a. 2D-gel Images (proteome level), b. Snapshot interactions (proteome & interacteome level), c. Inter-pathways & d. Effect on Metabolism (proteome, interacteome, and metabolic pathways), e. YTH Experiments (interactome), and f. CyanoCOG (proteome & genome).
Example of using "2D-gel image" tool to depict proteome results from selected condition. A list of identified proteins from protein spots (black spot in the image) is shown in the table, sorted by absolute value of fold-change. The asterisk marks before ORF names denote such proteins that are differentially expressed.
Example of using "Snapshot-Interaction" tool to visualize
(i) the PPI network around RbcS protein [SPLC1_S240080] of S. platensis C1, which is homologous to Slr0012 protein of Synechocystis sp. PCC 6803
, and (ii) differentially expressed after temperature down-shift in cytosol fraction.
Note: A notde marked by an octagon represents differential expression. In the node label, line 1 describes protein expression conditions and fractions (which colored marks); line 2 shows the corresponding Synechocystis ORF and protein name (blue text); and line 3 shows the protein homolog in Spirulina. The mark denotes expressed conditions: temperature up-shift (sun) and down-shift (umbrella/snow-man). The color of the marks, blue, green, and orange, represent the cytosol fraction, thylakoid membrane, and plasma membrane fraction, respectively. When using mouse-over on a node in the network, the corresponding homolog protein will move to the first row in the detail-table.
Example of using "Inter-pathways" tool for querying interactions between two pathways (left─syn00710: Carbon fixation; right─syn00480: glutathione metabolism). The interaction details between the two pahtways show that RbcS protein [SPLC1_S240080] can interact with RbcL protein [SPLC1_S240060] and with slr0697-homolog protein in glutathione metabolism. (The pathway image files were generated from KEGG Color Pathway tool by inputting our lists of differentially expressed proteins in each pathway.)
Alternatively, we are developing our own customizable SVG image that can be generated from KGML (KEGG PATHWAY xml file), but such files are not able to have a transparently translated.[see example]
Example of using "Effect on Metabolism" tool to see the overall proteome result mapped on carbon fixation metabolism.
NoteNumbers in blue, red (not shown in this figure), and green (not shown in this figure) represent protein found under temperature down-shift, up-shift and both up/down-shift conditions, repectively. (The pathway image files were generated from KEGG Color Pathway tool by inputting our lists of differentially expressed proteins in each pathway.)
Snapshot of using "YTH experiment" tools to visualize our experimentally verified interaction in S. platensis C1 by yeast two-hybrid screening. All nodes are Spirulina proteins. The pink, blue and grey edges are PPI inferred from Synechocystis, positive bait-prey pair of S. platensis, and negative bait-prey pair of S. platensis, respectively.
Example of using "CyanoCOG" for querying Rbc proteins in S.platensis C1 and Synechocystis.
Example of using tool to visualize protein domains by ticking at "protein domains" checkbox, and multiple sequence alignment among protein homologs by clicking <msa> under ortholog id.