NaviCell Web Service Data visualization tutorial

NaviCell Web Service: description Map: Data: Copy number variations mRNA expression Mutations NaviCell Web Service is a powerful data visualization tool that allow users to load, manage and visualize a large number of experimental data types in the context of molecular interaction maps. The user can upload expression data for mRNA, microRNA, proteins, mutation, copy-number data, and simple gene lists. The input data format is a standard tab-delimited text file. Users can upload sample annotation files that can be used to automatically calculate average values for defined groups of samples. Different options are available to display data values: heatmaps, barplots, glyphs and map staining. Data visualization example 1

Load data In the Data visualization menu click ‘Load Data’: Chose File: table in a tab-delimited text file format (e.g. tcga_expression.txt) Name: type name of dataset ( e.g. expression) Type: indicate type of data (e.g. mRNA expression data) Import (several datasets can be loaded one after another) Done 2

Load annotation table In the Data visualization menu click ‘Sample Annotations’: Step 1 Chose File: table in a tab-delimited text file format (e.g. ovca_sampleinfo.txt) or Sample annotation URL: to upload the annotation file Import annotations Step 2 Sample Annotations: Check boxes to create groups (e.g. IntrinsicExprClassJCI) Apply Done Step 1 Step 2 3

Check your data In the Data visualization menu click ‘My Data’: Check available types of data, samples, gene list, group created according to the annotation table, etc. 4

visualize copy number data using heatmap In the Data visualization menu click ‘Drawing Configuration’: Step1 Chart Type: Heatmap/ Apply/ click ‘configuration’ Step 2 Heatmap Configuration Editor: Select a sample or group (e.g. TCGA_041332, TCGA_24_1560)/ Select a data table (e.g. ‘copynumber’)/ Size (e.g. Medium)/ click ‘config’ Step 3 copynumber Datatable Color Configuration: Samples/assign color to value/ Apply Step 1 Step 2 Step 3 5

Copy number variations-heatmap Samples: TCGA_24_1560 tetraploid, prolifirative TCGA_04_1332 tetraploid, mesenchimal Zoom in on Cyclin E*: Clicking on the heatmap opens the heatmap configuration editor where values can be viewed 6

visualize copy number data using barplot In the Data visualization menu click ‘Drawing Configuration’: Step1Chart Type: Barplot/ Apply/ click ‘configuration’ Step 2 Barplot Configuration Editor: Select a sample or group (e.g. TCGA_041332, TCGA_24_1560)/ Select a data table (e.g. ‘copynumber’)/ Size (e.g. Medium)/ click ‘config’ Step 3 copynumber Datatable Color Configuration: Samples/assign color to value/ Apply Step 1 Step 2 Step 3 7

Copy number variations-bar plot Samples: TCGA_24_1560 tetraploid, prolifirative TCGA_04_1332 tetraploid, mesenchimal Zoom in on Cyclin E*: Clicking on the heat map opens the heat map configuration editor where values can be viewed 8

visualize mutations data using glyph In the Data visualization menu click ‘Drawing Configuration’: Step1 Glyphs: Glyph 1/ Apply/ click ‘configuration’ Step 2 Glypg 1 Configuration Editor: Sample or group (e.g. TCGA_25_1624)/ in ‘Shape, ‘Color’ and ‘Size’, chose ‘mutations’, click ‘config’ on each one of the configurations Step 3 mutations Datatable Shape Configuration: Samples/assign shape of glyphs to value/ Apply Step 4 mutations Datatable Color Configuration: : Samples/assign color to value/ Apply Step 5 mutations Size Shape Configuration: : Samples/chose value for glyphs size/ Apply Step 1 Step 2 Step 3 Step 4 Step 5 9

Mutations-glyph Zoom in on mutated genes: p53, p130*, RBM25 Distribution of mutated gene on the map Sample: TCGA_25_1634 tetraploid, mildly proliferative 10

In the Data visualization menu click ‘Drawing Configuration’: Step1 Map staining: Apply/ click on ‘configuration’ Step 2 Map staining Configuration Editor: Sample or group (e.g. TCGA_24_1560)/ in ‘Color’ chose ‘expression’/ click ‘config’ Step 3 expression Datatable Color Configuration: Samples/assign color to value/ Apply visualize expression data using map staining Step 1 Step 2 Step 3 11

Expression-map staining TCGA_04_1332 tetraploid, mesenchymal TCGA_24_1560 tetraploid, proliferative The patters of mRNA expression visualized as map staining are different in mesenchymal and proliferative types of ovarian cancer samples. 12

Several type of data can be visualized at the same map using a combination of visualization modes described previous in the tutorial. In the Data visualization menu click ‘Drawing Configuration’: Step1 Click Heatmap, Glyphs, Map Staining/ click ‘config’ on each one of the configurations Step2 Heatmap Configuration Editor: follow instructions indicated on the page 5 Step 3 Glypg 1 Configuration Editor: follow instructions indicated on the page 9 Step 4 Map staining Configuration Editor: follow instructions indicated on the page 11 visualize several type of data simultaneously Step 1 Step 2 Step 3 Step 4 13

Mutations-glyph Copy number-heat map Expression-map staining TCGA_25_1634 tetraploid, proliferative Zoom in on p130* in several complexes 14

In the Data visualization menu click ‘Drawing Configuration’: Step1 Map staining: Apply/ click on ‘configuration’ Step 2 Map staining Configuration Editor: Sample or group (e.g. Differentiated)/ in ‘Color’ chose ‘expression’/click ‘config’ Step 3 expression Datatable Color Configuration: Groups/assign color to value/ Apply visualize expression data for groups of samples using map staining Step 1 Step 2 Step 3 15

Expression-map staining on group of samples Differentiated Mesenchymal ImmunoreactiveProliferative Groups: Intrinsic expression classes The patters of mRNA expression visualized as map staining are varying in four intrinsic classes of ovarian cancer samples, indicating different regulation of processes depicted on the map. 16