Coexpression cluster:C50
From FANTOM5_SSTAR
Full id: C50_chorionic_placenta_amniotic_migratory_smallcell_chronic_choriocarcinoma
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
| p.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 3.29024809202456e-08 | 2.08272704225154e-05 | 9 | 265 | Cytokine-cytokine receptor interaction (KEGG):04060 |
| 0.000204113675808259 | 0.032300989196657 | 5 | 204 | Endocytosis (KEGG):04144 |
| 0.000441933534205271 | 0.0466239878586561 | 2 | 12 | IL-1 Signaling Pathway (Wikipathways):WP195 |
| 0.000188769247202179 | 0.032300989196657 | 2 | 8 | Glucocorticoid & Mineralcorticoid Metabolism (Wikipathways):WP237 |
| 0.000131682277901484 | 0.032300989196657 | 4 | 98 | EGFR1 down reg. targets (Netpath):NetPath_4 |
| 0.000271542738102093 | 0.034377310643725 | 5 | 217 | IL-4 up reg. targets (Netpath):NetPath_16 |
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:0019955 | cytokine binding | 1.49272708389083e-08 |
| GO:0005886 | plasma membrane | 7.61070928536705e-07 |
| GO:0005887 | integral to plasma membrane | 7.61070928536705e-07 |
| GO:0031226 | intrinsic to plasma membrane | 7.61070928536705e-07 |
| GO:0044459 | plasma membrane part | 8.62302001552363e-07 |
| GO:0019965 | interleukin binding | 1.8985367683814e-06 |
| GO:0007154 | cell communication | 1.8985367683814e-06 |
| GO:0032502 | developmental process | 5.30326663034162e-06 |
| GO:0032501 | multicellular organismal process | 1.94977006594127e-05 |
| GO:0004896 | hematopoietin/interferon-class (D200-domain) cytokine receptor activity | 1.94977006594127e-05 |
| GO:0005515 | protein binding | 2.18122820349288e-05 |
| GO:0004907 | interleukin receptor activity | 3.92941151866108e-05 |
| GO:0004871 | signal transducer activity | 4.97688454155484e-05 |
| GO:0060089 | molecular transducer activity | 4.97688454155484e-05 |
| GO:0007165 | signal transduction | 0.000669259796048789 |
| GO:0016021 | integral to membrane | 0.00102460498252477 |
| GO:0017106 | activin inhibitor activity | 0.00102460498252477 |
| GO:0031224 | intrinsic to membrane | 0.00102460498252477 |
| GO:0007275 | multicellular organismal development | 0.00102460498252477 |
| GO:0007167 | enzyme linked receptor protein signaling pathway | 0.00104650539691135 |
| GO:0019838 | growth factor binding | 0.00109245987129696 |
| GO:0048869 | cellular developmental process | 0.00123243246071054 |
| GO:0030154 | cell differentiation | 0.00123243246071054 |
| GO:0006702 | androgen biosynthetic process | 0.00130184789904941 |
| GO:0007166 | cell surface receptor linked signal transduction | 0.00147011725200007 |
| GO:0001637 | G-protein chemoattractant receptor activity | 0.00147011725200007 |
| GO:0004950 | chemokine receptor activity | 0.00147011725200007 |
| GO:0007169 | transmembrane receptor protein tyrosine kinase signaling pathway | 0.0015099549151185 |
| GO:0019956 | chemokine binding | 0.0015099549151185 |
| GO:0019098 | reproductive behavior | 0.0015099549151185 |
| GO:0007617 | mating behavior | 0.0015099549151185 |
| GO:0001573 | ganglioside metabolic process | 0.00259865329927433 |
| GO:0004908 | interleukin-1 receptor activity | 0.00259865329927433 |
| GO:0004888 | transmembrane receptor activity | 0.00259865329927433 |
| GO:0019966 | interleukin-1 binding | 0.00399237479762478 |
| GO:0044425 | membrane part | 0.00399580670302256 |
| GO:0008209 | androgen metabolic process | 0.00448878922135019 |
| GO:0016494 | C-X-C chemokine receptor activity | 0.00448878922135019 |
| GO:0009605 | response to external stimulus | 0.0044964507567263 |
| GO:0004872 | receptor activity | 0.0044964507567263 |
| GO:0006700 | C21-steroid hormone biosynthetic process | 0.00454302260027451 |
| GO:0045072 | regulation of interferon-gamma biosynthetic process | 0.00454302260027451 |
| GO:0051705 | behavioral interaction between organisms | 0.00454302260027451 |
| GO:0019958 | C-X-C chemokine binding | 0.00454302260027451 |
| GO:0007618 | mating | 0.00454302260027451 |
| GO:0042095 | interferon-gamma biosynthetic process | 0.00521665560383364 |
| GO:0001568 | blood vessel development | 0.00521665560383364 |
| GO:0001944 | vasculature development | 0.00532862574840074 |
| GO:0022414 | reproductive process | 0.00532862574840074 |
