Co-expression Network Analysis

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

📊 Global Network of evm.model.Ap2.2104
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.Ap2.2104
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.Ap2.2104--1positive
Arg_357--1.00positive
Thr_3612--1.00positive
Thr_3737--1.00positive
Thr_4662--1.00positive
Thr_4665--1.00positive
evm.model.Ap1.1150CXC DOMAIN-CONTAINING PROTEIN-RELATED1.00positive
evm.model.Ap1.1953NATTERIN-41.00positive
evm.model.Ap10.1519OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap10.1531HISTAMINE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap11.1007--1.00positive
evm.model.Ap11.1359LOC100145250 PROTEIN1.00positive
evm.model.Ap11.846--1.00positive
evm.model.Ap12.1033PROTEIN CBG266941.00positive
evm.model.Ap12.1911--1.00positive
evm.model.Ap13.1136MITOCHONDRIAL BASIC AMINO ACIDS TRANSPORTER-RELATED1.00positive
evm.model.Ap13.1558--1.00positive
evm.model.Ap13.2297LD33695P1.00positive
evm.model.Ap13.2877GLUTAREDOXIN FAMILY MEMBER1.00positive
evm.model.Ap14.201--1.00positive
evm.model.Ap2.2103--1.00positive
evm.model.Ap2.2740--1.00positive
evm.model.Ap3.1524--1.00positive
evm.model.Ap3.2075--1.00positive
evm.model.Ap4.1624--1.00positive
evm.model.Ap4.3710--1.00positive
evm.model.Ap4.6734HISTAMINE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap4.7080OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap5.2167_evm.model.Ap5.2177-1.00positive
evm.model.Ap5.281NEUROPEPTIDE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap6.1194--1.00positive
evm.model.Ap6.396--1.00positive
evm.model.Ap7.1548DNA HELICASE RECQ FAMILY MEMBER1.00positive
evm.model.Ap7.20052 KDA REPRESSOR OF THE INHIBITOR OF THE PROTEIN KINASE-LIKE PROTEIN-RELATED1.00positive
evm.model.Ap7.2082PROTEIN CBG266941.00positive
evm.model.Ap7.240DISKS LARGE-ASSOCIATED PROTEIN DAP SAP90/PSD-95-ASSOCIATED PROTEIN1.00positive
evm.model.Ap7.2865--1.00positive
evm.model.Ap8.1089--1.00positive
evm.model.Ap8.2011--1.00positive
evm.model.Ap8.2720NIEMANN PICK TYPE C2 PROTEIN NPC2-RELATED1.00positive
evm.model.Ap8.891LEXA REPRESSOR-RELATED1.00positive
evm.model.Ap9.1526FE2OG DIOXYGENASE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap9.2762FAM11A, B PROTEIN1.00positive
evm.model.Ap9.520--1.00positive
evm.model.Ap9.98--1.00positive
Gln_773--1.00positive
evm.model.Ap6.1952--0.99positive
Thr_4610--0.99positive
evm.model.Ap4.5926BETA-1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE0.99positive
evm.model.Ap12.1290G-PROTEIN COUPLED RECEPTOR0.99positive
evm.model.Ap9.2674REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.99positive
evm.model.Ap7.2050_evm.model.Ap7.2071--0.99positive
evm.model.Ap4.4374REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.99positive
evm.model.Ap2.3363RETROTRANSPOSON0.98positive
evm.model.Ap8.2418VANG-LIKE PROTEIN0.98positive
evm.model.Ap12.293OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.98positive
evm.model.Ap8.307TRANSMEMBRANE PROTEIN 151 HOMOLOG0.97positive
evm.model.Ap4.4439--0.97positive
evm.model.Ap11.37NON-LTR RETROLELEMENT REVERSE TRANSCRIPTASE-LIKE PROTEIN-RELATED0.97positive
evm.model.Ap13.2260REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.97positive
Thr_70--0.97positive
evm.model.Ap12.2294REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.96positive
evm.model.Ap14.1190REVERSE TRANSCRIPTASE0.96positive
evm.model.Ap9.2439SET DOMAIN-CONTAINING PROTEIN-RELATED0.95positive
evm.model.Ap1.911--0.94positive
evm.model.Ap2.3296TRANSMEMBRANE PROTEIN 790.94positive
Thr_1416--0.94positive
evm.model.Ap9.1328--0.94positive
evm.model.Ap9.2442SET DOMAIN-CONTAINING PROTEIN-RELATED0.94positive
evm.model.Ap2.3890--0.93positive
evm.model.Ap6.2232HISTAMINE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR0.92positive
evm.model.Ap2.3955--0.91positive
evm.model.Ap6.1900--0.91positive
evm.model.Ap2.2072--0.91positive
Ala_2789--0.91positive
evm.model.Ap5.1689--0.90positive
evm.model.Ap9.1960REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.90positive
evm.model.Ap1.1130NON-LTR RETROLELEMENT REVERSE TRANSCRIPTASE-LIKE PROTEIN-RELATED0.90positive
evm.model.Ap6.2317THO COMPLEX SUBUNIT 10.89positive
evm.model.Ap3.1732--0.89positive
evm.model.Ap4.4245--0.89positive
evm.model.Ap1.3698--0.88positive
evm.model.Ap1.1662SHIPPO-1-RELATED0.88positive
evm.model.Ap1.339--0.87positive
evm.model.Ap10.1493HISTAMINE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR0.87positive
evm.model.Ap3.951--0.87positive
evm.model.Ap7.2273--0.87positive
evm.model.Ap4.4898--0.87positive
evm.model.Ap5.1419SI:CH211-243P7.3-RELATED0.87positive
evm.model.Ap13.517OPSIN0.86positive
evm.model.Ap13.914--0.86positive
evm.model.Ap13.1231TRANSMEMBRANE PROTEIN 229 FAMILY MEMBER0.85positive
evm.model.Ap8.1534REVERSE TRANSCRIPTASE0.84positive
Thr_1474--0.84positive
evm.model.Ap1.740--0.83positive
evm.model.Ap8.592--0.83positive
evm.model.Ap4.2372DDE_TNP_1_7 DOMAIN-CONTAINING PROTEIN0.83positive
evm.model.Ap2.2731OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.82positive
evm.model.Ap5.1415SI:CH211-243P7.3-RELATED0.82positive
evm.model.Ap2.43--0.81positive
evm.model.Ap9.1143--0.81positive
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 3616 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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