these Amoebas is huge, some smaller. How it is possible to do the gene expression of the 12 genes between these species? Is that even possible?

I am sorry I just started to analyse what should be my next step of the PhD project, this is the reason if the question is "stupid" please take my apologize.

Thank you very much

Dorota

[Ginsea Chen]

Hi Dorota

you means you have some coding sequences and RNA-seq data of different species, you want to find the different expression of these genes through RNA-seq data analysis.

If what I said is ture, I think you can learn Tophat and cufflinks and cummeRbund packages of R. These days I was learning the operation of this analysis, I think we can communicate with each other.

The function of Tophat and cufflinks is to map your reads to reference genome and R packages is used to obtain rpkm value of the genes.

Answer 1

[Istvan Albert]

One possibility is to characterize the gene expression levels within one species then compare those relative expression across species.

For example:

1. it is possible to find one gene to be differentially expressed in one species but not in others.
2. it is possible to find the entire group of genes to be expressed say above average in one species and under the average in one or more of the others
3. it is possible to find genes with a specific functional role expressed above average in one species and under average levels in one ore more of the others

etc. there are many such observations that one could test.

What is important to pose the question correctly and use the correct statistical test and properly correct for the multiple comparisons that you may be making.