What are the data formats accepted by miRNet?

There are two main data types: a list of miRNAs, miR-SNPs, genes, small molecules, etc.; or a data table from qPCR, microarray or RNAseq for mRNA or miRNA experiments. The list data is a list of IDs with optional fold change values. The expression data is a table in tab delimited text file format with miRNAs/gene IDs in rows and samples in columns. The first column is for gene or probe IDs. The following common ID types are supported:

  • miRNA IDs: miRNA names or Accession numbers based on current miRBase. At the moment, miRNet supports miRBase IDs (preferred for older version IDs) and Accession numbers from version 15 to current (version 22). In addition, miRNet can automatically link miRNA precursor to their mature forms. For example, if you enter a miRNA precursor (e.g. hsa-mir-3140), miRNet will convert to its mature forms: hsa-miR-3140-5p and hsa-miR-3140-3p. Then, both precursor and mature forms will be searched in the internal database for their targets. (Note, please make sure your entry is valid miRBase ID);
  • miR-SNP IDs: rsID (reference SNP ID number) or chromosome:position based on GRCh37/hg19 reference;
  • Gene IDs: Entrez ID, Ensembl gene ID, official gene symbols, Ensembl transcript ID, GenBank Accession, and RefSeq ID (note, the support for last three IDs are only available for human and mouse);
  • Probe IDs: A total of 40 popular microarray platforms from Affymetrix, Illumina and Agilent are supported;