Co-expression Network Analysis

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

📊 Global Network of evm.model.Ap4.4287
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.Ap4.4287
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.Ap4.4287--1positive
Thr_2486--1.00positive
Thr_2863--1.00positive
Thr_3107--1.00positive
Thr_4008--1.00positive
Thr_885--1.00positive
evm.model.Ap1.1131--1.00positive
evm.model.Ap1.1242--1.00positive
evm.model.Ap1.1910BTB DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap1.1970--1.00positive
evm.model.Ap1.2403BTB/POZ DOMAIN-CONTAINING1.00positive
evm.model.Ap1.2431BTB/POZ DOMAIN-CONTAINING1.00positive
evm.model.Ap1.2554--1.00positive
evm.model.Ap1.2933GLYCOPROTEIN HORMONE RECEPTOR1.00positive
evm.model.Ap1.3095APPLE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap1.3197HISTONE H41.00positive
evm.model.Ap1.3481RAPSYN-RELATED1.00positive
evm.model.Ap10.1080OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap11.439OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap11.458RETROTRANSPOSON1.00positive
evm.model.Ap11.494BTB/POZ DOMAIN-CONTAINING1.00positive
evm.model.Ap11.948APPLE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap12.1561NEUROPEPTIDE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR1.00positive
evm.model.Ap12.2286--1.00positive
evm.model.Ap13.149OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap14.1695T-COMPLEX-ASSOCIATED-TESTIS-EXPRESSED 1/ DYNEIN LIGHT CHAIN1.00positive
evm.model.Ap14.1792NUCLEOREDOXIN-LIKE PROTEIN 21.00positive
evm.model.Ap2.1988PHOSPHATIDYLSERINE DECARBOXYLASE1.00positive
evm.model.Ap2.3376--1.00positive
evm.model.Ap3.1922OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap3.2013DNA HELICASE RECQ FAMILY MEMBER1.00positive
evm.model.Ap4.295OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap4.3152THAP DOMAIN PROTEIN1.00positive
evm.model.Ap4.3264--1.00positive
evm.model.Ap4.346--1.00positive
evm.model.Ap4.357--1.00positive
evm.model.Ap4.3580RETROTRANSPOSON1.00positive
evm.model.Ap4.4393AP ENDONUCLEASE1.00positive
evm.model.Ap4.5526--1.00positive
evm.model.Ap4.6418G PROTEIN-COUPLED RECEPTOR1.00positive
evm.model.Ap4.6552REVERSE TRANSCRIPTASE1.00positive
evm.model.Ap5.2404OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1.00positive
evm.model.Ap5.2856NECTIN-RELATED1.00positive
evm.model.Ap6.2897BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR, TWIST1.00positive
evm.model.Ap6.2899BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR, TWIST1.00positive
evm.model.Ap6.401--1.00positive
evm.model.Ap6.684ZINC FINGER PROTEIN1.00positive
evm.model.Ap7.1183--1.00positive
evm.model.Ap7.1227EARLY GAMETOCYTE ENRICHED PHOSPHOPROTEIN EGXP1.00positive
evm.model.Ap7.1708RETROTRANSPOSON1.00positive
evm.model.Ap7.2676--1.00positive
evm.model.Ap8.2156C2H2-TYPE DOMAIN-CONTAINING PROTEIN1.00positive
evm.model.Ap8.476F-BOX DOMAIN CONTAINING PROTEIN, EXPRESSED1.00positive
evm.model.Ap8.953--1.00positive
evm.model.Ap9.1134SYNDECAN1.00positive
evm.model.Ap9.2312--1.00positive
evm.model.Ap4.7091--1.00positive
evm.model.Ap5.2429REVERSE TRANSCRIPTASE1.00positive
evm.model.Ap9.148--1.00positive
evm.model.Ap10.2048CARNITINE O-ACYLTRANSFERASE1.00positive
evm.model.Ap3.1739BTB/POZ DOMAIN-CONTAINING0.98positive
evm.model.Ap4.7207EXPRESSED PROTEIN0.98positive
evm.model.Ap7.1804REVERSE TRANSCRIPTASE0.97positive
evm.model.Ap1.264OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.97positive
evm.model.Ap5.2750REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.97positive
evm.model.Ap14.898--0.97positive
Thr_2464--0.96positive
evm.model.Ap4.3966--0.96positive
Thr_2371--0.95positive
evm.model.Ap12.1126HISTAMINE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR0.95positive
evm.model.Ap4.1855--0.94positive
evm.model.Ap4.4101--0.93positive
evm.model.Ap1.98G-PROTEIN COUPLED RECEPTOR0.93positive
Gly_428--0.92positive
Thr_2613--0.92positive
Thr_1643--0.91positive
evm.model.Ap9.344ATP-DEPENDENT DNA HELICASE0.91positive
evm.model.Ap2.437--0.90positive
evm.model.Ap12.1013METABOTROPIC GLUTAMATE RECEPTOR0.90positive
evm.model.Ap9.850L1 TRANSPOSABLE ELEMENT-RELATED0.89positive
evm.model.Ap1.4017--0.89positive
evm.model.Ap9.1678ANK_REP_REGION DOMAIN-CONTAINING PROTEIN-RELATED0.89positive
evm.model.Ap5.2409--0.89positive
evm.model.Ap13.367--0.89positive
evm.model.Ap1.3184--0.88positive
evm.model.Ap13.1883TORSIN0.88positive
evm.model.Ap4.1083NON-LTR RETROLELEMENT REVERSE TRANSCRIPTASE-LIKE PROTEIN-RELATED0.88positive
evm.model.Ap2.653NON-LTR RETROLELEMENT REVERSE TRANSCRIPTASE-LIKE PROTEIN-RELATED0.88positive
evm.model.Ap2.3439_evm.model.Ap2.3445MUCIN 4-RELATED0.88positive
evm.model.Ap13.2763--0.88positive
Thr_1848--0.87positive
evm.model.Ap11.1541DRAB11-RELATED0.87positive
evm.model.Ap4.3819--0.87positive
Thr_1659--0.87positive
evm.model.Ap4.808OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.87positive
evm.model.Ap4.4768SET DOMAIN-CONTAINING PROTEIN-RELATED0.87positive
evm.model.Ap3.569--0.86positive
evm.model.Ap8.1831--0.86positive
evm.model.Ap2.2971--0.86positive
evm.model.Ap2.713OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.85positive
evm.model.Ap5.472--0.85positive
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 4113 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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