Here you can find several examples of gene/protein list analysis by BioProfiling.de tools. From these examples you get a quick impression of what you get by using our tools.
Example 1: regions with copy number alteration in Sezary syndrome
Many clinical studies currently are designed to reveal possible pathogenesis mechanisms and novel therapeutic targets for complex deceases with a very specific phenotypes. Sezary syndrome is an aggressive cutaneous T-cell lymphoma/leukemia. In (Vermeer et al.,Cancer Res 2008) high-resolution array-based comparative genomic hybridization was done on malignant T cells from 20 patients to reveal highly recurrent genetic alterations typical of Sezary syndrome. Minimal common regions with copy number alteration occurring in at least 35% of patients were reported comprising in total ~ 360 candidate genes (table 1 in the paper).
Exampe 2: Bosutinib protein targets.
Bosutinib is a novel drug (promiscuous kinase inhibitor). In this example, BioProfiling.de was used to understand properties of Bosutinib protein targets which were identified by chemical proteomics. We particularly draw your attentions to results produced by ProfCom_PROT_MOTIF , a new tool in BioProfiling.de collection. In this case you get logical combinations of amino acid triplets which are highly discriminative between the list of Bosutinib protein targets and the whole human proteome. For example, logical pattern "((DFG and HRD) not (LPY, HEE))" was present in 50 (out of 55) Bosutinib protein targets while only 305 (out of ~25 000) proteins in the whole genome have this pattern. The P-value of the enrichment adjusted by Bonferoni correction for multiple testing is 2.4e-81. Such strong bias in amino acid triplet composition suggests that the presence of this logical pattern predefines interaction between Bosutinib and the protein.
In addition, results by PPI spider suggest that Bosutinib protein targets form densely interaction pattern. This result supports novel Network pharmacology paradigm in drug discovery: to be effective the drug should target multiple functionally dependent targets.
This link to download input gene list for this example.