Co-expression Network Analysis

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

📊 Global Network of evm.model.Ap4.1855
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.Ap4.1855
Gene ID Description PCC Relationship
evm.model.Ap4.1855--1positive
Thr_2486--0.94positive
Thr_2863--0.94positive
Thr_3107--0.94positive
Thr_4008--0.94positive
Thr_885--0.94positive
evm.model.Ap1.1131--0.94positive
evm.model.Ap1.1242--0.94positive
evm.model.Ap1.1910BTB DOMAIN-CONTAINING PROTEIN0.94positive
evm.model.Ap1.1970--0.94positive
evm.model.Ap1.2403BTB/POZ DOMAIN-CONTAINING0.94positive
evm.model.Ap1.2431BTB/POZ DOMAIN-CONTAINING0.94positive
evm.model.Ap1.2554--0.94positive
evm.model.Ap1.2933GLYCOPROTEIN HORMONE RECEPTOR0.94positive
evm.model.Ap1.3095APPLE DOMAIN-CONTAINING PROTEIN0.94positive
evm.model.Ap1.3197HISTONE H40.94positive
evm.model.Ap1.3481RAPSYN-RELATED0.94positive
evm.model.Ap10.1080OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.94positive
evm.model.Ap11.439OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.94positive
evm.model.Ap11.458RETROTRANSPOSON0.94positive
evm.model.Ap11.494BTB/POZ DOMAIN-CONTAINING0.94positive
evm.model.Ap11.948APPLE DOMAIN-CONTAINING PROTEIN0.94positive
evm.model.Ap12.1561NEUROPEPTIDE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR0.94positive
evm.model.Ap12.2286--0.94positive
evm.model.Ap13.149OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.94positive
evm.model.Ap14.1695T-COMPLEX-ASSOCIATED-TESTIS-EXPRESSED 1/ DYNEIN LIGHT CHAIN0.94positive
evm.model.Ap14.1792NUCLEOREDOXIN-LIKE PROTEIN 20.94positive
evm.model.Ap2.1988PHOSPHATIDYLSERINE DECARBOXYLASE0.94positive
evm.model.Ap2.3376--0.94positive
evm.model.Ap3.1922OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.94positive
evm.model.Ap3.2013DNA HELICASE RECQ FAMILY MEMBER0.94positive
evm.model.Ap4.295OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.94positive
evm.model.Ap4.3152THAP DOMAIN PROTEIN0.94positive
evm.model.Ap4.3264--0.94positive
evm.model.Ap4.346--0.94positive
evm.model.Ap4.357--0.94positive
evm.model.Ap4.3580RETROTRANSPOSON0.94positive
evm.model.Ap4.4287--0.94positive
evm.model.Ap4.4393AP ENDONUCLEASE0.94positive
evm.model.Ap4.5526--0.94positive
evm.model.Ap4.6418G PROTEIN-COUPLED RECEPTOR0.94positive
evm.model.Ap4.6552REVERSE TRANSCRIPTASE0.94positive
evm.model.Ap5.2404OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.94positive
evm.model.Ap5.2856NECTIN-RELATED0.94positive
evm.model.Ap6.2897BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR, TWIST0.94positive
evm.model.Ap6.2899BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR, TWIST0.94positive
evm.model.Ap6.401--0.94positive
evm.model.Ap6.684ZINC FINGER PROTEIN0.94positive
evm.model.Ap7.1183--0.94positive
evm.model.Ap7.1227EARLY GAMETOCYTE ENRICHED PHOSPHOPROTEIN EGXP0.94positive
evm.model.Ap7.1708RETROTRANSPOSON0.94positive
evm.model.Ap7.2676--0.94positive
evm.model.Ap8.2156C2H2-TYPE DOMAIN-CONTAINING PROTEIN0.94positive
evm.model.Ap8.476F-BOX DOMAIN CONTAINING PROTEIN, EXPRESSED0.94positive
evm.model.Ap8.953--0.94positive
evm.model.Ap9.1134SYNDECAN0.94positive
evm.model.Ap9.2312--0.94positive
evm.model.Ap4.4101--0.93positive
Thr_3221--0.91positive
evm.model.Ap8.1444REVERSE TRANSCRIPTASE0.88positive
Thr_3801--0.71positive
evm.model.Ap2.594REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.70positive
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 1771 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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