Co-expression Network Analysis

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

📊 Global Network of evm.model.Ap1.263
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.Ap1.263
Gene ID Description PCC Relationship
evm.model.Ap1.263OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR1positive
evm.model.Ap6.229G-PROTEIN COUPLED RECEPTOR0.84positive
evm.model.Ap1.1429DNA HELICASE RECQ FAMILY MEMBER0.84positive
evm.model.Ap13.367--0.83positive
evm.model.Ap5.2409--0.83positive
evm.model.Ap3.780P-LOOP CONTAINING NUCLEOTIDE TRIPHOSPHATE HYDROLASE0.83positive
Gly_2366--0.81positive
Gly_2367--0.81positive
Ser_24--0.81positive
Ser_4648--0.81positive
Thr_2434--0.81positive
Thr_2504--0.81positive
Thr_3183--0.81positive
Thr_3195--0.81positive
Thr_3925--0.81positive
evm.model.Ap1.1866PROTEIN CBG266940.81positive
evm.model.Ap1.206--0.81positive
evm.model.Ap1.2247SERINE/THREONINE-PROTEIN KINASE RIO10.81positive
evm.model.Ap1.3786REVERSE TRANSCRIPTASE0.81positive
evm.model.Ap1.4187REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.81positive
evm.model.Ap1.735--0.81positive
evm.model.Ap1.861--0.81positive
evm.model.Ap10.511OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.81positive
evm.model.Ap10.967--0.81positive
evm.model.Ap11.117--0.81positive
evm.model.Ap11.169--0.81positive
evm.model.Ap11.1744--0.81positive
evm.model.Ap11.55ZINC FINGER PROTEIN0.81positive
evm.model.Ap11.855SPOT14 FAMILY MEMBER0.81positive
evm.model.Ap12.114RNA AND EXPORT FACTOR BINDING PROTEIN0.81positive
evm.model.Ap12.1244--0.81positive
evm.model.Ap12.585REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.81positive
evm.model.Ap12.67HISTAMINE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR0.81positive
evm.model.Ap12.753HISTAMINE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR0.81positive
evm.model.Ap13.1--0.81positive
evm.model.Ap13.1608-0.81positive
evm.model.Ap13.2727REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.81positive
evm.model.Ap13.2904--0.81positive
evm.model.Ap13.739L1 TRANSPOSABLE ELEMENT-RELATED0.81positive
evm.model.Ap14.1202--0.81positive
evm.model.Ap14.272--0.81positive
evm.model.Ap14.492RIBITOL-5-PHOSPHATE XYLOSYLTRANSFERASE 10.81positive
evm.model.Ap14.686RETROTRANSPOSON0.81positive
evm.model.Ap2.1300REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.81positive
evm.model.Ap2.2776REVERSE TRANSCRIPTASE0.81positive
evm.model.Ap2.2827--0.81positive
evm.model.Ap2.3481REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.81positive
evm.model.Ap3.1633OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.81positive
evm.model.Ap3.2247--0.81positive
evm.model.Ap3.402ALPHA- 1,3 -FUCOSYLTRANSFERASE0.81positive
evm.model.Ap4.1235INTEGRASE CATALYTIC DOMAIN-CONTAINING PROTEIN-RELATED0.81positive
evm.model.Ap4.1408RETROTRANSPOSON0.81positive
evm.model.Ap4.1597--0.81positive
evm.model.Ap4.1640--0.81positive
evm.model.Ap4.2022--0.81positive
evm.model.Ap4.2143L1 TRANSPOSABLE ELEMENT-RELATED0.81positive
evm.model.Ap4.2420SET DOMAIN-CONTAINING PROTEIN-RELATED0.81positive
evm.model.Ap4.3011--0.81positive
evm.model.Ap4.3897C2H2-TYPE DOMAIN-CONTAINING PROTEIN0.81positive
evm.model.Ap4.5167--0.81positive
evm.model.Ap4.7OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.81positive
evm.model.Ap5.2038OPSIN0.81positive
evm.model.Ap5.20395-HYDROXYTRYPTAMINE RECEPTOR0.81positive
evm.model.Ap5.2618TRANSMEMBRANE PROTEIN 1870.81positive
evm.model.Ap5.2795PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 120.81positive
evm.model.Ap6.1275BTB/POZ DOMAIN-CONTAINING0.81positive
evm.model.Ap6.1595FORKHEAD BOX PROTEIN0.81positive
evm.model.Ap6.1600FORKHEAD BOX PROTEIN0.81positive
evm.model.Ap6.1601FORKHEAD BOX PROTEIN0.81positive
evm.model.Ap6.3013--0.81positive
evm.model.Ap6.3234RIBOSOMAL PROTEIN L130.81positive
evm.model.Ap7.1413--0.81positive
evm.model.Ap7.204SKICH DOMAIN-CONTAINING PROTEIN0.81positive
evm.model.Ap7.410REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.81positive
evm.model.Ap7.497RETROTRANSPOSON0.81positive
evm.model.Ap7.790--0.81positive
evm.model.Ap8.1329--0.81positive
evm.model.Ap8.1427--0.81positive
evm.model.Ap8.1453--0.81positive
evm.model.Ap8.1529PROTEIN CBG237640.81positive
evm.model.Ap8.155OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.81positive
evm.model.Ap8.156OLFACTORY RECEPTOR AND ADENOSINE RECEPTOR0.81positive
evm.model.Ap8.232--0.81positive
evm.model.Ap8.892TRANSMEMBRANE PROTEIN 151 HOMOLOG0.81positive
evm.model.Ap9.1964--0.81positive
evm.model.Ap9.653--0.81positive
evm.model.Ap13.174REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN0.78positive
evm.model.Ap1.32315-HYDROXYTRYPTAMINE RECEPTOR0.71positive
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 3491 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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