RFLOMICS can handle three types of omics (transcriptomics (RNAseq), proteomics and metabolomics) and several datasets per omics generated from similar experimental design. Each dataset must have a complete design.
Below each input file is detailed.
This file provides the experimental design table. The first column indicates the sample names. Next columns indicate experimental conditions (called biological factors or technical/batch factors) and metadata (optional). Each row describes a sample by specifying the level for each experimental condition. This file is edited by the user and must contain a header with column names corresponding respectively to the factor names and metadata names.
It is advised that each factor’s level starts with a letter (for example, for a factor called Month, it is better to write M1 rather than 1).
For each omics: The matrix-like file with abundance of omics data is needed. The first column indicates feature names (genes, proteins, or metabolites), column headers indicate the sample names.
For RNAseq data the values correspond to raw read counts per genes or transcripts.
For proteomics data the values correspond to intensity of proteins.
For metabolomics data the values correspond to intensity of metabolites.
This file contains annotation about biological functions of genes/proteins/metabolites, or their implication in biological pathways. This annotation is needed to compute Over Representation Analysis (ORA). This file must contain at least 2 columns, names of features (identical to the ones used in the abundance matrix) and term identifiers (ex. GO term accession : GO:0034599). It is possible to add 2 more columns: names of terms (ex. cellular response to oxidative stress) and the domain of annotation (ex. biological_process).
| Gene ID | GO term accession | GO term name | GO domain |
|---|---|---|---|
| AT4G36648 | GO:0006412 | translation | biological_process |
| AT4G36648 | GO:0030533 | triplet codon-amino acid adaptor activity | molecular_function |
| AT1G18745 | GO:0006396 | RNA processing | biological_process |
| AT1G18745 | GO:0005730 | nucleolus | cellular_component |
| AT3G00980 | GO:0006396 | RNA processing | biological_process |
| AT3G00980 | GO:0005730 | nucleolus | cellular_component |