Humboldt-Universität zu Berlin - Mathematisch-Naturwissenschaftliche Fakultät - Wissensmanagement in der Bioinformatik


Screenshot What are the risk factors of treating G6PD-deficient malaria patiens with primaquine? The query entered in Ali Baba was "primaquine malaria g6pd deficiency".
The graph shows the connection between G6PD (deficiency), vivax malaria (patients), and their treatment with primaquine. The risk factors hemolytic anemia/hemolysis are directly connected to G6PD and primaquine.
Other nodes in the graph present more information on studied populations, the viral origin, infected cells, and informations on the disease.

Screenshot What are the known or suspected genes that are associated with Parkinson's disease? The query entered in Ali Baba was "parkinson disease genetic cause".
Shown in the graph is the node Parkinson's disease (blue border) and all associated proteins (red border). In the view on the right side, a list of 16 proteins is shown for Parkinson's diease. Current confirmed proteins are: LRRK2, parkin/PRKN, UCHL1/Ubiquitin carboxyl-terminal hydrolase isozyme L1, HFE, PINK1/PTEN induced kinase 1, DJ-1/PARK7, PARK12 (not in UniProt), SNCA/alpha-Synuclein/SI, Hcy, GDNF; Nix, JNK. Known interactions (according to UniProt) include: LRRK2 - PARK2/PRKN2/Parkin; PRKN2 - SCNAIP; PRNK2 - Syt11.
Note that MeSH distinguishes between Parkinson's disease and parkinsonism, thus there is an extra node for parkinsonism. This node is connected to some of the same and also to other proteins.

Screenshot A Patient with cough becomes unresponsive after normal dosage of codeine -- what is going on? The query entered in Ali Baba was "codeine intoxication".
Ali Baba shows the relationship between codeine (marked in the graph with blue frame), cough, morphine, and poisioning. Poisioning is also connected to morphine and CYP2D6. The solution thus is that codeine is bioactivated by CYP2D6 into morphine, certain patients show an ultrarapid form of this metabolism, which leads to a life-threatening intoxication (see Gasche et al. (2004)). The connection codeine->CYP2D6->morphine is directly visible in Ali Baba.
To make this example a bit more concise and focused on the central problem, we used the minimum degree filter (in the menu, see Preferences|Filter preferences). This allows to remove all nodes without any neighbors (unconnected nodes) using the 'Degree' slider on the bottom panel.

Screenshot The query was for "IFN gamma signaling pathway".
IFN gamma signaling takes place through a IFN receptor (grouped as IFNs in the graph). Jak1/2 phosporylates STAT(1α), which then transduces the signal into transcriptional events. SOCS3 is known to negatively regulate cytokines that signal through this JAK/STAT pathway. IL-10 inhibits cytokines like IGN-gamma, GM-CSF and TNF-α. G-CSF belongs to the IL-6 superfamily.
Sources: UniProt entries for SOCS3_HUMAN and IL10_HUMAN; IFN gamma signaling pathway from BioCarta

Screenshot Here we show the results for the query "FADD". (Pro-)Caspase-8 binds to the FADD adapter molecule as one of the first steps during apoptosis signaling induced by TNFRSF1A. FADD associates with Fas, the receptor for TNFFS6/FasLG. RIP1 is known to activate JNK.
Sources: UniProt entries for CASP8_HUMAN and TNR6_HUMAN

Screenshot The Wnt signaling pathway loaded into AliBaba, directly from the KEGG web server.