How to find cumulative gene score for gene list?

Question

[John]

Hi there,

How to find cumulative gene score for particular gene list, to show the cumulative gene expression(around 100 genes) across multiple samples (using line graph) of RNA seq data.

Thanks

[Ram]

What is a "gene score"? Also, this is a multi-step question. What have you tried? What does your dataset look like right now?

[John]

thanks for the response,

I have RNA seq data set with six columns. I want to show particular list of genes have increased/decreased in every column. How I can I do this?

I don't want to do heat Map for every gene. I want something like cumulative gene expression value/score

[Kevin Blighe]

six columns

...and what are these 6 columns? We cannot see them from here (?)

Where have you read about this 'cumulative gene expression value/score' - please link us to the literature sources.

[John]

I'm sorry, I just created the term, because I didn't 't know how to explain it. I don't find any literature for what I want to do.

I have gene expression matrix, with columns= 6 different treatments, rows= genes.

I want to plot 100 gene's expression (y axis) vs 6 treatments (x axis). Is there any way to do this without plotting for each and every gene. My graph should show whether those genes are unregulated/enriched in every treatment.

please help.

[Kevin Blighe]

Like either of these?

• A: Network/Pathway Analysis from Mass Spec data
• A: Boxplot in ggplot2

[John]

Yeah , I liked the box plot. but still I can't really show the differences using Boxplots. Can we calculate expression score for each gene, by comparing the all columns, them sum up? Something like this? I don't know whether I will endup writing new code.