Co-expression Network Analysis

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

📊 Global Network of evm.model.Ap4.3992
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.Ap4.3992
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.Ap4.3992--1positive
Thr_4257--1.00positive
evm.model.Ap1.1312EXONUCLEASE, PHAGE-TYPE/RECB, C-TERMINAL DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap1.1351--1.00positive
evm.model.Ap1.170--1.00positive
evm.model.Ap1.1740--1.00positive
evm.model.Ap1.1807RAPSYN-RELATED1.00positive
evm.model.Ap1.1858RAPSYN-RELATED1.00positive
evm.model.Ap1.2748HYPOXIA-INDUCIBLE FACTOR 1 ALPHA INHIBITOR-RELATED1.00positive
evm.model.Ap1.3080HISTAMINE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap1.3612RIBONUCLEASE P SUBUNIT P301.00positive
evm.model.Ap1.4149NEUROPEPTIDE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap1.637TETRATRICOPEPTIDE REPEAT PROTEIN1.00positive
evm.model.Ap1.906CYTOCHROME P450 508A4-RELATED1.00positive
evm.model.Ap10.1322OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap10.161--1.00positive
evm.model.Ap10.1756G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap10.1927ACTIN1.00positive
evm.model.Ap10.742PROPERDIN1.00positive
evm.model.Ap10.974UBIQUITIN-LIKE PROTEASE 4-RELATED1.00positive
evm.model.Ap11.1559--1.00positive
evm.model.Ap11.1738TRANSPOSON1.00positive
evm.model.Ap11.1813METALLOPROTEASE TLDD1.00positive
evm.model.Ap11.583G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap11.593_evm.model.Ap11.597BONUS, ISOFORM C-RELATED1.00positive
evm.model.Ap11.624BTB/POZ DOMAIN-CONTAINING1.00positive
evm.model.Ap11.999BTB/POZ DOMAIN-CONTAINING1.00positive
evm.model.Ap12.1323--1.00positive
evm.model.Ap12.145OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap12.1467BTB/POZ DOMAIN-CONTAINING1.00positive
evm.model.Ap12.147OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap12.1770ESSENTIAL MCU REGULATOR, MITOCHONDRIAL1.00positive
evm.model.Ap12.2255--1.00positive
evm.model.Ap12.688--1.00positive
evm.model.Ap13.1421--1.00positive
evm.model.Ap13.169339S RIBOSOMAL PROTEIN L40, MITOCHONDRIAL1.00positive
evm.model.Ap13.1954--1.00positive
evm.model.Ap13.2140INTEGRASE CATALYTIC DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap13.2235--1.00positive
evm.model.Ap13.2291RAPSYN-RELATED1.00positive
evm.model.Ap13.2384OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap13.707--1.00positive
evm.model.Ap14.1008--1.00positive
evm.model.Ap14.1241INTEGRASE CATALYTIC DOMAIN-CONTAINING PROTEIN-RELATED1.00positive
evm.model.Ap14.1520--1.00positive
evm.model.Ap14.1604HISTONE H3 METHYLTRANSFERASE1.00positive
evm.model.Ap14.1723RAPSYN-RELATED1.00positive
evm.model.Ap14.451MYOSIN LIGHT CHAIN 1, 31.00positive
evm.model.Ap14.524OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap14.640--1.00positive
evm.model.Ap2.1116ADRENERGIC RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap2.1316--1.00positive
evm.model.Ap2.14014.1 G PROTEIN1.00positive
evm.model.Ap2.1704HISTAMINE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap2.1868COMPLEMENT COMPONENT C61.00positive
evm.model.Ap2.2223TROPOMYOSIN1.00positive
evm.model.Ap2.3019KINESIN-RELATED1.00positive
evm.model.Ap2.749OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap2.819--1.00positive
evm.model.Ap3.1176HEAT SHOCK PROTEIN 70KDA1.00positive
evm.model.Ap3.1396BONUS, ISOFORM C-RELATED1.00positive
evm.model.Ap3.1397BONUS, ISOFORM C-RELATED1.00positive
evm.model.Ap3.1567NEUROPEPTIDE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap3.1568--1.00positive
evm.model.Ap3.1588NEUROPEPTIDE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap3.1859RNA-DEPENDENT RNA POLYMERASE1.00positive
evm.model.Ap3.1871LD33804P1.00positive
evm.model.Ap3.2135LD33695P1.00positive
evm.model.Ap4.1275--1.00positive
evm.model.Ap4.1278--1.00positive
evm.model.Ap4.2229SIMILAR TO RIKEN CDNA E130308A191.00positive
evm.model.Ap4.2284--1.00positive
evm.model.Ap4.2453--1.00positive
evm.model.Ap4.246--1.00positive
evm.model.Ap4.2504--1.00positive
evm.model.Ap4.2589L1 TRANSPOSABLE ELEMENT-RELATED1.00positive
evm.model.Ap4.2980--1.00positive
evm.model.Ap4.3222--1.00positive
evm.model.Ap4.3348RAS-ASSOCIATING DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap4.3386--1.00positive
evm.model.Ap4.3397--1.00positive
evm.model.Ap4.3418--1.00positive
evm.model.Ap4.3656C2H2-TYPE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap4.5083COMM DOMAIN-CONTAINING PROTEIN 4-8 FAMILY MEMBER1.00positive
evm.model.Ap4.5130PROTEIN CBG266941.00positive
evm.model.Ap4.5241--1.00positive
evm.model.Ap4.5520--1.00positive
evm.model.Ap4.5521--1.00positive
evm.model.Ap4.5591SENTRIN-SPECIFIC PROTEASE1.00positive
evm.model.Ap4.7213ENDO/EXONUCLEASE/PHOSPHATASE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap4.7287TRANSFORMER-2 SEX-DETERMINING PROTEIN-RELATED1.00positive
evm.model.Ap5.1138INTEGRASE CATALYTIC DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap5.1649PROPERDIN1.00positive
evm.model.Ap5.2480--1.00positive
evm.model.Ap5.2544XYLOSIDE XYLOSYLTRANSFERASE 11.00positive
evm.model.Ap5.307--1.00positive
evm.model.Ap5.636--1.00positive
evm.model.Ap5.706--1.00positive
evm.model.Ap6.1011POLYCOMB GROUP PROTEIN PC1.00positive
evm.model.Ap6.2098--1.00positive
evm.model.Ap6.2107--1.00positive
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 5050 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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