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Mind mapping

This feature allows researchers to focus in on specific content (e.g. interactions or protein or sub network) while at the same time maintaining a sense of its overall context within a pathway/ global map. See figure 3 and figure 4 give below for illustrative explanation. This feature allows researchers to organize their ideas and data in a non-linear format guided by pathways as framework that facilitate creative problem solving. Scientists, students and physicians can quickly transform a jumble of ideas, documents and files into one seamless mind map (save it all in one file) -- giving them access to their most valuable data related to pathways from one place.

Use KCPAVS as effective thinking tool
  • Use symbols to represent your concepts from the collection of >120 bio-concepts symbol library.
  • Visual representation of the concepts described in the following text fosters thinking and hypothesis generiation. 

Example 1:  Farell et al in their publication describes sex differences in mechanisms for cardiac exciation-contraction coupling (EC coupling) in rat ventricular myocytes {Farrell, 2010 #300}. They explain Sex differences in the properties of EC coupling may arise from sex differences in ryanodine receptors (RYR) protein and mRNA levels. The expression level were found higher in females than in males shown with red (increased expression) and green color overlay (decreased expression) on RYR protein with male and female symbols overlaid next to the marked protein (Figure 2). 

Example 2: If you have a experimental data obtained from a journal describing few of the molecular  expression levels (as up regulation and down regulation) obtained in a particular condition like disease, such data can be quickly located and mapped onto the pathway diagram using KCPAVS. Marking the pathways with the symbols like up arrow and down arrows can help to better visualize the role and mechanisms on a pathway. 

Example 3: Figure 3 was as produced by mapping information on to ER Stress Pathway map. Contains all the information as shown in a model (Figure 4). But unlike Figure 4, Figure 3 helps researchers interpret the experimental data in context of larger biological system. Interpreting data in context of greater details ( large pathways / maps) helps to make more accurate findings and frame relevant hypothesis than just only interpreting results based  on simple "A to B" relationships.


Figure 1:  Partial list of KCPAVS symbol library ( > 100 biological concepts in symbol library)



Figure 2: The expression level were found higher in females than in males shown with red (increased expression) and green color overlay (decreased expression) on RYR protein with male and female symbols overlaid next to the marked protein


Figure 3: Representation of information given in Figure 4 on KEGG Pathway (hsa04141) in KcPAVS.

This way of representing information allows researchers to focus in on specific relevant pathway components while at the same time maintaining a sense of its overall context ( in mist of the complete details) within the pathway. The overall context and a detailed back-ground information is missing in a simplistic illustrative figures like figure 4.




Figure 4: Expression level changes during endoplasmic reticulum stress response. See figure 3 showing similar schematic representation as this figure, that can be created by users dynamically on KEGG patwhays during brain storming sessions.



Figure 5: another example in which text, arrow and various symbols were used in annotating pathway to mark the protein expressions in various organisms and tissues. The proteins of interest to the current hypothetical project is painted with red color on a KEGG pathway (cell cycle signaling).



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