Co-expression Network Analysis

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

📊 Global Network of g27715.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 g27715.t1
Gene ID Description PCC Relationship
g27715.t1POLY A -SPECIFIC RIBONUCLEASE/TARGET OF EGR1, MEMBER 11positive
g28249.t1BATTENIN0.94positive
g6395.t1SORTING NEXIN-40.92positive
g7567.t1GEO07735P1-RELATED-RELATED0.92positive
g8218.t1RNA POLYMERASE II-ASSOCIATED PROTEIN 10.91positive
g33745.t1ANKYRIN REPEAT PROTEIN0.91positive
g22005.t1ZINC FINGERS AND HOMEOBOXES PROTEIN 1, ISOFORM 20.91positive
g13350.t1TRANSMEMBRANE PROTEIN INDUCED BY TUMOR NECROSIS FACTOR ALPHA0.89positive
g2220.t1FOLATE RECEPTOR0.89positive
g1199.t1AMINO ACID TRANSPORTER0.89positive
g22701.t1CYTOPLASMIC TRNA 2-THIOLATION PROTEIN 20.88positive
g8648.t1LIPOPOLYSACCHARIDE CHOLINEPHOSPHOTRANSFERASE LICD0.88positive
g6497.t1ENDOPLASMIC RETICULUM MEMBRANE-ASSOCIATED RNA DEGRADATION PROTEIN0.87positive
g30324.t1CYTOCHROME P450 FAMILY 46 SUBFAMILY A0.85positive
g33333.t1BONUS, ISOFORM C-RELATED0.84positive
g8268.t1CALCIUM AND INTEGRIN BINDING FAMILY MEMBER 20.82positive
g31004.t1UBIQUITIN CARBOXYL-TERMINAL HYDROLASE0.81positive
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 48 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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