Co-expression Network Analysis

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

📊 Global Network of evm.model.Ap2.2443
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.Ap2.2443
Note: a hub gene can be co-expressed with thousands of genes, so each query gene is limited to its 100 strongest partners (positive and negative counted separately). Both the networks above and the table below show only those — this is not the complete network of the query genes.
Gene ID Description PCC Relationship
evm.model.Ap2.2443--1positive
Ala_1338--1.00positive
Ile_1464--1.00positive
Ser_1405--1.00positive
Ser_1815--1.00positive
Thr_191--1.00positive
Thr_30--1.00positive
Thr_3284--1.00positive
Thr_558--1.00positive
Thr_782--1.00positive
evm.model.Ap1.1003PROTEIN CBG051311.00positive
evm.model.Ap1.1126L1 TRANSPOSABLE ELEMENT-RELATED1.00positive
evm.model.Ap1.1147--1.00positive
evm.model.Ap1.1369ANK_REP_REGION DOMAIN-CONTAINING PROTEIN-RELATED1.00positive
evm.model.Ap1.1620--1.00positive
evm.model.Ap1.1753--1.00positive
evm.model.Ap1.2521--1.00positive
evm.model.Ap1.267METABOTROPIC GLUTAMATE RECEPTOR1.00positive
evm.model.Ap1.3236FE2OG DIOXYGENASE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap1.3479RAPSYN-RELATED1.00positive
evm.model.Ap1.4139--1.00positive
evm.model.Ap1.548KRUEPPEL-LIKE TRANSCRIPTION FACTOR1.00positive
evm.model.Ap10.1231LEUCOKININ RECEPTOR-RELATED1.00positive
evm.model.Ap10.1535HISTAMINE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap10.1548HISTAMINE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap10.414TETRATRICOPEPTIDE REPEAT PROTEIN (AFU_ORTHOLOGUE AFUA_6G03870)1.00positive
evm.model.Ap10.714--1.00positive
evm.model.Ap11.1026POLY A -SPECIFIC RIBONUCLEASE/TARGET OF EGR1, MEMBER 11.00positive
evm.model.Ap11.1570--1.00positive
evm.model.Ap11.1603EGL NINE HOMOLOG-RELATED1.00positive
evm.model.Ap11.1764ADRENERGIC RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap11.436G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap11.577--1.00positive
evm.model.Ap12.1243--1.00positive
evm.model.Ap12.1404TRACE AMINE-ASSOCIATED RECEPTOR 19N-RELATED1.00positive
evm.model.Ap12.1476--1.00positive
evm.model.Ap12.344ENDONUCLEASE-RELATED1.00positive
evm.model.Ap13.2315L1 TRANSPOSABLE ELEMENT-RELATED1.00positive
evm.model.Ap13.2583--1.00positive
evm.model.Ap13.2687--1.00positive
evm.model.Ap13.2692--1.00positive
evm.model.Ap13.2726UPF0669 PROTEIN C6ORF1201.00positive
evm.model.Ap13.277HEPARAN SULFATE 6-O-SULFOTRANSFERASE 31.00positive
evm.model.Ap13.372BINDING PROTEIN, PUTATIVE (AFU_ORTHOLOGUE AFUA_1G14430)-RELATED1.00positive
evm.model.Ap13.5305-HYDROXYTRYPTAMINE RECEPTOR1.00positive
evm.model.Ap14.1594OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap14.1916--1.00positive
evm.model.Ap14.1933--1.00positive
evm.model.Ap14.2038O-FUCOSYLTRANSFERASE 301.00positive
evm.model.Ap2.105--1.00positive
evm.model.Ap2.1812SPROUTY1.00positive
evm.model.Ap2.2627OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap2.4000GEO11136P1-RELATED1.00positive
evm.model.Ap3.112OPSIN1.00positive
evm.model.Ap3.1694BTB/POZ DOMAIN-CONTAINING1.00positive
evm.model.Ap4.1157OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap4.161--1.00positive
evm.model.Ap4.1851--1.00positive
evm.model.Ap4.1858RETROTRANSPOSON1.00positive
evm.model.Ap4.2631--1.00positive
evm.model.Ap4.3097PROTEIN CBG266941.00positive
evm.model.Ap4.3628--1.00positive
evm.model.Ap4.365PROTEIN CBG237641.00positive
evm.model.Ap4.5446--1.00positive
evm.model.Ap4.6441--1.00positive
evm.model.Ap4.6541-1.00positive
evm.model.Ap4.66795-HYDROXYTRYPTAMINE RECEPTOR1.00positive
evm.model.Ap4.976REVERSE TRANSCRIPTASE1.00positive
evm.model.Ap5.1085--1.00positive
evm.model.Ap5.1302--1.00positive
evm.model.Ap5.1311DUF3504 DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap5.1314--1.00positive
evm.model.Ap5.567CADHERIN DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap6.1738OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap6.1936PROTEIN CBG170251.00positive
evm.model.Ap6.3119OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap6.477--1.00positive
evm.model.Ap6.500--1.00positive
evm.model.Ap6.988INTEGRASE CORE DOMAIN CONTAINING PROTEIN1.00positive
evm.model.Ap7.1156TRANSLIN AND TRANSLIN ASSOCIATED PROTEIN X1.00positive
evm.model.Ap7.1180CARBOHYDRATE SULFOTRANSFERASE1.00positive
evm.model.Ap7.769--1.00positive
evm.model.Ap7.779--1.00positive
evm.model.Ap8.1832PHD-TYPE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap8.19185-HYDROXYTRYPTAMINE RECEPTOR1.00positive
evm.model.Ap8.422BTB/POZ DOMAIN-CONTAINING1.00positive
evm.model.Ap8.52TRANSPOSASE, PUTATIVE-RELATED1.00positive
evm.model.Ap8.618VOLTAGE-GATED POTASSIUM CHANNEL1.00positive
evm.model.Ap9.1224REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap9.1362REVERSE TRANSCRIPTASE1.00positive
evm.model.Ap9.1398--1.00positive
evm.model.Ap9.1550DISEASE RESISTANCE PROTEIN RP1.00positive
evm.model.Ap9.2465DNA HELICASE RECQ FAMILY MEMBER1.00positive
evm.model.Ap9.282REVERSE TRANSCRIPTASE1.00positive
evm.model.Ap9.603PROTEIN CBG170251.00positive
evm.model.Ap2.3831--1.00positive
evm.model.Ap4.3748--0.99positive
evm.model.Ap1.3153SH3 DOMAIN-CONTAINING0.99positive
Thr_415--0.99positive
evm.model.Ap13.1126--0.97positive
evm.model.Ap12.2571C2H2-TYPE DOMAIN-CONTAINING PROTEIN0.97positive
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 5035 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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