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
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).  |
KCPAVS features >
