Difference between revisions of "Cellular Networks KnowledgeBase"
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These gene types are derived from the GO annotation associated with a gene name. | These gene types are derived from the GO annotation associated with a gene name. | ||
| + | ===Selected Marker List=== | ||
| − | The | + | The Selected Markers List table contains activated markers moved over from the Activated Markers table. In addition to the columns defined for the Activated Marker List, the Selected Marker List adds the following: |
| − | + | ||
| − | + | # Entrez Id: The Entrez ID of the gene name. When present, the Entrez ID is hyperlinked to the relevant entry within Entrez Gene . | |
| − | + | # GO Term: Associated GO Term. Users can browse the GO terms associated with a gene (using an AmiGO browser-like interface) and select one of those terms for display. | |
| − | + | # Prot-Prot #: number of protein-protein interactions (reported in the CNKB) involving the gene. | |
| − | + | # Prot-DNA #: number of protein-DNA interactions (reported in the CNKB) involving the gene. | |
| − | + | ||
| − | + | Additionally, each row has check-boxes that can be used to designate whether protein-protein, protein-DNA, or both types of interactions should be used. | |
| − | + | ||
| − | Additionally, each row has | + | ===Preferences=== |
| − | Using a “preferences”-type tab user can control how many of the columns listed above | + | Using a “preferences”-type tab, the user can control how many of the columns listed above are visible within the Selected Markers table. |
| + | |||
| + | ===Throttle Graph=== | ||
Throttle graph: The graph allows users to throttle (for the genes in the Selected Markers table) which interactions to work with using as a criterion the interactions’ confidence indicator. The X axis of the graph ranges from 0 to 1, in increments of 0.01. For any value 0<=a<=1 on the X-axis, the throttle graph contains the point (a, y) where y is computed as follows: | Throttle graph: The graph allows users to throttle (for the genes in the Selected Markers table) which interactions to work with using as a criterion the interactions’ confidence indicator. The X axis of the graph ranges from 0 to 1, in increments of 0.01. For any value 0<=a<=1 on the X-axis, the throttle graph contains the point (a, y) where y is computed as follows: | ||
a. Consider the set GS of all genes in the Selected Markers table. | a. Consider the set GS of all genes in the Selected Markers table. | ||
Revision as of 17:14, 18 May 2007
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Contents
Outline
This tutorial contains
- . an overview of the Cellular Networks KnowledgeBase and
- . instructions....
Overview
The Cellular Network Knowledge Base (CNKB) is a repository of interactions between pairs of proteins (these interactions can be either computationally or experimentally derived). Both direct, physical interactions can be captured as well as indirect transcriptional relationships (where an interaction is between a transcription factor and its gene target). Each pairwise interaction has an associated confidence indicator (a value between 0 and 1) reflecting the strength of the underlying data, whether experimental or computational.
This component allows the user to select a group of markers and specify for each the interaction type of interest (Protein-Protein and/or Protein-DNA). All interactions (of the designated types) involving the selected markers are retrieved from the CNKB and displayed (along with associated information such as GO annotation, interaction attributes, etc) both in the CNKB component and also in Cytoscape.
GUI
The CNKB component displays a list of markers that have been activated in the Markers component. The user can select from these markers by double-clicking them; those selected will be added to the Selected Marker List just below.
Activated Marker List
This table contains three columns: Marker, Gene (the gene name corresponding to the marker, if available), and Gene Type. The possible values in the Gene Type column are
- TF - Transcription Factor,
- K - Kinase,
- P - Phosphatase, and
- (no entry) - type is unknown.
These gene types are derived from the GO annotation associated with a gene name.
Selected Marker List
The Selected Markers List table contains activated markers moved over from the Activated Markers table. In addition to the columns defined for the Activated Marker List, the Selected Marker List adds the following:
- Entrez Id: The Entrez ID of the gene name. When present, the Entrez ID is hyperlinked to the relevant entry within Entrez Gene .
- GO Term: Associated GO Term. Users can browse the GO terms associated with a gene (using an AmiGO browser-like interface) and select one of those terms for display.
- Prot-Prot #: number of protein-protein interactions (reported in the CNKB) involving the gene.
- Prot-DNA #: number of protein-DNA interactions (reported in the CNKB) involving the gene.
Additionally, each row has check-boxes that can be used to designate whether protein-protein, protein-DNA, or both types of interactions should be used.
Preferences
Using a “preferences”-type tab, the user can control how many of the columns listed above are visible within the Selected Markers table.
Throttle Graph
Throttle graph: The graph allows users to throttle (for the genes in the Selected Markers table) which interactions to work with using as a criterion the interactions’ confidence indicator. The X axis of the graph ranges from 0 to 1, in increments of 0.01. For any value 0<=a<=1 on the X-axis, the throttle graph contains the point (a, y) where y is computed as follows: a. Consider the set GS of all genes in the Selected Markers table. b. For each G in GS, let Y(G) be defined as follows: If both checkboxes are selected for G, then Y (G) = S (G, a). If only the protein-protein checkbox is selected for G, then Y (G) = SPP(G, a). If only the protein-DNA checkbox is selected for G, then Y(G) = SPD(G, a). If neither check box is selected for G, then Y(G) = empty set. c. The value y for the graph point (a, y) is then defined as the size of the set that results from the union of all the Y(G), for all G in GS. Note that this is an algebraic union, i.e., there is no double counting of interactions (for interactions I(A, B) where both A and B belong to GS). d. Users can select a value for the X-axis by using either the graph slider (has a range of 0-1 and moves in intervals of 0.01) or the associated threshold box (only positive real values between 0-1 are allowed in that box; values are rounded to the closest second decimal point). When a value X=a is selected by the user for the X axis, the GUI is modified as follows: • The vertical bar indicator on the graph moves on the X-axis, to the position X=a. • For each gene G in the Selected Markers table, the contents of the columns Prot-Prot # and Prot-DNA # are updated as follows: o Prot-Prot # = SPP(G, a). Prot-DNA # = SPD(G, a). o If the Protein-Protein checkbox is not selected for G, then the contents if the “Prot-Prot #” column appears grayed-out (but the number therein is still visible). The graying out indicates that this group of interactions will not be taken into account when building the Cytoscape network (see below). o If the Protein-DNA checkbox is not selected for G, then the contents if the “Prot-DNA #” column appear grayed-out (number therein is still visible). As above, in this case the Prot-DNA interactions will not be taken into account when building the Cytoscape network. So, as the user interacts with the throttle graph slider the contents of the Selected Markers table (specifically, the contents of the “Prot-Prot #” and “Prot-DNA” columns) are updated on the fly, using the numbers specified above.
