Co-expression Network Analysis

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

📊 Global Network of evm.model.Ap4.7207
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.Ap4.7207
Gene ID Description PCC Relationship
evm.model.Ap4.7207EXPRESSED PROTEIN1positive
evm.model.Ap4.7091--0.98positive
Thr_2486--0.98positive
Thr_2863--0.98positive
Thr_3107--0.98positive
Thr_4008--0.98positive
Thr_885--0.98positive
evm.model.Ap1.1131--0.98positive
evm.model.Ap1.1242--0.98positive
evm.model.Ap1.1910BTB DOMAIN-CONTAINING PROTEIN0.98positive
evm.model.Ap1.1970--0.98positive
evm.model.Ap1.2403BTB/POZ DOMAIN-CONTAINING0.98positive
evm.model.Ap1.2431BTB/POZ DOMAIN-CONTAINING0.98positive
evm.model.Ap1.2554--0.98positive
evm.model.Ap1.2933GLYCOPROTEIN HORMONE RECEPTOR0.98positive
evm.model.Ap1.3095APPLE DOMAIN-CONTAINING PROTEIN0.98positive
evm.model.Ap1.3197HISTONE H40.98positive
evm.model.Ap1.3481RAPSYN-RELATED0.98positive
evm.model.Ap10.1080OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.98positive
evm.model.Ap11.439OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.98positive
evm.model.Ap11.458RETROTRANSPOSON0.98positive
evm.model.Ap11.494BTB/POZ DOMAIN-CONTAINING0.98positive
evm.model.Ap11.948APPLE DOMAIN-CONTAINING PROTEIN0.98positive
evm.model.Ap12.1561NEUROPEPTIDE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR0.98positive
evm.model.Ap12.2286--0.98positive
evm.model.Ap13.149OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.98positive
evm.model.Ap14.1695T-COMPLEX-ASSOCIATED-TESTIS-EXPRESSED 1/ DYNEIN LIGHT CHAIN0.98positive
evm.model.Ap14.1792NUCLEOREDOXIN-LIKE PROTEIN 20.98positive
evm.model.Ap2.1988PHOSPHATIDYLSERINE DECARBOXYLASE0.98positive
evm.model.Ap2.3376--0.98positive
evm.model.Ap3.1922OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.98positive
evm.model.Ap3.2013DNA HELICASE RECQ FAMILY MEMBER0.98positive
evm.model.Ap4.295OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.98positive
evm.model.Ap4.3152THAP DOMAIN PROTEIN0.98positive
evm.model.Ap4.3264--0.98positive
evm.model.Ap4.346--0.98positive
evm.model.Ap4.357--0.98positive
evm.model.Ap4.3580RETROTRANSPOSON0.98positive
evm.model.Ap4.4287--0.98positive
evm.model.Ap4.4393AP ENDONUCLEASE0.98positive
evm.model.Ap4.5526--0.98positive
evm.model.Ap4.6418G PROTEIN-COUPLED RECEPTOR0.98positive
evm.model.Ap4.6552REVERSE TRANSCRIPTASE0.98positive
evm.model.Ap5.2404OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.98positive
evm.model.Ap5.2856NECTIN-RELATED0.98positive
evm.model.Ap6.2897BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR, TWIST0.98positive
evm.model.Ap6.2899BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR, TWIST0.98positive
evm.model.Ap6.401--0.98positive
evm.model.Ap6.684ZINC FINGER PROTEIN0.98positive
evm.model.Ap7.1183--0.98positive
evm.model.Ap7.1227EARLY GAMETOCYTE ENRICHED PHOSPHOPROTEIN EGXP0.98positive
evm.model.Ap7.1708RETROTRANSPOSON0.98positive
evm.model.Ap7.2676--0.98positive
evm.model.Ap8.2156C2H2-TYPE DOMAIN-CONTAINING PROTEIN0.98positive
evm.model.Ap8.476F-BOX DOMAIN CONTAINING PROTEIN, EXPRESSED0.98positive
evm.model.Ap8.953--0.98positive
evm.model.Ap9.1134SYNDECAN0.98positive
evm.model.Ap9.2312--0.98positive
evm.model.Ap11.152--0.92positive
evm.model.Ap1.2447REVERSE TRANSCRIPTASE0.76positive
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 1713 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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