| GO:0044421 | extracellular region part | 0.00585547116203293 |
| GO:0016020 | membrane | 0.00711638043454994 |
| GO:0008201 | heparin binding | 0.00711638043454994 |
| GO:0008207 | C21-steroid hormone metabolic process | 0.00789940474589652 |
| GO:0032609 | interferon-gamma production | 0.00871149685800637 |
| GO:0006687 | glycosphingolipid metabolic process | 0.00954755989468845 |
| GO:0042802 | identical protein binding | 0.0104102169548371 |
| GO:0006952 | defense response | 0.0134330951685002 |
| GO:0048731 | system development | 0.0134862223130983 |
| GO:0019957 | C-C chemokine binding | 0.0140390320707872 |
| GO:0016493 | C-C chemokine receptor activity | 0.0140390320707872 |
| GO:0002376 | immune system process | 0.0174946863345362 |
| GO:0005539 | glycosaminoglycan binding | 0.0174946863345362 |
| GO:0048856 | anatomical structure development | 0.0189458534462492 |
| GO:0007267 | cell-cell signaling | 0.0189458534462492 |
| GO:0006664 | glycolipid metabolic process | 0.0189458534462492 |
| GO:0030247 | polysaccharide binding | 0.0191438607355616 |
| GO:0006672 | ceramide metabolic process | 0.0205506931634331 |
| GO:0001871 | pattern binding | 0.0205506931634331 |
| GO:0006955 | immune response | 0.0205506931634331 |
| GO:0005333 | norepinephrine transmembrane transporter activity | 0.0205506931634331 |
| GO:0008115 | sarcosine oxidase activity | 0.0205506931634331 |
| GO:0007619 | courtship behavior | 0.0205506931634331 |
| GO:0060018 | astrocyte fate commitment | 0.0205506931634331 |
| GO:0005334 | norephinephrine:sodium symporter activity | 0.0205506931634331 |
| GO:0008386 | cholesterol monooxygenase (side-chain-cleaving) activity | 0.0205506931634331 |
| GO:0030526 | granulocyte macrophage colony-stimulating factor receptor complex | 0.0205506931634331 |
| GO:0015874 | norepinephrine transport | 0.0205506931634331 |
| GO:0008049 | male courtship behavior | 0.0205506931634331 |
| GO:0004513 | neolactotetraosylceramide alpha-2,3-sialyltransferase activity | 0.0205506931634331 |
| GO:0050031 | L-pipecolate oxidase activity | 0.0205506931634331 |
| GO:0060179 | male mating behavior | 0.0205506931634331 |
| GO:0001525 | angiogenesis | 0.0208753141373089 |
| GO:0046519 | sphingoid metabolic process | 0.0215838713303297 |
| GO:0044464 | cell part | 0.0217108781624752 |
| GO:0006954 | inflammatory response | 0.0241089520879431 |
| GO:0008081 | phosphoric diester hydrolase activity | 0.0241089520879431 |
| GO:0007610 | behavior | 0.0244194813017395 |
| GO:0007399 | nervous system development | 0.0244194813017395 |
| GO:0048514 | blood vessel morphogenesis | 0.0277675870270528 |
| GO:0008528 | peptide receptor activity, G-protein coupled | 0.0277675870270528 |
| GO:0001653 | peptide receptor activity | 0.0277675870270528 |
| GO:0008283 | cell proliferation | 0.0280524718892925 |
| GO:0042446 | hormone biosynthetic process | 0.0280524718892925 |
| GO:0019221 | cytokine and chemokine mediated signaling pathway | 0.0280524718892925 |
| GO:0048646 | anatomical structure formation | 0.0280524718892925 |
| GO:0004435 | phosphoinositide phospholipase C activity | 0.0280524718892925 |
| GO:0004434 | inositol or phosphatidylinositol phosphodiesterase activity | 0.0280524718892925 |
| GO:0005615 | extracellular space | 0.0280524718892925 |
| GO:0043511 | inhibin complex | 0.0280524718892925 |
| GO:0043512 | inhibin A complex | 0.0280524718892925 |
| GO:0001574 | ganglioside biosynthetic process | 0.0280524718892925 |
| GO:0004910 | interleukin-1, Type II, blocking receptor activity | 0.0280524718892925 |
| GO:0033057 | reproductive behavior in a multicellular organism | 0.0280524718892925 |
| GO:0045077 | negative regulation of interferon-gamma biosynthetic process | 0.0280524718892925 |
| GO:0019968 | interleukin-1, Type II, blocking binding | 0.0280524718892925 |
| GO:0045650 | negative regulation of macrophage differentiation | 0.0280524718892925 |
| GO:0004912 | interleukin-3 receptor activity | 0.0280524718892925 |
| GO:0045523 | interleukin-27 receptor binding | 0.0280524718892925 |
| GO:0005011 | macrophage colony stimulating factor receptor activity | 0.0280524718892925 |
