Question: which feature is considered as expression level ?
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gravatar for aaponcseku
5.1 years ago by
aaponcseku10
Bangladesh
aaponcseku10 wrote:

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 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM647461

there are ID_REF and value(normalized log2 expression) column. Can I use this value as expression value of each miRNA ?

again for the same sample the mRNA profiling here http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM133565 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 :)

gene rna-seq R genome • 1.2k views
ADD COMMENTlink modified 5.1 years ago by cpad011214k • written 5.1 years ago by aaponcseku10
2
gravatar for cpad0112
5.1 years ago by
cpad011214k
India
cpad011214k wrote:

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.

ADD COMMENTlink written 5.1 years ago by cpad011214k

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

ADD REPLYlink written 5.1 years ago by aaponcseku10
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