Coexpression cluster:C39
From FANTOM5_SSTAR
Full id: C39_epididymis_ductus_seminal_testis_acute_thyroid_CD133
Phase1 CAGE Peaks
Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data
No results for this coexpression
Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0042742 | defense response to bacterium | 2.57358103660875e-17 |
| GO:0009617 | response to bacterium | 5.75568533087663e-17 |
| GO:0051707 | response to other organism | 2.65519661258531e-13 |
| GO:0009607 | response to biotic stimulus | 1.5706494034578e-11 |
| GO:0051704 | multi-organism process | 7.6126961140875e-11 |
| GO:0006952 | defense response | 5.21198666657427e-09 |
| GO:0030414 | protease inhibitor activity | 8.34111943821792e-07 |
| GO:0004866 | endopeptidase inhibitor activity | 7.59444133361891e-06 |
| GO:0004867 | serine-type endopeptidase inhibitor activity | 7.59444133361891e-06 |
| GO:0004857 | enzyme inhibitor activity | 1.92678201597427e-05 |
| GO:0004522 | pancreatic ribonuclease activity | 0.00103973182225395 |
| GO:0016892 | endoribonuclease activity, producing 3'-phosphomonoesters | 0.00174869510084071 |
| GO:0016894 | endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters | 0.00199396234918022 |
| GO:0006629 | lipid metabolic process | 0.00231003462070621 |
| GO:0019953 | sexual reproduction | 0.00328427593768674 |
| GO:0007338 | single fertilization | 0.0106024648605205 |
| GO:0009566 | fertilization | 0.0110716057967754 |
| GO:0004519 | endonuclease activity | 0.0130618980962842 |
| GO:0004521 | endoribonuclease activity | 0.0187160920694898 |
| GO:0007283 | spermatogenesis | 0.0375243664717349 |
| GO:0048232 | male gamete generation | 0.0375243664717349 |
| GO:0004540 | ribonuclease activity | 0.0375243664717349 |
| GO:0045087 | innate immune response | 0.0375243664717349 |
| GO:0051149 | positive regulation of muscle cell differentiation | 0.0375243664717349 |
| GO:0004617 | phosphoglycerate dehydrogenase activity | 0.0375243664717349 |
| GO:0005982 | starch metabolic process | 0.0375243664717349 |
| GO:0043416 | regulation of skeletal muscle regeneration | 0.0375243664717349 |
| GO:0019747 | regulation of isoprenoid metabolic process | 0.0375243664717349 |
| GO:0015633 | zinc transporting ATPase activity | 0.0375243664717349 |
| GO:0004608 | phosphatidylethanolamine N-methyltransferase activity | 0.0375243664717349 |
| GO:0005983 | starch catabolic process | 0.0375243664717349 |
| GO:0051155 | positive regulation of striated muscle cell differentiation | 0.0375243664717349 |
| GO:0043415 | positive regulation of skeletal muscle regeneration | 0.0375243664717349 |
| GO:0009917 | sterol 5-alpha reductase activity | 0.0375243664717349 |
| GO:0051153 | regulation of striated muscle cell differentiation | 0.0375243664717349 |
| GO:0004518 | nuclease activity | 0.0386689632252155 |
| GO:0005184 | neuropeptide hormone activity | 0.0401226071427917 |
| GO:0007276 | gamete generation | 0.0472744431405105 |
| GO:0006810 | transport | 0.0479396339481545 |
Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>
| Ontology term | p-value | n |
|---|---|---|
| male genital duct | 1.71e-66 | 3 |
| internal male genitalia | 1.71e-66 | 3 |
| epididymis | 1.46e-50 | 1 |
| vas deferens | 2.42e-50 | 1 |
| spermatic cord | 2.42e-50 | 1 |
| duct of male reproductive system | 3.11e-50 | 4 |
| male reproductive organ | 4.07e-41 | 11 |
| male organism | 3.99e-21 | 22 |
| male reproductive system | 3.99e-21 | 22 |
| duct | 1.55e-11 | 19 |
| reproductive organ | 3.32e-10 | 48 |
| internal genitalia | 5.06e-09 | 25 |
| reproductive structure | 1.83e-08 | 59 |
| reproductive system | 1.83e-08 | 59 |
| mesonephric epithelium | 1.49e-07 | 8 |
| mesonephric tubule | 1.49e-07 | 8 |
