Co-expression Network Analysis

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

📊 Global Network of g1561.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 g1561.t1
Gene ID Description PCC Relationship
g1561.t1ENDOGLIN/TGF-BETA RECEPTOR TYPE III1positive
g9965.t1HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN-RELATED0.98positive
g16658.t1CONTACTIN 50.98positive
g10188.t1RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR AT 64C, ISOFORM A0.98positive
g35598.t1RNA-BINDING PROTEIN MUSASHI HOMOLOG RBP60.98positive
g13062.t1SODIUM/CHLORIDE DEPENDENT TRANSPORTER0.98positive
g4019.t1NETRIN/LAMININ-RELATED0.97positive
g60.t1COMPLEMENT COMPONENT 1, S SUBCOMPONENT-RELATED0.97positive
g9966.t1HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN-RELATED0.97positive
g515.t1SRCR DOMAIN-CONTAINING PROTEIN0.97positive
g11179.t1FER-1-LIKE0.97positive
g18413.t1HOMEOBOX PROTEIN ARISTALESS0.97positive
g4426.t1BETA-1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE0.97positive
g33275.t1--0.97positive
g16657.t1RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE0.97positive
g2770.t1HOMEOBOX PROTEIN0.97positive
g18412.t1HOMEOBOX PROTEIN ARISTALESS0.97positive
g11216.t1ENHANCER OF MRNA-DECAPPING PROTEIN 40.97positive
g12658.t1CATION TRANSPORTING ATPASE0.96positive
g601.t1TETRATRICOPEPTIDE REPEAT PROTEIN 130.96positive
g25255.t1--0.96positive
g34242.t1--0.96positive
g23615.t1POLY A POLYMERASE0.95positive
g23431.t1GRANULIN0.95positive
g34253.t1GH28348P0.94positive
g26823.t1--0.92positive
g19093.t1URICASE0.92positive
g21407.t1--0.90positive
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 98 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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