Co-expression Network Analysis

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

📊 Global Network of g2113.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 g2113.t1
Gene ID Description PCC Relationship
g2113.t1--1positive
g7.t1NEUROTRANSMITTER GATED ION CHANNEL1.00positive
g10390.t1--0.99positive
g15439.t1--0.99positive
g13536.t1SODIUM/CALCIUM EXCHANGER0.99positive
g10672.t1--0.99positive
g17806.t1COLLAGEN ALPHA0.99positive
g10642.t1COLLAGEN ALPHA0.99positive
g13454.t1NEUROTRANSMITTER GATED ION CHANNEL0.99positive
g3648.t1RETICULON-LIKE PROTEIN0.99positive
g26424.t1CYTOCHROME P450 FAMILY 30.99positive
g4784.t1POLYCYSTIN FAMILY MEMBER0.99positive
g27238.t1TRYPTASE-RELATED0.99positive
g25187.t1--0.99positive
g2901.t1ANKYRIN REPEAT PROTEIN0.99positive
g6614.t1COLLAGEN ALPHA0.99positive
g7546.t1--0.99positive
g31660.t1SH3 DOMAIN-CONTAINING0.99positive
g10644.t1COLLAGEN0.99positive
g4722.t1CONTACTIN 50.99positive
g192.t1COLLAGEN ALPHA0.99positive
g8733.t1CALCIUM-ACTIVATED POTASSIUM CHANNEL ALPHA CHAIN0.99positive
g3925.t1UBIQUITIN-PROTEIN LIGASE E3C0.99positive
g28150.t1--0.99positive
g34787.t1C-REACTIVE PROTEIN-RELATED0.99positive
g5650.t1--0.99positive
g32703.t1ACTIN0.99positive
g3382.t1--0.99positive
g14798.t1T-BOX PROTEIN-RELATED0.99positive
g5248.t1COLLAGEN ALPHA0.99positive
g11603.t1TRANSFERRIN0.99positive
g14447.t1MONOCARBOXYLATE TRANSPORTER0.99positive
g15438.t1--0.99positive
g1952.t1--0.99positive
g34672.t1COLLAGEN ALPHA0.99positive
g9705.t1ENOLASE (DUF1399)0.98positive
g28439.t1COLLAGEN ALPHA0.98positive
g27821.t1L1 TRANSPOSABLE ELEMENT-RELATED0.98positive
g15548.t1--0.98positive
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 204 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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