which feature is considered as expression level ?

Question

[aaponcseku]

I have 2 questions. I am very new in bioinformatics field. I am working on NCI-60 Cancer cell lines to find out miRNA and their target mRNA with computational methods by Machine Learning.

For the miRNA expression profiling in this sample. there are ID_REF and value(normalized log2 expression) columns. Can I use this value as expression value of each miRNA?

Again for the same sample the mRNA profiling here gives many columns (ID_REF, CHPPairs, CHPPairUsed, Value, CHPDetection and CHPDetectionPvalue).

Which column can be used as the expression value of each mRNA (if possible)?

Besides, if you give short notes or reference about those headers (CHPPairs, CHPPairUsed, Value, ...) it will be very helpful.

Thank you for reading :)

Answer 1

[cpad0112]

I would use corresponding GSE series for microRNA profiling (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26375) and mRNA profiling (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5720) for any correlation between miRNA and mRNA expression studies in the same cell lines.

[aaponcseku]

ah ! yes ! i found series matrix files and they gives a matrix like representation. thank you !!! :D