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gographviz [2010/06/02 19:29]
sgoetz
gographviz [2017/05/24 10:36] (current)
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 +===== GoGraphViz - a Gene Ontology Graph Viewer =====
 +
 +Interactive and highlighted Gene Ontology Graph Visualization
 +
 +==== Introduction ====
 +
 +The GoGraphViz tool generates joined (multiple annotation sets) gene ontology graphs (directed acyclic graphs (DAGs)) to create overviews of the functional context of groups of sequences. **Interactive** graph visualization allows the navigation of large and unwieldy graphs often generated when trying to biologically explore large sets of sequence annotations. Zoom and graph navigation is provided through the DAG viewer Java Web Start tool.
 +
 +Graph **coloring** and highlighted information content are provided through a colour scale proportional to annotation weight. A term annotation weight can be computed as the number of sequences annotated to that term or as an annotation confluence score. This confluence score (Node-Score) takes into account the number of sequences converging at one GO term and penalizes by the distance to the term where each sequence actually was annotated. Assigned sequences and **Node-Scores** can be also displayed at the term's level. Additionally, the visualization of a user-provided score was added to e.g. be able to visualize two groups of GO terms by separating under- and over-represented terms with two different colors.
 +
 +The graph **term filtering** adds the ability to display the annotation result for a set of sequences on the Gene Ontology DAG. However, when the number of sequences to display is large, GO graphs can become extremely large and difficult to navigate. Additionally, the relevant information in these cases is frequently concentrated in a relatively small subset of terms. We have introduced **graph pruning functions** to simplify DAG structures to display only the most relevant information. A cut-off on the number of sequences or the score value can be set to filter out GO terms. The number of omitted GO terms is given for each branch, which is an indication of the level of local compression applied.
 +
 +
 +==== Some Example Output ====
 +
 +Graph colored by the Annot-Score method
 +\\ 
 +{{ :example_data:gographviz:graph1.jpg?750 |Graph colored by the Annot-Score method}}
 +
 +Graph colored by a user defined score
 +\\
 +{{ :example_data:gographviz:graph2.jpg?750 |Graph colored by a user defined score}}\\ 
 +
 +
 +==== Input Parameters ====
 +
 +  * **Association File**: A tabulator separated file indicating first the Annotation Unit (a sequence, a cluster, a gene set, etc.) and than the GO-term(s). As a third column a score value  (0-1) can be set optional and is used for coloring issues when graph-coloring mode "input score" is selected.
 +
 +**File format example**
 +<file>   Seq1 GO:0000001 0.1
 +   Seq2 GO:0000011 0.8
 +   Seq3 GO:0000015 0.6
 +   Seq4 GO:0000015 0.12
 +   Seq5 GO:0000027 0.45
 +   ...
 +   ...</file>
 +
 +
 +  * **GO Category**: The GO category you wish to visualize.
 +  * **ID Node Filter:** Filter out GO-terms with less then the given number of annotation units assigned.
 +  * **Mode of Graph-Coloring:** Select which graph feature to visualize.
 +    * **ID-count:** Colorize by the number of IDs united at a term.
 +    * **Annot-score:** Colorize by the Annot-Score of a term. 
 +    * **Input-score:** Colorize by the score defined in the input file.
 +  
 +  * **Annot-Score parameter:** This parameter adjusts the alpha of the Annot-Score formula (GO Annot-Score = sum( number_of_ids x exp( alpha, distance to origin)))
 +  * **Annot-Score Node Filter:** Thin out graphs by the Annot-Score. 
 +  * **Color:** Main graph color (at the moment disabled)
 +
 +==== Output ====
 +
 +Several images (jpg, svg, png) of the generated graph are given as Output. The graphs can also be downloaded in form of a textual representation. Further, a link (.jnlp) starts automatically the interactive graph visualization tool in form of a Java Web Start application.
 +
 +
 +====== Examples ======
 +===== Example 1 =====
 +
 +We have a list of genes that are known to be involved in breast cancer. We want to inspect the joint biological meaning of this set of genes. How to proceed?
 +
 +Take the {{:example_data:gographviz:brca2_brca1_up.txt|list}} of genes (human) and find their annotations with "create annotation" tool under "processing data" in Babelomics. Therefore you have to upload the list of genes under "data upload" and select "ID-list->Genes". Once the list in loaded into Babelomics you go the "create annotation" tool. Here you have to "browse" your data and select the list you uploaded. Deselect "all genome". Afterwards you have to select the organism and the type of annotations you want to recover. Select all three GO categories. The output format has to be "extended".\\
 +
 +{{:example_data:gographviz:create_annotation.png?400|}}
 +
 +Than use the generated annotations with the GO Graph Viewer to visualize the ontologies (Babelomics --> Utilities --> GO Graph Viewer)
 +Use the browse button to select the generated annotation, select the corresponding GO category and press "RUN".
 +\\ 
 +{{:example_data:gographviz:make_graph.png?400|}}
 +
 +Once the results are obtained you can download the graph as an image (png, jpg) or in a textual representation.
 +Additionally you have the option to view the graph with the interactive GOGraphViz tool by clicking in this icon: 
 +{{:example_data:gographviz:gographvizlogomini.png|}}
 +
 +
 +
 +===== Example 2 =====
 +
 +==== Example Files ===
 +{{:example_data:gographviz:gographviz_annotations.txt|An association file containing in each line a gene id with its GO annotation separated by a tabulator.}}
 +\\
 +
 +{{:example_data:gographviz:gographviz_goscores.txt|An association file example which simply visualizes a list of gene ontology terms with an associated intensity value}}
 +
  
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