Case studies using DNNESCAN

Identification of TFBSs in Yeast Genomic Regions

DNNESCAN can be used to search for putative transcription factor binding sites (TFBSs) in given DNA sequences extracted from the Saccharomyces Cerevisiae genome. The users can search for the occurrences of BSs of a single TF or multiple TFs. In this case study, we search for BSs of the ABF1 protein in five genomic sequences (in the 'test_abf1.fasta'). Seven binding sites are found for the ABF1 protein in these DNA sequences. The DNNESCAN report can be seen here.

Identification of Gene Regulators

DNNESCAN can be also used to find the TF proteins that regulate a particular gene. In this case study, we search for potential regulators for three genes: YBR146W, YAL053W and YNL118C (in the 'ident_regulators.orf'). The scan results show that YBR146W is likely to be regulated by ABF1 only, YAL053W is likely to be regulated by eleven TFs (PHD1, UME6, SUT1, FKH1, FHL1, CBF1, REB1, ABF1, SWI5, SWI4 and DIG1) and YNL118C is likely to be regulated by five TFs(ABF1, REB1, SUT1, SWI5 and SKN7). The DNNESCAN report can be seen here.

Identification of TF Target Genes

Identifying the target genes of a TF is an important step towards understanding the transcriptional gene regulatory network (GRN) of an organism. DNNESCAN can be used for this purpose as it scans the promoters of a list of genes and identify potential targets. In this case study, we look for potential targets for the REB1 transcription factor in a list of 100 genes (in the 'ident_targs.orf'). The scan results show that around 70 genes are likely to be regulated by REB1. The DNNESCAN report can be seen here.

Case Studies Data

The data files used to generate the HTML reports of these three case studies can be downloaded with DNNESCAN program from the download page.