Co-expression Network Analysis

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

📊 Global Network of g5546.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 g5546.t1
Gene ID Description PCC Relationship
g5546.t1--1positive
g6446.t1ENDOGLIN/TGF-BETA RECEPTOR TYPE III1.00positive
g15941.t1FACIOGENITAL DYSPLASIA PROTEIN0.99positive
g15827.t160S RIBOSOMAL PROTEIN L3-RELATED0.99positive
g14393.t1COMPLEMENT COMPONENT-RELATED SUSHI DOMAIN-CONTAINING0.99positive
g19151.t1VOLTAGE-GATED CATION CHANNEL CALCIUM AND SODIUM0.99positive
g520.t1VITELLOGENIN RECEPTOR-LIKE PROTEIN-RELATED-RELATED0.99positive
g32703.t1ACTIN0.99positive
g36688.t1--0.99positive
g13536.t1SODIUM/CALCIUM EXCHANGER0.99positive
g3693.t1ORAL-FACIAL-DIGITAL SYNDROME 1 PROTEIN HOMOLOG0.99positive
g27468.t1SOLUTE CARRIER FAMILY 22 MEMBER0.99positive
g1484.t1MITOGEN-ACTIVATED PROTEIN KINASE0.99positive
g418.t1VOLTAGE-GATED CATION CHANNEL CALCIUM AND SODIUM0.99positive
g16168.t1LEUCINE RICH REPEAT FAMILY PROTEIN0.99positive
g21670.t1MACROGLOBULIN / COMPLEMENT0.99positive
g24840.t1--0.99positive
g12224.t1--0.99positive
g14564.t1RING FINGER AND CHY ZINC FINGER DOMAIN-CONTAINING PROTEIN 10.99positive
g12225.t1--0.99positive
g35439.t1--0.99positive
g26445.t1--0.98positive
g3104.t1ANK_REP_REGION DOMAIN-CONTAINING PROTEIN0.98positive
g4719.t1PROTEIN PHOSPHATASE0.98positive
g25631.t1RETROTRANSPOSON0.98positive
g13519.t1GRANULIN0.98positive
g16890.t1--0.98positive
g35270.t1THAP DOMAIN PROTEIN0.97positive
g17336.t1UNCHARACTERIZED0.95positive
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 116 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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