{{userText}}
{{dataSize}} Results
{{page}} of {{lastPage}}
| Show More | Showing {{pageSize}} of {{dataSize}} |
Loading
| {{column.title == null ? column.name : column.title}} | |
|---|---|
| {{value}} | |
{{c.text}}
{{model[c.name]}}
Log in with your user
Create a new user
User profile
Remember password
{{computeToolName()}}
{{computeStatus()}}
{{computeDate()}}
{{table.dataSize}} job{{table.dataSize != 1 ? 's' : ''}}
{{table.page}} of {{table.lastPage}}
Job launched
Job {{status}}
{{file.name}}
{{study.description}}
{{study.type}}
{{study.status}}
{{study.diskUsage}} bytes
Microarray
Expression
One channel
Two channels
Data matrix
ID list
Annotation
Other
{{file.name}}
{{bioformatText}}
{{bread}}
{{files.length}} item{{files.length != 1 ? 's' : ''}}
The files must be on the server to select them.
You can upload files using the button
You can upload files using the button
You can create folders using the button
{{selectedStudy.name}}/{{selectedFile.path}}
PATHiVAR - {{jobItem.name}} {{computeDate()}}
{{tissueSelected}}
{{ctypesSelected}}
{{warningMessage}}
{{genesWarningText}}
{{g}}
,
{{pathwaysMap[selectedPathway].text}} - {{selectedPathway}}
File
- New session...
- Save session...
- Open session...
- Manage sessions...
- Import
- Network from SIF...
- Network from XLSX...
- Network from Text...
- Node attributes ...
- Edge attributes ...
- Export
- Network as SIF
- Network as SVG
- Node attributes as file
- Edge attributes as file
Network
- Edit network...
- Import network
- Reactome...
- Kegg...
- Intact...
- Select
- Nodes by attributes...
- Edges by attributes...
- All nodes
- First neighbourhood nodes
- Invert node selection
- All edges
- Adjacent edges
- Everything
- Layout
- Force directed
- Default
- Configure...
- Tree
- Circle
- Unsorted
- {{column.title}}
- Random
- Force directed
Attributes
- Edit node attributes...
- Edit edge attributes...
- Node visualization settings...
- Edge visualization settings...
- Import attributes from Cellbase...
Analysis
- Network analysis
- Communities structure detection
- Topological study
- Functional analysis
- Network enrichment
- Gene set network enrichment
- Single enrichment
Examples
- PPIs related to histone exchange and removal during nucleosome assembly and disassembly
- Reactome pathway of Insulin Synthesis and Processing
- PPI network with attributes
Configure
- Circle
- Square
- Ellipse
- Rectangle
- None
- Low
- Medium
- High
- Invisible
- 10
- 20
- 30
- 40
- 50
- 60
- 70
- 80
- 90
- 100
- 120
- 140
- 160
- 1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 9
- 10
- None
- 8
- 10
- 12
- 14
- 16
- 18
- Directed
- Undirected
- Inhibited
- Dot
- Dot o
- 1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 9
- 10
- None
- 8
- 10
- 12
- 14
- 16
- 18
- Force directed
- Circle
- Random
- All nodes
- First neighbour nodes
- Invert node selection
- All edges
- Adjacent edges
- Everything
- 45
- 90
- 180
- -45
- -90
- -180
Nodes:
{{networkViewer.vAttr.data.length}}
Edges:
{{networkViewer.eAttr.data.length}}
File: {{networkViewer.lastLoadedFileName}}
Session manager
You must be logged in to save your sessions.
No sessions found.
{{session.name}}
{{session.dateString}}
Import a network SIF file
{{table.dataSize}} item{{table.dataSize != 1 ? 's' : ''}}
{{table.page}} of {{table.lastPage}}
Import a network Text file
- Tab
- Comma
- Semicolon
- {{index}}
- none
- {{index}}
- {{index}}
{{table.dataSize}} item{{table.dataSize != 1 ? 's' : ''}}
{{table.page}} of {{table.lastPage}}
Import a network XLSX file
- {{sheet}}
- {{index}}
- none
- {{index}}
- {{index}}
{{table.dataSize}} item{{table.dataSize != 1 ? 's' : ''}}
{{table.page}} of {{table.lastPage}}
Import {{type}} attributes file
{{table.dataSize}} {{type}} attribute{{table.dataSize != 1 ? 's' : ''}}
{{table.page}} of {{table.lastPage}}
Edit Network
{{interactionMessage}}
{{table.dataSize}} {{view}}{{table.dataSize != 1 ? 's' : ''}}
{{table.page}} of {{table.lastPage}}
Edit and filter {{type}} attributes
Edit
Filters
No filters to show.
