Results table

A description on how to interpret the results


The results are reported as a table, ranked by their significance. By default, a threshold of FDR<0.05 is applied. If you want to see the full result table, or if you have no "significant" result, you can select all predictions in the Main menue, and the entire table will be shown.

IndexFactor Fp-valueFDRFPF & G+no F & G+F & G-no F & G-Logo
1 V$NMYC_01 0 0.000005 0.000005 6 45 94 33307
2 V$MYC_Q2 0 0.000126 0.000252 5 46 95 33306

In the following, each column of the table is explained in detail:
  • Index: The row number.
  • Factor F: The name of positional freuquency matrix from Transfac. The binding sites are predicted using the positional frequency matrices from the Transfac database (for the version and links to the database, see our about page). The name of these matrices are composed out of V$ (which means vertebrate), then the name of the transcription factor, its family or another name describing it, and a quality or version number. Note that each factor may correspond to more than one of these matrices. Since Transfac is a proprietary database, we cannot include more information here - we instead provide a link to a page from the Gene Set Enrichment Analysis project, which provides some more information about the factor.
  • p-value: result of Fisher's excact test. For each of the matrices we have computed affinities to the promoters. Then we test, whether the high-affinity matches for the matrix are significantly enriched in the promoters of your submitted gene group (when compared to the reference group). This test is done using the Fisher's exact test, whose p-values are reported in this column. We do not recommend to rank by these p-values, but to take the multiple-testing-corrected values in the next column
  • FDR: false discovery rate. Since many matrices/factors are tested for enrichment, one needs to perform multiple testing correction. We use FDR, which is the false discovery rate. If you e.g. have a FDR below 0.05 this means that, on average, 5% of the enriched factors will be wrong.
  • FP: number of estimated false predictions at this p-value.
  • F & G+: number of predictions for this matrix/transcription factor among the submitted group of genes.
  • no F & G+: number of genes in the submitted group for which  this factor is not predicted to have a high affinity.
  • F + G-: number of predictions for this factor in the background set.
  • no F & G-: number of genes where this factor is not predicted in the background group.
  • Logo: Sequence logo visualising the positional frequency matrix for this factor. Sequence logos are a way to visualize the positional frequency matrix.