Co-expression Network Analysis

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

📊 Global Network of evm.model.Ap1.236
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 evm.model.Ap1.236
Gene ID Description PCC Relationship
evm.model.Ap1.236TRANSMEMBRANE PROTEIN 1631positive
Thr_517--0.89positive
Thr_3843--0.86positive
evm.model.Ap4.6042--0.86positive
Thr_1440--0.85positive
Thr_1641--0.85positive
Thr_3325--0.85positive
Thr_4140--0.85positive
evm.model.Ap1.110--0.85positive
evm.model.Ap1.1778--0.85positive
evm.model.Ap1.1911BTB DOMAIN-CONTAINING PROTEIN0.85positive
evm.model.Ap1.4026--0.85positive
evm.model.Ap1.445LUPUS LA PROTEIN-RELATED0.85positive
evm.model.Ap1.742CARBOHYDRATE SULFOTRANSFERASE0.85positive
evm.model.Ap10.746--0.85positive
evm.model.Ap10.952--0.85positive
evm.model.Ap11.1055CARBOHYDRATE SULFOTRANSFERASE0.85positive
evm.model.Ap11.291HISTAMINE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR0.85positive
evm.model.Ap11.309MONOACYLGLYCEROL LIPASE0.85positive
evm.model.Ap11.395NADH-UBIQUINONE OXIDOREDUCTASE B12 SUBUNIT0.85positive
evm.model.Ap11.628BTB/POZ DOMAIN-CONTAINING0.85positive
evm.model.Ap11.629BTB/POZ DOMAIN-CONTAINING0.85positive
evm.model.Ap11.764--0.85positive
evm.model.Ap12.1312--0.85positive
evm.model.Ap12.1428BTB/POZ DOMAIN-CONTAINING0.85positive
evm.model.Ap12.790REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.85positive
evm.model.Ap13.103--0.85positive
evm.model.Ap13.2841--0.85positive
evm.model.Ap13.336CALCIUM-ACTIVATED POTASSIUM CHANNEL SUBUNIT BETA0.85positive
evm.model.Ap13.721--0.85positive
evm.model.Ap14.1299CXC DOMAIN-CONTAINING PROTEIN-RELATED0.85positive
evm.model.Ap2.2770--0.85positive
evm.model.Ap2.2877--0.85positive
evm.model.Ap2.3648--0.85positive
evm.model.Ap3.1259--0.85positive
evm.model.Ap3.1926E3 UBIQUITIN-PROTEIN LIGASE NHLRC1-RELATED0.85positive
evm.model.Ap4.2822--0.85positive
evm.model.Ap4.3015--0.85positive
evm.model.Ap4.3763--0.85positive
evm.model.Ap4.3951ATP-DEPENDENT DNA HELICASE0.85positive
evm.model.Ap4.5139RAS-ASSOCIATING DOMAIN-CONTAINING PROTEIN0.85positive
evm.model.Ap4.5447--0.85positive
evm.model.Ap4.6051OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.85positive
evm.model.Ap4.6056OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.85positive
evm.model.Ap4.857PHD-TYPE DOMAIN-CONTAINING PROTEIN0.85positive
evm.model.Ap6.1425--0.85positive
evm.model.Ap6.2930RETROTRANSPOSON0.85positive
evm.model.Ap6.297--0.85positive
evm.model.Ap6.3065--0.85positive
evm.model.Ap6.533RHO FAMILY GTPASE0.85positive
evm.model.Ap6.688ZINC FINGER PROTEIN0.85positive
evm.model.Ap6.717KRAB AND ZINC FINGER DOMAIN-CONTAINING0.85positive
evm.model.Ap7.2134ENDO/EXONUCLEASE/PHOSPHATASE DOMAIN-CONTAINING PROTEIN0.85positive
evm.model.Ap7.227--0.85positive
evm.model.Ap7.646--0.85positive
evm.model.Ap8.1645--0.85positive
evm.model.Ap8.2641--0.85positive
evm.model.Ap8.388--0.85positive
evm.model.Ap8.401--0.85positive
evm.model.Ap8.999--0.85positive
evm.model.Ap9.511TRANSCRIPTASE, PUTATIVE-RELATED-RELATED0.85positive
evm.model.Ap9.717--0.85positive
Thr_388--0.79positive
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 1892 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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