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

• Layout
• Filter
• Export
• Nodes
• Edges
• Compare

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