Example: Knocked-out study

At the moment, one of the most popular experimental approaches to investigate gene function is based on generation of omics data in experimental models where the gene of interest has been manipulated (knocked-out, silenced or overexpressed). However, often, identification of the causative relationship between knocked-out gene and modulated genes is not obvious. The Gene vs Gene list procedure of BioProfiling could provide statistical evidences that modulated genes are located on signalling/interaction network in close vicinity to the manipulated gene.

Gene expression profiling of mouse organs from genetically modified models are commonly employed to identify molecular functionality related to a biological phenotype associated to the gene of interest. For example, TAp73 deficient mice (TAp73-/- mice) display a complex and heterogeneous phenotype that ranges from enhanced tumourigenesis to infertility. The study reported a gene expression analysis in TAp73-/- ovary with ~50 genes whose expression have been significantly upregulated by TAp73 knock-out. To use novel functionality of BioProfiling we have compiled 2 gene lists: gene list "a" covering only one gene (TAp73) and gene list "b" covering upregulated genes.

BioProfiling network model inferred using Intact protein interactions network. Out of ~50 upregulated genes 22 genes could be mapped to Intact network and all of them are located within 2-3 steps from TAp73. P-value computed by resampling procedure ( ~ 0.02) validates that upregulated genes are located in significant vicinity to TAp73.

BioProfiling Result Page

Your Submission Details:

Organism: MOUSE (TAX_ID: 10090 )

Mapping Statistics

Gene List 1: mapping details

Gene List 2: mapping details

!!! Please note that TAp73 is not annotated in Reactome database (Mouse genome) thus making this type of analyses inapplicable.

Links to Results

Reference NetworkLink to Results
REACTOME ERROR MESSAGE
INTACT link to results

Line color (Red, Yellow or Grey) indicates significance of the best model:

Redp-value < 0.01
Yellowp-value ~ (0.01 -0.05)
Greyinsignificant