Co-expression Network Analysis

Interactive visualization of gene co-expression networks, expression and funtional enrichment analysis.

📊 Global Network of g7802.t1
Co-expression Network View
Network Legend
Yellow: Query proteins
Green: Interaction proteins
Pink line: Own interaction + positive co-expression
Blue line: Own interaction + negative co-expression
Node size reflects how many connections the gene has (hubs are drawn larger). Hover any node to see the annotation of the gene it stands for (PANTHER / InterPro / GO description, or NR when the others are absent) and a link to its gene page.
📋 View Detailed Network Information
Co-expressed Genes of g7802.t1
Gene ID Description PCC Relationship
g7802.t1ATP-DEPENDENT DNA HELICASE1positive
g35990.t1ZINC FINGER CCCH DOMAIN-CONTAINING PROTEIN 140.97positive
g4804.t1FACTOR VIII-ASSOCIATED GENE 10.96positive
g12080.t1LYSINE-SPECIFIC DEMETHYLASE0.96positive
g5569.t1PROTEIN KINASE C, MU0.96positive
g3319.t1RETINOIC ACID INDUCED 1/TRANSCRIPTION FACTOR 200.96positive
g12698.t1TOPOISOMERASE II-ASSOCIATED PROTEIN PAT10.96positive
g3739.t1PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR0.96positive
g18695.t1SYNTROPHIN0.96positive
g16754.t1HEME OXYGENASE0.96positive
g8000.t1E3 UBIQUITIN-PROTEIN LIGASE HECTD30.96positive
g5818.t1CYCLIC-AMP RESPONSE ELEMENT BINDING PROTEIN0.96positive
g3410.t1M7GPPPN-MRNA HYDROLASE0.95positive
g16763.t1--0.95positive
g12187.t1--0.95positive
g4813.t1HEADCASE PROTEIN0.95positive
g32586.t1--0.95positive
g36570.t1--0.95positive
g19976.t1PROLINE-SERINE-THREONINE PHOSPHATASE INTERACTING PROTEIN 10.95positive
Further Analysis for Network Members
Next Step: Dynamic Expression View

What this does. Everything above treats every gene the same way. Dynamic Expression View redraws this same network but colours each node by how much that gene changes between two conditions, so you can see which part of the network responds. It needs one input the network itself does not carry: a per-gene expression ratio.

Where the ratio comes from. CnidoSite holds an RNA-seq expression matrix for this species, so the ratio can be built here rather than elsewhere: pick the samples for each side of your comparison and every gene gets log2((mean of group A + 1) / (mean of group B + 1)). This network has 77 gene pairs and one run of Dynamic Expression View draws at most 10, so the button below carries the 10 with the strongest |PCC|.

Gene pairs carried over (10)
Opens the ratio builder with these pairs already loaded. It computes the ratios, then hands both the pairs and the ratios to the network view in one step.
Or take the pairs by hand
Click to select all, then paste into step 2 of Dynamic Expression View as GeneA GeneB, one pair per line. Its step 3 still needs the expression ratios.
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