Co-expression Network Analysis

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

📊 Global Network of g24689.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 g24689.t1
Gene ID Description PCC Relationship
g24689.t1FIBRINOGEN/TENASCIN/ANGIOPOEITIN1positive
g34672.t1COLLAGEN ALPHA0.99positive
g13536.t1SODIUM/CALCIUM EXCHANGER0.99positive
g24840.t1--0.99positive
g192.t1COLLAGEN ALPHA0.98positive
g7.t1NEUROTRANSMITTER GATED ION CHANNEL0.98positive
g10390.t1--0.98positive
g5746.t1CRUMBS FAMILY MEMBER0.98positive
g9311.t1TETRASPANIN0.98positive
g14118.t1ENDO/EXONUCLEASE/PHOSPHATASE DOMAIN-CONTAINING PROTEIN0.98positive
g14245.t1ACROSIN-RELATED0.98positive
g2176.t1SRCR DOMAIN-CONTAINING PROTEIN0.97positive
g261.t1UNCHARACTERIZED0.93positive
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 28 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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