Improving miRNA target prediction with gene expression profiles
TargetExpress requires a plain text file (*.txt or *.tab) with expression information of the cellular condition of interest. This file must have two columns, the first column must contain RefSeq ids (Reference Sequence) used by NCBI to identify transcripts and the second column numerical expression values. These expression values can be the output from any high-throughput technology like microarrays, RNA-seq, qPCR, etc. The values do not need to be normalized in any particular way, as long as they can be used to rank the transcripts by descending order. The RefSeq ids can be quoted or not and the two columns have to be separated by a tab or a white space. The following example shows the first lines from an RNA-seq experiment with expression values in RPKM:
NM_001101 114.156 NM_001402 143.874 NM_006472 26.705 NM_001927 1.196 NM_002084 6.146
Note: if you have any other type of identifier you can convert them to RefSeq ids using the DAVID gene ID conversion tool.