Co-expression Network Analysis

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

📊 Global Network of g4055.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 g4055.t1
Gene ID Description PCC Relationship
g4055.t1--1positive
g528.t1FCH AND DOUBLE SH3 DOMAINS PROTEIN0.99positive
g4434.t1FIBRINOGEN/TENASCIN/ANGIOPOEITIN0.99positive
g3365.t1--0.99positive
g18961.t1G-PROTEIN COUPLED RECEPTOR FAMILY 1 MEMBER0.99positive
g12030.t1COLLAGEN ALPHA0.99positive
g10112.t1CENTROSOMAL PROTEIN 20.99positive
g28319.t1CYSTEINE-RICH SECRETORY PROTEIN-RELATED0.99positive
g18965.t1CARBOHYDRATE SULFOTRANSFERASE0.99positive
g16362.t1KELCH PROTEIN0.99positive
g5679.t1--0.99positive
g27828.t1--0.99positive
g15545.t1--0.99positive
g3648.t1RETICULON-LIKE PROTEIN0.99positive
g7546.t1--0.99positive
g27742.t1--0.99positive
g167.t1ENDOCHITINASE0.99positive
g16653.t1CALCIUM BINDING PROTEIN0.99positive
g10642.t1COLLAGEN ALPHA0.99positive
g35995.t1T-COMPLEX-ASSOCIATED-TESTIS-EXPRESSED 1/ DYNEIN LIGHT CHAIN0.99positive
g34854.t1SULFOTRANSFERASE DOMAIN-CONTAINING PROTEIN0.99positive
g23746.t1--0.99positive
g5611.t1--0.99positive
g6365.t1LANC-LIKE PROTEIN0.99positive
g27945.t1--0.99positive
g2642.t1SRCR DOMAIN-CONTAINING PROTEIN0.99positive
g29471.t1PROLYL 4-HYDROXYLASE ALPHA SUBUNIT0.99positive
g10057.t1HOMEOBOX PROTEIN GBX0.99positive
g2102.t1COLLAGEN ALPHA0.99positive
g19186.t1TNF RECEPTOR ASSOCIATED FACTOR0.99positive
g12092.t1RIBULOKINASE0.99positive
g32539.t1--0.99positive
g7280.t1AMILORIDE-SENSITIVE SODIUM CHANNEL-RELATED0.99positive
g28123.t1POTASSIUM CHANNEL, SUBFAMILY K0.99positive
g9745.t1--0.98positive
g26120.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 166 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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