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Contents
Contents ...................................................................................................................................................... 2
1. Overview ................................................................................................................................................. 4
1.1. Description........................................................................................................................................ 4
1.2. Launching the KUPNetViz ................................................................................................................ 4
1.3. How to use this guide ........................................................................................................................ 4
1.4. Issue reporting................................................................................................................................... 5
1.5. Quick start ........................................................................................................................................ 5
2. Using the KUPNetViz in single species mode .......................................................................................... 8
2.1. Searching for genes/proteins/miRNAs ............................................................................................... 9
2.2. Network description .......................................................................................................................... 9
2.2.1. Network initialization ................................................................................................................. 9
2.2.2. Node and edge description ........................................................................................................ 10
2.3. Network functionalities ................................................................................................................... 12
2.3.1. 1st and 2nd level neighbors ......................................................................................................... 12
2.3.2. Hiding nodes/edges .................................................................................................................. 14
2.3.3. Deleting nodes/edges ................................................................................................................ 15
2.3.4. Restoring the network ............................................................................................................... 15
2.4. Element annotation.......................................................................................................................... 15
2.4.1. Node annotation ....................................................................................................................... 16
2.4.2. Edge annotation ........................................................................................................................ 17
2.5. Adding KUPKB data ....................................................................................................................... 18
2.5.1. The KUPKB gene/protein data panel ........................................................................................ 18
2.5.2. The KUPKB miRNA data panel ............................................................................................... 22
2.5.3. The Displayed interactions panel .............................................................................................. 23
2.5.4. Displaying neighbors ................................................................................................................ 24
2.6. Adding functional and pathway data ................................................................................................ 24
2.6.1. The Gene Ontology panel ......................................................................................................... 24
2.6.2. The KEGG pathways panel....................................................................................................... 25
2.6.3. The miRBase microRNA panel................................................................................................. 27
2.7. Advanced options ............................................................................................................................ 28
2.7.1. The Search options panel .......................................................................................................... 28
2.7.2. The Coloring options panel ....................................................................................................... 30
2.7.3. Other advanced options ............................................................................................................ 32
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