PROFAT is a computational tool to quantify the thermogenic potential
(BAT content) of adipose tissue samples from whole-genome expression
profiles
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Either a single sample or better multiple samples with a mixture of BAT and WAT.
Multiple samples with only BAT or WAT is not supported due to automatic batch removal.


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Step 1: Selecting files for the analysis

Microarray Data. Microarray datasets can be uploaded in two formats: normalized MicroArray data and raw CEL file (also in the compressed format). Only raw CEL data from Affymetrix platforms are supported. Data should always be log-based and the correct chip type has to be chosen.
RNA-seq Data. To analyze RNA-seq data, the user must upload a data file containing the raw reads count. Raw fastq/BAM files are not supported.
Notes: The upload must not exceed 60MB in size. Uploaded files may be raw CEL and text files or compressed using .gz, .tar.gz and .zip.

Step 2: Input file format

Microarray Data. With the exception of raw CEL files from microarray analyses, all other files should be formatted as it follows: 1st row, without leading tab: Sample name; 1st column: ENSEMBL genes IDs (e.g., ENSG00000109424); Following columns contain log-based intensity values. Please see the example below.
Example file: normalized mouse MicroArray
RNA-seq Data. RNA-seq data files should be formatted as it follows: 1st row, without leading tab: Sample name; 1st column: ENSEMBL genes IDs (e.g., ENSG00000109424); Following columns contain raw reads count. Please see the example below.
Example file: mouse RNA-Seq
To generate a data file with raw reads count, the following steps are recommended:
  1. The reference genome and gene annotation file for Homo sapiens and Mus musculus (gtf file format) can be downloaded from Ensembl FTP repository ftp://ftp.ensembl.org/pub/release-81/gtf/
  2. For genome alignment, RNA-seq fastq files can be processed with Tophat software package (https://ccb.jhu.edu/software/tophat/index.shtml)
    tophat -G gtf_file -o results_dir bowtie_index fastq_file
  3. Raw reads count files can be generated using htseq-count software http://htseq.readthedocs.io/en/release_0.9.0
    htseq-count -s no sam_file gtf_file raw_reads_file





FAQ

Can I upload multiple samples?

Since all uploaded samples will be treated as one batch, only one batch should be uploaded at once. This can otherwise seriously affect analysis and prediction.

When I press “compute”, nothing happens?

First try to reload the page using CTLR-R (PC) or CMD-R (Mac) and see if it persists. Check that Javascript is enabled and you use a current web browser. Check with your network administrator whether a proxy interferes.

When I select raw CEL data file, I could not find my chip type?

We only support Affymetrix platforms for the raw data. You could upload the normalised data if the data are generated using other platforms.

The calculation seems to hang?

It may take about 5-10 mins.

Error: length of 'dimnames' [2] not equal to array extent?

Check whether you have chosen the correct species.

Error: requires numeric/complex matrix/vector arguments

Check the first line of your data file. It should have the sample names in the first line without a leading tab.