BioCichlid is a 3D visualization system of time-course microarray data on molecular networks. It aims to interpret gene expression data by transcriptional relationships based on the central dogma with physical and genetic interactions. BioCichlid enables us to:
1) visualize the regulatory networks in both the physical and genetic layer,
2) create animation of time-course gene expression data on these molecular networks,
3) interpret time-course gene expression data and obtain biological insights,
4) provide beautiful images and appealing movies for your presentation.

Here, we show a use case which describes "what you can do by the BioCichlid", and demonstrate the capabilities described above through a use case. We also present a practical usage for interactive control of the BioCichlid. More information on the usage for interactive control, see the Cichlid web page.
Usecase: gene expression on glycolysis pathway under hypoxic stress
Before starting the BioCichlid, we first prepared 1) a physical and a genetic interaction datasets of glycolysis pathway, 2) a gene expression dataset under hypoxic stress, 3) a transcriptional regulation (physical to genetic interaction) dataset (hypoxia responsive SREBF1 regulation of gene expressions) (shown in yellow link). Interaction datasets are manually collected from literature and public pathway databases. Datasets used in this use case are available here.

Second, we inputted these datasets on the BioCichlid website. We can also input these datases by uploading files on the BioCichlid web site. After starting the biocichlid server by clicking "Starting BioCichlid" button, we launched the biocichlid client, and interactively manipulated the client software as described below.

For your information about stress testing, BioCichlid can smoothly visualize gene expression data on the molecular networks composed by about five thousands of genes and proteins, respectively.


I. Start BioCichlid View1: before starting the visualization View2: overview
1. Start visualization and animation: press "a" on the keyboard.
2. Left-click and right-click the mouse: changing the 3D model position and scaling (zoom-in/out).
View 2) physical, genetic (glycolysis pathway) and transcriptional interactions (hypoxia responsive SREBF1 regulation of gene expressions) are visualized, and animation of time-course gene expression data is displayed by red cylinder* on the genetic network layer. You can find the three genes which are regulated by SREBF1 on the glycolysis pathway.
*Color scheme of gene expression values: BioCichlid visualizes gene expression values associated with the changing colors based on redcolor color scheme (low expression: green, high expression: red).


II. Interactive manipulation of the 3D model
3. Mouse mode: BioCichlid (Cichlid) client has three mouse modes for 3D visualization: "POINT" mode, "CAMERA MOVE" mode (default mode), and "DATA MOVE" mode*. Users can select the mouse mode by selecting the radio button of the mouse mode section in tool-bar window. In the "CAMERA MOVE" mode, users can interactively manipulate the 3D model (zoom-in/out, rotete, etc.).
In the "POINT" mode, users can only "point" at and select an individual node and link by mouse (users cannot use the functions of zoom-in/out, rotate, etc.). And, users can retrieve the node name by right-clicking on the node of interest. The retrieved node name will be displayed in the text box of node label in tool-bar window (see next section 3). When you finish retrieving node name, select the "CAMERA MOVE" radio button to move back to "CAMERAMOVE" mode.
4. Edit network: users can manipulate position, color, shape, size of pointed nodes and links. Users can change position, color, shape, size of nodes and links by changing the corresponding properties in edit network section in tool-bar window. After changing properies, by clicking on "update network" button, network manipulation will be reflected. Users also can do removal of an individual node and link by selecting the "NONE" node/link style. Moreover, users can undo/redo/reset function of network manipulation by clicking "undo/redo/reset" button in command section in tool-bar window.
5. Statistics: users can retrieve correlation value between two gene-expression profiles. When users pointed at two genes, by clicking on "calc correlation" button, correlation value will be displayed in statistics section in tool-bar window.
*Please see details of modes here.

