Co-expression Network Analysis

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

📊 Global Network of evm.model.Ap4.7
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.Ap4.7
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.Ap4.7OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1positive
Gly_2366--1.00positive
Gly_2367--1.00positive
Ser_24--1.00positive
Ser_4648--1.00positive
Thr_2434--1.00positive
Thr_2504--1.00positive
Thr_3183--1.00positive
Thr_3195--1.00positive
Thr_3925--1.00positive
evm.model.Ap1.1866PROTEIN CBG266941.00positive
evm.model.Ap1.206--1.00positive
evm.model.Ap1.2247SERINE/THREONINE-PROTEIN KINASE RIO11.00positive
evm.model.Ap1.3786REVERSE TRANSCRIPTASE1.00positive
evm.model.Ap1.4187REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap1.735--1.00positive
evm.model.Ap1.861--1.00positive
evm.model.Ap10.511OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap10.967--1.00positive
evm.model.Ap11.117--1.00positive
evm.model.Ap11.169--1.00positive
evm.model.Ap11.1744--1.00positive
evm.model.Ap11.55ZINC FINGER PROTEIN1.00positive
evm.model.Ap11.855SPOT14 FAMILY MEMBER1.00positive
evm.model.Ap12.114RNA AND EXPORT FACTOR BINDING PROTEIN1.00positive
evm.model.Ap12.1244--1.00positive
evm.model.Ap12.585REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap12.67HISTAMINE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap12.753HISTAMINE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap13.1--1.00positive
evm.model.Ap13.1608-1.00positive
evm.model.Ap13.2727REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap13.2904--1.00positive
evm.model.Ap13.739L1 TRANSPOSABLE ELEMENT-RELATED1.00positive
evm.model.Ap14.1202--1.00positive
evm.model.Ap14.272--1.00positive
evm.model.Ap14.492RIBITOL-5-PHOSPHATE XYLOSYLTRANSFERASE 11.00positive
evm.model.Ap14.686RETROTRANSPOSON1.00positive
evm.model.Ap2.1300REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap2.2776REVERSE TRANSCRIPTASE1.00positive
evm.model.Ap2.2827--1.00positive
evm.model.Ap2.3481REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap3.1633OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap3.2247--1.00positive
evm.model.Ap3.402ALPHA- 1,3 -FUCOSYLTRANSFERASE1.00positive
evm.model.Ap4.1235INTEGRASE CATALYTIC DOMAIN-CONTAINING PROTEIN-RELATED1.00positive
evm.model.Ap4.1408RETROTRANSPOSON1.00positive
evm.model.Ap4.1597--1.00positive
evm.model.Ap4.1640--1.00positive
evm.model.Ap4.2022--1.00positive
evm.model.Ap4.2143L1 TRANSPOSABLE ELEMENT-RELATED1.00positive
evm.model.Ap4.2420SET DOMAIN-CONTAINING PROTEIN-RELATED1.00positive
evm.model.Ap4.3011--1.00positive
evm.model.Ap4.3897C2H2-TYPE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap4.5167--1.00positive
evm.model.Ap5.2038OPSIN1.00positive
evm.model.Ap5.20395-HYDROXYTRYPTAMINE RECEPTOR1.00positive
evm.model.Ap5.2618TRANSMEMBRANE PROTEIN 1871.00positive
evm.model.Ap5.2795PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 121.00positive
evm.model.Ap6.1275BTB/POZ DOMAIN-CONTAINING1.00positive
evm.model.Ap6.1595FORKHEAD BOX PROTEIN1.00positive
evm.model.Ap6.1600FORKHEAD BOX PROTEIN1.00positive
evm.model.Ap6.1601FORKHEAD BOX PROTEIN1.00positive
evm.model.Ap6.3013--1.00positive
evm.model.Ap6.3234RIBOSOMAL PROTEIN L131.00positive
evm.model.Ap7.1413--1.00positive
evm.model.Ap7.204SKICH DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap7.410REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap7.497RETROTRANSPOSON1.00positive
evm.model.Ap7.790--1.00positive
evm.model.Ap8.1329--1.00positive
evm.model.Ap8.1427--1.00positive
evm.model.Ap8.1453--1.00positive
evm.model.Ap8.1529PROTEIN CBG237641.00positive
evm.model.Ap8.155OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap8.156OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap8.232--1.00positive
evm.model.Ap8.892TRANSMEMBRANE PROTEIN 151 HOMOLOG1.00positive
evm.model.Ap9.1964--1.00positive
evm.model.Ap9.653--1.00positive
Ser_90--0.99positive
evm.model.Ap11.1001--0.98positive
evm.model.Ap13.34--0.98positive
evm.model.Ap2.570--0.98positive
evm.model.Ap10.125--0.98positive
evm.model.Ap14.1934--0.97positive
evm.model.Ap12.882_evm.model.Ap12.880KELCH PROTEIN0.97positive
evm.model.Ap1.1429DNA HELICASE RECQ FAMILY MEMBER0.96positive
evm.model.Ap1.810THAP DOMAIN PROTEIN0.94positive
evm.model.Ap13.310--0.93positive
evm.model.Ap11.1829REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.92positive
evm.model.Ap12.1150HISTAMINE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR0.92positive
evm.model.Ap2.3741REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.91positive
evm.model.Ap6.229G-PROTEIN COUPLED RECEPTOR0.90positive
evm.model.Ap12.2331CENTROSOMAL PROTEIN 20.90positive
evm.model.Ap4.5255LEUCOKININ RECEPTOR-RELATED0.89positive
evm.model.Ap8.1565--0.89positive
evm.model.Ap14.769REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.88positive
evm.model.Ap8.1642--0.88positive
Phe_863--0.87positive
evm.model.Ap2.3667REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.87positive
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 4853 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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