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

input_file_formats.txt · Last modified: 2012/04/18 16:44 by mbleda
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