Table of Contents
Input file formats
RENATO currently accepts input data in two formats: gene list and ranked gene list. The suitable file format must be used according to the functional enrichment method selected. Users can import their own regulatory annotations. Detailed information about the accepted formats is described below.
Here we also describe the supported identifiers.
Gene list
A list of unordered gene identifiers. There must be a single identifier per line. See an example of Homo sapiens identifiers list:
RUNDC3A RFX4 MKRN2 MAN2C1 HNRNPA3 GABRD FOXO1B ABLIM2 UBE2S TUBA8 ZNF852 ALPK1 ARSD BRPF1
This file format is suitable for the FatiGo method described in the Simple enrichment analysis section.
Ranked gene list
A two-column tab-delimited file containing the gene identifier in the first column followed by a value in the second column. For example:
HBG1 -11.7442369229016 APOL1 -11.5357469878867 MTSS1 -11.3757989614021 DPP4 -11.1635599336843 COL1A1 -10.0255643036678 RASL10A -9.97415705415455 MARCH8 -9.82174217995803 FUT2 -9.82119578502124 MYB 15.4342043731427 H2AFZ 15.9175276150186 IRAK3 16.0536043782225 ERG 16.3175493727468 FUT4 16.8855259613026 HMGN2P3 18.1188653702586
Values are any parameter that orders the list preferably based on experimental information. Ranking values are generally obtained from a differential expression analysis and represent the phenotype studied in the experiment when two experimental conditions are compared (case and control, time series, etc). However, other type of values such those from large-scale genotyping or evolutionary analysis can be used.
This is the suitable input for a Gene set analysis.
Annotation file
RENATO offers the possibility to use your own regulatory annotations instead of the ones provided (TFBSs and miRNA targets). The input format for regulatory annotations consists of a two-column file delimited by tab. The first column must indicate the target gene and the second column the regulator. Example:
BRCA2 hsa-miR-146a-3p CADM1 hsa-miR-192-3p CD59 hsa-miR-124-3p EMP1 hsa-miR-34a-3p FBXO28 hsa-miR-145-3p FOS hsa-miR-101-5p GAB1 hsa-miR-17-5p GATA6 hsa-miR-181c-3p KLK1 hsa-miR-224-3p PHKB hsa-miR-15a-5p PTEN hsa-miR-217
Supported identifiers
RENATO currently supports the following gene identifiers:
Human
Mouse
