Co-expression Network Analysis

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

📊 Global Network of g16653.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 g16653.t1
Gene ID Description PCC Relationship
g16653.t1CALCIUM BINDING PROTEIN1positive
g3648.t1RETICULON-LIKE PROTEIN0.99positive
g34854.t1SULFOTRANSFERASE DOMAIN-CONTAINING PROTEIN0.99positive
g27588.t1MYOTROPHIN0.99positive
g2102.t1COLLAGEN ALPHA0.99positive
g5935.t1--0.99positive
g6365.t1LANC-LIKE PROTEIN0.99positive
g12092.t1RIBULOKINASE0.99positive
g1953.t1--0.99positive
g31603.t1--0.99positive
g16362.t1KELCH PROTEIN0.99positive
g4055.t1--0.99positive
g14893.t1PROTEIN CBR-CLEC-780.99positive
g18965.t1CARBOHYDRATE SULFOTRANSFERASE0.99positive
g27106.t1AGAP001623-PA0.99positive
g19265.t1--0.99positive
g23002.t1CYTOCHROME P450 FAMILY 30.99positive
g14390.t1--0.99positive
g34678.t1--0.99positive
g10057.t1HOMEOBOX PROTEIN GBX0.99positive
g3385.t1NOTCH LIGAND FAMILY MEMBER0.99positive
g9390.t1MULTIPLE INOSITOL POLYPHOSPHATE PHOSPHATASE-RELATED0.99positive
g2375.t1ANK_REP_REGION DOMAIN-CONTAINING PROTEIN0.99positive
g28319.t1CYSTEINE-RICH SECRETORY PROTEIN-RELATED0.99positive
g4084.t1ANTHRAX TOXIN RECEPTOR0.99positive
g34691.t1CONTACTIN 50.99positive
g14798.t1T-BOX PROTEIN-RELATED0.99positive
g25495.t1G-PROTEIN COUPLED RECEPTOR0.99positive
g8334.t1--0.99positive
g2583.t1POTASSIUM CHANNEL, SUBFAMILY K0.99positive
g34676.t1COLLAGEN ALPHA0.99positive
g12983.t1--0.98positive
g4242.t1USP DOMAIN-CONTAINING PROTEIN0.98positive
g15452.t1RAS-ASSOCIATING DOMAIN-CONTAINING PROTEIN0.97positive
g4750.t1--0.92positive
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 149 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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