Co-expression Network Analysis

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

📊 Global Network of g3302.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 g3302.t1
Gene ID Description PCC Relationship
g3302.t1IQ DOMAIN-CONTAINING PROTEIN K1positive
g16799.t1KH DOMAIN CONTAINING RNA BINDING PROTEIN0.97positive
g723.t1ARMADILLO-LIKE HELICAL DOMAIN CONTAINING PROTEIN 10.97positive
g28180.t1CHROMOSOME-ASSOCIATED KINESIN KIF4A-RELATED0.97positive
g30241.t1PROTEIN C21ORF590.97positive
g20268.t1--0.97positive
g10969.t1SAM DOMAIN-CONTAINING PROTEIN-RELATED0.97positive
g3531.t1ZINC FINGER MYND DOMAIN-CONTAINING PROTEIN 120.96positive
g2833.t1EF-HAND DOMAIN C-TERMINAL CONTAINING PROTEIN0.96positive
g10361.t1ANKYRIN REPEAT FAMILY PROTEIN0.96positive
g3793.t1NISCHARIN RELATED0.96positive
g8989.t1CILIA- AND FLAGELLA-ASSOCIATED PROTEIN 1570.95positive
g6307.t1EPHRIN0.95positive
g10451.t1WD-40 REPEAT PROTEIN0.95positive
g20121.t1CARBOHYDRATE SULFOTRANSFERASE0.95positive
g31592.t1--0.93positive
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 56 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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