Co-expression Network Analysis

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

📊 Global Network of g13630.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 g13630.t1
Gene ID Description PCC Relationship
g13630.t1-1positive
g6326.t1EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TRANSPORTER0.95positive
g14350.t1SH3 AND MULTIPLE ANKYRIN REPEAT DOMAINS PROTEIN0.94positive
g27157.t1COILED-COIL DOMAIN-CONTAINING PROTEIN 1710.94positive
g9756.t1PDZ DOMAIN-CONTAINING PROTEIN 80.94positive
g3272.t1UROCANATE HYDRATASE0.93positive
g4487.t1--0.93positive
g10462.t1NIPPED-B-LIKE PROTEIN DELANGIN SCC2-RELATED0.92positive
g7126.t14.1 G PROTEIN0.92positive
g9303.t1SERUM RESPONSE FACTOR HOMOLOG0.92positive
g22614.t1--0.92positive
g7348.t1--0.91positive
g20715.t1F-BOX ONLY PROTEIN 30.91positive
g31351.t1CHOLESTEROL OXIDASE0.90positive
g8050.t1SH3 DOMAIN-BINDING PROTEIN 50.90positive
g12374.t1SERINE/THREONINE-PROTEIN KINASE TNNI3K-RELATED0.87positive
g28705.t1RIBOSOMAL PROTEIN S6 KINASE0.87positive
g14924.t1LEUCINE AMINOPEPTIDASE-RELATED0.85positive
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 80 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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