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Author: Admin | 2025-04-28
Use a different naming convention than the genes in the data file,and thus with a cross reference file it is possible to match a gene in the datafile with its annotation in the annotation file even when the symbol used in the datafile does not appear in the annotation file.Note that the cross reference file is only used to map between gene symbol.Any symbols on the same line are considered to be equivalent where symbols are delimited by tabs,a pipe(|), a comma (',') or a semicolon (;). The file can either be in plain text or gzipped version of a text file in this format.Sample cross reference file:GeneA SymbolAGeneB SymbolBGeneC SymbolC3. Options (Optional, iDREM can run without specifying options)The options can be used to provide optional data sets or search setting for model prediction.model searching optionsThe model searching options include "Gene Annotations", "GO Analysis", "DECOD Options", "Expression Scaling Options","Filtering Options", "Search Options" and "Model Selection Options".Note users can use the default parameters provided (no need to specify those options).Please refer to the manual for detailed description of those options if users want to changethe model searching parameters.datasets optionsThere are 3 additional datasets options including "microRNA Option", "Epigenomics Option" and "Proteomics Option".This optional datasets can provide additional regulatory information, which is helpful for iDREM model prediction.microRNA OptionUsers are able to specify the miRNA information (It’s optional.If the miRNA information is available, if will help to predict the regulatory model). There are severalmajor fields for this option dialog.microRNA-gene Interaction SourceThis specifies the miRNA-gene interaction. By default, we provided the miRNA-gene interaction predicted by miRanda for Human, Rat, Mouse, Fruitfly and Mematode.microRNA-gene Interaction FileUsers are also able to use customized miRNA-gene interaction files. The miRNA-gene interaction must follow the following format requirement. 1st column: miRNA ID 2nd column: gene symbol 3rd column: regulation (It can be binary 1/0 or a float binding score in range [0,1]) The columns are tab-delimited.example file: MIRNA GENE INPUT dme-miR-1 CG18769 1 dme-miR-1 CG11710 1 dme-miR-1 CG5522 1 dme-miR-1 apt 1 dme-miR-1 CG3338 1 dme-miR-1 LIMK1 1microRNA Expression Data FileThis field specifies the microRNA expression data file.The microRNA
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