Viewing oPOSSUM Results

Choose Genes List Analysis Tools in the main menu.
Click Analyze a gene list. A page displays the gene lists to which you have access.
Click the gene list for which you want to view oPOSSUM results.
Click the Promoter tab. The Promoter page displays with results organized into tables by the type of analysis performed.
Click a row in the oPOSSUM Results table. The oPOSSUM Results page displays the parameters used in the oPOSSUM analysis. It also displays transcription factors based on the One-Tailed Fisher Extract Probability Analysis and the Z-score Analysis.

Take a look

oPOSSUM Results Table

The table contains the results from oPOSSUM, ordered by p-value from most to least significant (lower to higher p-value). The columns are:

Column Name	Description
TF	The name of the transcription factor.
TF Class	The class of transcription factors to which the transcription factor belongs.
TF SuperGroup	The taxonomic supergroup to which this transcription factor belongs.
IC	The information content or specificity of this TFBS profile's position weight matrix.
Background Gene Hits	The number of genes in the background set for which this TFBS was predicted within the conserved non-coding regions.
Background Gene Non-Hits	The number of genes in the background set for which this TFBS was NOT predicted within the conserved non-coding regions.
Target Gene Hits	The number of genes in the included target set for which this TFBS was predicted within the conserved non-coding regions.
Target Gene Non-Hits	The number of genes in the included target set for which this TFBS was NOT predicted within the conserved non-coding regions.
Background TFBS Hits	The number of times this TFBS was detected within the conserved non-coding regions of the background set of genes.
Background TFBS rate	The rate of occurrence of this TFBS within the conserved non-coding regions of the background set of genes. The rate is equal to the number of times the site was predicted (background hits) multiplied by the TFBS profile, divided by the total number of nucleotides in the conserved non-coding regions of the background gene set.
Target TFBS hits	The number of times this TFBS was detected within the conserved non-coding regions of the target set of genes.
Target TFBS rate	The rate of occurrence of this TFBS within the conserved non-coding regions of the included target set of genes. The rate is equal to the number of times the site was predicted (target hits) multiplied by the TFBS profile, divided by the total number of nucleotides in the conserved non-coding regions of the included target gene set.
Z-score	The likelihood that the number of TFBS nucleotides detected for the included target genes is significant as compared with the number of TFBS nucleotides detected for the background set. Z-score is expressed in units of magnitude of the standard deviation.
Fisher score	The probability that the number of hits vs. non-hits for the included target genes could have occurred by random chance based on the hits vs. non-hits for the background set.
P-value	The probability that the number of hits vs. non-hits for the included target genes could have occurred by random chance based on the hits vs. non-hits for the background set.

Click a TF ID to open the JASPER website for that transcription factor.
Click a link in the Target Gene Hits column to view a list of associated genes for that link. The Associated Genes page displays.

Click a link in the Target TFBS Hits column to view a list of associated genes for that link. The Associated Genes page displays.