Click
Click
Attribute: {{filter.attributeName}}
rule: {{filter.match}} {{filter.attributeType}}
Value: {{filter.queryString}}
String
Number
Exact
Contains
Not contains
Equals
Not equal to
Greater than
Greater than or equal to
Less than
Less than or equal to
{{table.dataSize}} {{type}}{{table.dataSize != 1 ? 's' : ''}}
{{table.page}} of {{table.lastPage}}
Select {{type}}s by attributes
String
Number
Exact
Contains
Not contains
Equals
Not equal to
Greater than
Greater than or equal to
Less than
Less than or equal to
No active filters to show.
Attribute:
{{filter.attributeName}}
Rule:
{{filter.match}} {{filter.attributeType}}
Value:
{{filter.queryString}}
Node visualization settings
Label attr:
Label offset:
Label size:
Opacity:
Shape:
Color:
Stroke color:
Size:
Stroke size:
Area:
Stroke area:
X:
Y:
Edge visualization settings
Label attr:
Label size:
Opacity:
Shaft:
Head:
Bidirectional:
Color:
Size:
{{displayProperty}} render configuration
{{column.title}}
Categorical
Continuous
String
List
Attribute value
Render value
{{model.attribute}}
{{displayProperty}} rendering configuration
{{column.title}}
Categorical
Continuous
String
List
Attribute value
Render value
{{model.attribute}}
{{displayProperty}} rendering configuration
{{column.title}}
Attribute value
Render value
{{model.attribute}}
Import Cellbase attributes
{{spe.name}}
{{column.title}}
{{item.boxLabel}}
{{item.boxLabel}}
{{item.boxLabel}}
Import IntAct
{{spe.name}}
{{column.title}}
Network analysis: Communities structure detection
Fastgreedy
Walktrap
Infomap
No
Yes
No
Yes
{{column.title}}
A color has been assigned to the top communities.
Communities results are available as node attributes
Global modularity: {{results['Global modularity']}}
Number of communities with more than 2 nodes: {{results['Number of communities with more than 2 nodes']}}
Total number of communities: {{results['Total number of communities']}}
Network analysis: Topological study
Yes
No
Yes
No
{{column.title}}
Topology results are available as node attributes
Average nodes per component: {{results['Average nodes per component']}}
Average shorthest path length: {{results['Average shorthest path length']}}
Clustering coefficient: {{results['Clustering coefficient']}}
Diameter: {{results['Diameter']}}
Number of components: {{results['Number of components']}}
Number of edges: {{results['Number of edges']}}
Number of nodes: {{results['Number of nodes']}}
Kegg import
{{item.text}}
Reactome import
{{displayName}}
Force directed layout configuration
Node related settings
Edge related settings
Global settings
Network enrichment form
Gene set network enrichment form
Single enrichment form
Single enrichment
Reactome FI form
PATHiVAR
Overview
PATHiVAR estimates the functional impact that mutations have over the human signalling network.
PATHiVAR analyses VCF files, extract the deleterious mutations, locate them over the signalling
pathways in the selected tissue (with the appropriate expression pattern) and provides a
comprehensive, graphic and interactive view of the predicted signal transduction probabilities
across the different signalling pathways.
Note:
PATHiVAR web application makes an intensive use of the HTML5 standard and other cutting-edge web
technologies such as
Web Components, so only modern web browsers are fully supported, these include Chrome 36+, Firefox 32+, IE
10+, Safari 7+
and Opera 24+.
Run
PATHiVAR
Computational Genomics Department
Principe Felipe Research Center, Valencia, Spain
2015