Ideas about what can I do with the raw data of gene expression and miRNA of Genechip Affymetrix?

Question

[agrandiadil]

Hello! I am an internship student and I have given the task to perform analysis in a given data, but now I should propose things to do with the data in order to obtain the most of them, I would really like to add value so I am eager to learn anything, but it should be in a time span of 2-3 months. Learnt: basics of R and Cytoscape.

The data obtained corresponds to Gene Expression and miRNA expression.

Experiment:

4 cell lines that received a pharmacological treatment.

Used:

-Human Gene 2.1 ST 24 array plate

-miRNA4.1 24 array plate

What I have:

-CEL files

-Full reports including the parameters to evaluate the quality of the experiment and the data of hybridation summarized with RMA algorithm.

-An Excel for each experiment, with the gene annotation, Fold Change, p-values etc...

If I should add any information say me and I will!

Con you give me any idea?

PS: I am a total begginer in Bioinformatics, my major is in Biotech.

Answer 1

[gandrescabrera]

I will ask you some items: RNAseq data? Tissue specific? Genome version (hg19/hg38?) Bibliography about drugs you used?

I think if you have RNAseq data that you could check about alternative splicing events on drug use. For that you can use a featureCounts (R package) for mapping the alignments to a exon.gtf file.

Idk if thats what you expect as an answer, Im also learning, but feel free to chat, I might help you or at least will try to throw some light (or more questions)

Cheers!