Cytoscape test4

Details

Transcriptome profiling

hCAGE	{{{profile_hcage}}}
RNA-seq	{{{profile_rnaseq}}}
smallRNA seq	{{{profile_srnaseq}}}
nanoCAGEscan	{{{profile_cagescan}}}

Sample info

strain	{{{sample_strain}}}
tissue	{{{sample_tissue}}}
dev_stage	{{{sample_dev_stage}}}
sex	{{{sample_sex}}}
age	{{{sample_age}}}
ethnicity	{{{sample_ethnicity}}}
cell_type	{{{sample_cell_type}}}
cell_line	{{{sample_cell_line}}}
collaboration	{{{sample_collaboration}}}
Experimental condition	{{{sample_experimental_condition}}}
disease	{{{sample_disease}}}
cell_lot	{{{sample_cell_lot}}}
cell_catalog	{{{sample_cell_catalog}}}
company	{{{sample_company}}}
donor(cell lot)	{{{sample_donor(cell lot)}}}
Note	{{{sample_note}}}

RNA info

sample_id	{{{sample_id}}}
tube_id	{{{rna_tube_id}}}
box	{{{rna_box}}}
position	{{{rna_position}}}
lot_number	{{{rna_lot_number}}}
catalog_number	{{{rna_catalog_number}}}
RIN	{{{rna_rin}}}
OD260/230	{{{rna_od260/230}}}
OD260/280	{{{rna_od260/280}}}
sample_type	{{{rna_sample_type}}}
extraction_protocol	{{{rna_extraction_protocol}}}
weight_ug	{{{rna_weight_ug}}}
concentration	{{{rna_concentration}}}

TF

, MOTIF

Promoter
TF-MOTIF Binding

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• Nodes
• Edges
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Layout: Force Directed Circle Radial Tree Recalculate Labels:

Nodes
Edges

Show edges:

TF-MOTIF Binding
Promoters

Promoter Z-Score filter:

Motif degree filter:

TF indegree filter:

TF outdegree filter: Source TF (Outdegree > 0)
Target TF (Outdegree = 0)

Show all nodes Show only selected nodes

Show all edges Show only selected edges

Export Network: graphml xgmml sif JSON Export Image: PDF PNG SVG

Load

Union: A || B
Intersection: A && B
Difference: A - B
Difference: B - A
Subnetwork: A
Subnetwork: B

About this network view.

Motifs shown are the top motifs in the sample (maximum 30). TFs shown have at least one CAGE promoter with at at least 10 TPM expression (RLE normalized) in the sample. Edges shown have a z-score of at least 1.5 (based on correlation between motif activity and promoter expression).

In the single sample view motifs are shown in orange, TFs are shown in blue. Promoter and z-score are attributes of the Motif to TF edges (blue arrow). TF to Motif edges are shown in orange.

How to interact with the network?

Zoom using the control panel in the lower right.
Click and drag to move nodes.
Double click to search for label in resource browser.
Mouse over nodes and edges to see additional attributes.
Hover over a node to highlight its first neighbors.
Click and drag or shift-click on the canvas to highlight many nodes and edges.
Right click on a node to select its first neighbors.
Right click to show only selected nodes.
When nodes are selected additional information is available in the pull out panel.
Addition filters are available within the pull out panel.

Acknowledgments

Analyst: Erik Arner
Application Developer: Jayson Harshbarger

Research Grant for RIKEN Omics Science Center from MEXT to Yoshihide Hayashizaki
Grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan to Yoshihide Hayashizaki