Regulatory Analysis
This page allows you to perform perliminary regulatory analysis on a set of genes. This means that it will identify transcription factor binding sites (TFBS) in putative regulatory
regions of submitted IRGs. This enables the determination of any common factors that control the transcription IRGS.
This region consists of 1000 bp immediately upstream of the transcription start site and includes the 5 UTR of the gene. A tick box allows the selection of putative promoters from all the transcripts
for a given gene.
The searchable TFBS include
TATA, ISRE, STAT, IRF, and NFKB. You can also specify a cutoff value (between 0 and 1) for the quality of the match between the sequence of the transcription factor
binding matrix. A core match indicates the quality of the match between the core sequence of the transcription factor matrix and part of the
input sequence, while matrix match indicated the quality of match between the core sequence and flanking regions of this core sequence with a part of
your input sequence. The default for core and matrix match cutoff is 0.80. The higher the cutoff value the more stringent the
match between the core sequence and the regions in your input sequence. Currently only generic TFBS are identified.
To perform regulatory analysis on your gene of interest insert your gene list to in the search field.
Then choose the TFBS that you are interested in, the species of your gene list as well as a specific
cut off value (default is 0.8). If you want all transcripts of your input genes, tick the Include All Transcripts box, and then Search. You output for your analysis should be similar to:
Without all transcripts:
With all transcripts:
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