III. Finding the node of your interest View3: search result
6. Incremental search: input the node name (label) of your interest, and click the "find" button. Then your interested node is highlighted with larger and bold label. Incremental search is avalable; multiple hit nodes are highlighted to find easily.
7. Time period: it indicates time period of time-course gene expression data.
8. Animation stop: press "server animation play/pause" button in tool-bar window.
View 3) we obtained an interesting snapshot during this animation by stopping the animation for saving images (write image to file by "w/W" on the keyboard). From this snapshot, we found that SREBF1 regulated genes, such as PFKL, GCK and PKLR, are mapped in glycolytic pathway, and also located in the glycolysis pathway.
9. Retrieval of node name: to retrieve a node name, users need to enter into the "POINT" mode. When users pointed at an individual node, the corresponding node name will be diplayed in node label of search panel in tool-bar window.
10. Retrieval of set of time-series gene expression data: in the "POINT" mode, users can retrieve time-series gene expression data. When users pointed at an individual node, the corresponding time-series gene expression data will be displayed in "expr data" section in tool-bar window.
11. Retrieval of node information (search on Ensembl or Google)**: in the "POINT" mode, users can retrieve node information by opening search results page (in default web browser) of Ensembl or Google searched by a node name.
Users can retrieve the node information by right-clicking on the node of interest. The search results page of Ensembl or Google (searched by a node name) will be opened in default web browser.
** This function is implemented for Windows and Mac OS X version. Linux (UNIX) users cannot utilize this function.

IV. Command keys to interactively manipulate the BioCichlid
"m/M" Step through "CAMERAMOVE" modes (each time one press the m/M button on the keyboard).
"FOCUS": The camera always aims at a particular point.
The mouse pans the camera around and zooms in and out, but it always points at the same place, changing direction as it moves.
"SLIDE": The mouse slides the camera in the plane of the screen, or in and out of it.
The camera always points the same direction.
"PAN": The mouse rotates the camera, keeping it at a fixed point, much like a person would move their head around, as well as move the camera forward or backward along it's current direction.
"PLANE": The camera moves in a pseudo-aircraft motion, pitching, rolling, and banking based upon the current speed and roll.
"w/W" These cause a copy of the current display to be written to disk in the form of a 24-bit uncompressed PPM 'rawbits' file.
The images will be named "dumpNNNN.ppm", with N starting at 1 and counting up, but existing images will not be overwritten.
"TAB" This option captures the images. The images will be stored in a pre-allocated buffer in memory, and written to disk when the buffer is full.
"l" Scene lighting modifies the colors of the scene's vertices, taking light source parameters into account.
"t" This modifies node shapes (each time one press "t" button on keyboard).
"g" Toggle guide lines / bounding boxes
"r/R" Reset options and camera (R => and graphs) to defaults.
This resets all of the window-level options to their default values, including the camera orientation.
More information on the usage for interactive control, see Cichlid usage.

V. Biological insight into hypoxia responsive regulation on glycolysis

a-c) Through hypoxia response, PKLR, a kinase of glyconeogenesis, is down-regulated, whereas PFKL and GCK are up-regulated with SREBF1.

Conclusion and discussion

In this use case, we describe a relationship between SREBF1 regulation and glycolysis pathway under hypoxic stress. On observation of visualization by the BioCichlid, we can find that three genes which are regulated by SREBF1 protein (PFKL, GCK and PKLR genes) are working on the glycolysis pathway. PFKL and GCK genes are up-regulated with up-regulation of SREBF1. On the other hand, PKLR gene, a kinase working on glyconeogenesis or TCA cycle, is down-regulated with down-regulation of PDHX gene on TCA cycle under hypoxic stress.

As described above, these three genes regulated by SREBF1 are working on both aerobic and anaerobic glycolysis pathway, and their gene expressions are up/down-regulated depending on hypoxic stress. Moreover, a gene which shows the least gene expression change on the glycolysis pathway is found to be PGK gene, a kinase whose gene expression is induced by HIF-1a.

That is, by observing the visualization of time-course gene expression data on molecular network using the BioCichlid, we revealed that, under hypoxic stress, up-regulation of SREBF1 gene does not always up-regulate gene expressions of its down-stream genes. We also revealed that a down-regulated gene under hypoxic stress is working on aerobic glycolysis pathway. Observations on time-course gene expression data of genes of interest (e.g., PGK gene) enable us to obtain novel knowledge. Thus, BioCichlid enables researchers to interpret time-course gene expression data to obtain biological insights. Furthermore, Biocichlid can provide beautiful images and appealing movies for your presentation.

Back to the BioCichlid website.
Dept. of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University