Data upload

There are 4 data files Paintomics will regularly accept:

  1. A tab-delimited file with transcriptomics data, containing genes in rows and samples in columns (Table 1). This is the only required parameter of the application. The first row must contain sample names, preferabily as short compact labels, and the first column must indicate gene identifiers. As a general rule Paintomics accepts EntrezGene IDs as gene identifiers, although for some model species (Table 2) other IDs such as ensembl IDs, refseq IDs, unigene IDs, as well as some affymetrix, agilent and illumina chips are also supported. Gene expression data should be in the log scale, positive values indicating over-expression and negative values indicating under-expression.


    Table 1: Transcriptomics data input format
    name treatment_1 treatment_2
    APOBEC3B -0.82 -0.1
    AA085955 -0.28 -0.32
    ATP11B 0.31 0.97
    AK092846 0.72 1.43
    DNAJA1 -1.68 -1.01
    THC2450799 0.19 -0.34
    EHMT2 0.15 0.45
    RPL23 0.09 0.32
    T12590 -0.18 0.59
    A_24_P704878 0.13 0.58
    RPS13 0.01 -0.13
    AK021474 0.25 -0.28
    HDDC3 -0.43 -1.53
    -- -- --



    Table 2: Species with authomatic gene ID convertion

    Name
    Arabidopsis thaliana
    Bos taurus
    Caenorhabditis elegans
    Danio rerio
    Drosophila melanogaster
    Homo sapiens
    Mus musculus
    Rattus norvegicus
    Saccharomyces cerevisiae


  2. A list of significant genes (optional). This is a ONE column text file with the names of a selection of genes from the previous file. Note that the type of gene indentifier used for the transcriptomics data and the significant list must coincide.

  3. A tab-delimited file with metabolite measurements (optional) for the same samples as in the transcriptomics dataset (Table 3). Metabolite names should be placed in rows and identical sample ID must label columns. Data should be also provided in log scale, negative values indicating reduced metabolite levels and positive values indicating increased metabolite levels.


    Table 3: Metabolomics data input format
    name treatment_1 treatment_2
    isoleucine 0.14 -0.04
    leucine 0.02 0.02
    valine 0.02 0.02
    phenylalanine 0.02 -0.01
    alanine -0.02 -0.02
    lactate 0.33 0.05
    acetate 0.01 -0.12
    pyruvate 0.09 -0.06
    citrate -0.01 -0.06
    -- -- --


  4. A list of significant metabolites (optional). Similarly to the gene data, this is a ONE column text file containing a subset of metabolites names from the metabolomics dataset.

  5. Organism. Currently Paintomics supports 101 species (see Appendix A). If your species is not available at the drop-down menu, please contact with the user support service at paintomics@cipf.es.

Once data is uploaded and the species of your choice is selected the application can be lanuched by cliking on the Run buttom.

Fernando Garcia-Alcalde and Ana Conesa