| nephric duct | 1.49e-07 | 8 |
| renal duct | 1.49e-07 | 8 |
| mesonephric duct | 1.49e-07 | 8 |
| pronephric duct | 1.49e-07 | 8 |
| testis | 1.69e-07 | 8 |
| mesonephros | 7.48e-07 | 9 |
| pronephros | 7.48e-07 | 9 |
| nephrogenic cord | 7.48e-07 | 9 |
| pronephric mesoderm | 7.48e-07 | 9 |
| rostral part of nephrogenic cord | 7.48e-07 | 9 |
| presumptive pronephric mesoderm | 7.48e-07 | 9 |
Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data
Novel motifs
JASPAR motifs
| Motifs | -log10(p-value) |
|---|---|
| MA0003.1 | 1.56221e-14 |
| MA0004.1 | 0.0182733 |
| MA0006.1 | 2.96123e-07 |
| MA0007.1 | 9.52701 |
| MA0009.1 | 0.0285521 |
| MA0014.1 | 8.87181e-15 |
| MA0017.1 | 0.319503 |
| MA0019.1 | 0.0760206 |
| MA0024.1 | 0.0016834 |
| MA0025.1 | 0.04539 |
| MA0027.1 | 0.808003 |
| MA0028.1 | 0.00154117 |
| MA0029.1 | 2.21031 |
| MA0030.1 | 0.465037 |
| MA0031.1 | 0.175964 |
| MA0038.1 | 0.734682 |
| MA0040.1 | 0.0244866 |
| MA0041.1 | 0.138893 |
| MA0042.1 | 0.0069652 |
| MA0043.1 | 0.000270166 |
| MA0046.1 | 5.8091 |
| MA0048.1 | 0.00229099 |
| MA0050.1 | 0.0125138 |
| MA0051.1 | 0.00182403 |
| MA0052.1 | 0.54625 |
| MA0055.1 | 0.0329027 |
| MA0056.1 | 0 |
| MA0057.1 | 0.00160292 |
| MA0058.1 | 0.0210508 |
| MA0059.1 | 0.0129936 |
| MA0060.1 | 5.45229e-05 |
| MA0061.1 | 1.76623e-05 |
| MA0063.1 | 0 |
| MA0066.1 | 5.28567 |
| MA0067.1 | 0.0142917 |
| MA0068.1 | 0.102998 |
| MA0069.1 | 1.59852 |
| MA0070.1 | 0.408466 |
| MA0071.1 | 0.829773 |
| MA0072.1 | 0.0938497 |
| MA0073.1 | 0 |
| MA0074.1 | 2.18378 |
| MA0076.1 | 1.24388e-05 |
| MA0077.1 | 1.71251 |
| MA0078.1 | 0.0682764 |
| MA0081.1 | 0.686222 |
| MA0083.1 | 0.930178 |
| MA0084.1 | 0.422216 |
| MA0087.1 | 0.387726 |
| MA0088.1 | 0.00370182 |
| MA0089.1 | 0 |
| MA0090.1 | 0.814152 |
| MA0091.1 | 0.138277 |
| MA0092.1 | 1.49684 |
| MA0093.1 | 0.014938 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.00684455 |
| MA0101.1 | 4.83198e-08 |
| MA0103.1 | 1.64629 |
| MA0105.1 | 3.66657e-12 |
| MA0106.1 | 0.497738 |
| MA0107.1 | 3.29298e-05 |
| MA0108.2 | 1.20892 |
| MA0109.1 | 0 |
| MA0111.1 | 0.0551304 |
| MA0113.1 | 3.56551 |
| MA0114.1 | 0.031877 |
| MA0115.1 | 0.037826 |
| MA0116.1 | 0.013035 |
| MA0117.1 | 0.0159819 |
| MA0119.1 | 0.31003 |
| MA0122.1 | 0.121631 |
| MA0124.1 | 0.515484 |
| MA0125.1 | 0.488172 |
| MA0130.1 | 0 |
| MA0131.1 | 0.00272331 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.32671 |
| MA0136.1 | 0.132797 |
| MA0139.1 | 4.40488e-05 |
| MA0140.1 | 1.45169 |
| MA0141.1 | 0.572146 |
| MA0142.1 | 1.67041 |
| MA0143.1 | 0.470329 |
| MA0144.1 | 1.92217 |
| MA0145.1 | 0.338178 |
| MA0146.1 | 2.31124e-11 |
| MA0147.1 | 1.16783e-06 |
| MA0148.1 | 0.522794 |
| MA0149.1 | 0.0964483 |
| MA0062.2 | 1.19606e-06 |
| MA0035.2 | 2.76684 |
| MA0039.2 | 0 |
| MA0138.2 | 0.425941 |
| MA0002.2 | 0.606886 |
| MA0137.2 | 0.925744 |
| MA0104.2 | 5.57381e-08 |
| MA0047.2 | 0.254871 |
| MA0112.2 | 1.80592 |
| MA0065.2 | 0.394931 |
| MA0150.1 | 0.462566 |
| MA0151.1 | 0 |
| MA0152.1 | 1.17562 |
| MA0153.1 | 1.14873 |
| MA0154.1 | 0.730531 |
| MA0155.1 | 0.00857764 |
| MA0156.1 | 0.0890634 |
| MA0157.1 | 0.645789 |
| MA0158.1 | 0 |
| MA0159.1 | 0.144399 |
| MA0160.1 | 1.54354 |
| MA0161.1 | 0 |
| MA0162.1 | 1.11044e-10 |
| MA0163.1 | 2.21954e-07 |
| MA0164.1 | 0.816754 |
| MA0080.2 | 0.503655 |
| MA0018.2 | 0.00676733 |
| MA0099.2 | 0.0137321 |
| MA0079.2 | 0 |
| MA0102.2 | 0.0618605 |
| MA0258.1 | 7.68691 |
| MA0259.1 | 2.92765e-05 |
| MA0442.1 | 0 |
ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
| TF | #promoters | Enrichment | p-value | q-value |
|---|---|---|---|---|
| ESR1#2099 | 28 | 1.87287150498332 | 0.00133367099868708 | 0.00885206643990338 |
Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data