| GO:0016647 | oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor | 0.0280524718892925 |
| GO:0009914 | hormone transport | 0.0280524718892925 |
| GO:0060014 | granulosa cell differentiation | 0.0280524718892925 |
| GO:0047291 | lactosylceramide alpha-2,3-sialyltransferase activity | 0.0280524718892925 |
| GO:0019978 | interleukin-3 binding | 0.0280524718892925 |
| GO:0046653 | tetrahydrofolate metabolic process | 0.0280524718892925 |
| GO:0009313 | oligosaccharide catabolic process | 0.0280524718892925 |
| GO:0007197 | muscarinic acetylcholine receptor, adenylate cyclase inhibiting pathway | 0.0280524718892925 |
| GO:0051704 | multi-organism process | 0.0280524718892925 |
| GO:0008610 | lipid biosynthetic process | 0.0280524718892925 |
| GO:0042578 | phosphoric ester hydrolase activity | 0.0352271326292445 |
| GO:0007626 | locomotory behavior | 0.0361189572560658 |
| GO:0006417 | regulation of translation | 0.0361189572560658 |
| GO:0004629 | phospholipase C activity | 0.0361189572560658 |
| GO:0019976 | interleukin-2 binding | 0.0361189572560658 |
| GO:0046640 | regulation of alpha-beta T cell proliferation | 0.0361189572560658 |
| GO:0004911 | interleukin-2 receptor activity | 0.0361189572560658 |
| GO:0051148 | negative regulation of muscle cell differentiation | 0.0361189572560658 |
| GO:0045578 | negative regulation of B cell differentiation | 0.0361189572560658 |
| GO:0004769 | steroid delta-isomerase activity | 0.0361189572560658 |
| GO:0032278 | positive regulation of gonadotropin secretion | 0.0361189572560658 |
| GO:0046881 | positive regulation of follicle-stimulating hormone secretion | 0.0361189572560658 |
| GO:0004914 | interleukin-5 receptor activity | 0.0361189572560658 |
| GO:0019980 | interleukin-5 binding | 0.0361189572560658 |
| GO:0051150 | regulation of smooth muscle cell differentiation | 0.0361189572560658 |
| GO:0030061 | mitochondrial crista | 0.0361189572560658 |
| GO:0046641 | positive regulation of alpha-beta T cell proliferation | 0.0361189572560658 |
| GO:0051151 | negative regulation of smooth muscle cell differentiation | 0.0361189572560658 |
| GO:0046635 | positive regulation of alpha-beta T cell activation | 0.0361189572560658 |
| GO:0042035 | regulation of cytokine biosynthetic process | 0.0371790017174161 |
| GO:0048513 | organ development | 0.0375810492059555 |
| GO:0048609 | reproductive process in a multicellular organism | 0.0375810492059555 |
| GO:0032504 | multicellular organism reproduction | 0.0375810492059555 |
| GO:0006928 | cell motility | 0.0378812828189273 |
| GO:0051674 | localization of cell | 0.0378812828189273 |
| GO:0031326 | regulation of cellular biosynthetic process | 0.0395216162600166 |
| GO:0045596 | negative regulation of cell differentiation | 0.0395216162600166 |
| GO:0042089 | cytokine biosynthetic process | 0.0395216162600166 |
| GO:0042277 | peptide binding | 0.0395216162600166 |
| GO:0042107 | cytokine metabolic process | 0.0395216162600166 |
| GO:0006665 | sphingolipid metabolic process | 0.0395216162600166 |
| GO:0001501 | skeletal development | 0.0395216162600166 |
| GO:0007341 | penetration of zona pellucida | 0.0395216162600166 |
| GO:0046882 | negative regulation of follicle-stimulating hormone secretion | 0.0395216162600166 |
| GO:0004563 | beta-N-acetylhexosaminidase activity | 0.0395216162600166 |
| GO:0045620 | negative regulation of lymphocyte differentiation | 0.0395216162600166 |
| GO:0015872 | dopamine transport | 0.0395216162600166 |
| GO:0046887 | positive regulation of hormone secretion | 0.0395216162600166 |
| GO:0032277 | negative regulation of gonadotropin secretion | 0.0395216162600166 |
| GO:0046686 | response to cadmium ion | 0.0395216162600166 |
| GO:0032276 | regulation of gonadotropin secretion | 0.0395216162600166 |
| GO:0046880 | regulation of follicle-stimulating hormone secretion | 0.0395216162600166 |
| GO:0046633 | alpha-beta T cell proliferation | 0.0395216162600166 |
| GO:0042541 | hemoglobin biosynthetic process | 0.0395216162600166 |
| GO:0030868 | smooth endoplasmic reticulum membrane | 0.0395216162600166 |
| GO:0046634 | regulation of alpha-beta T cell activation | 0.0395216162600166 |
| GO:0006689 | ganglioside catabolic process | 0.0395216162600166 |
| GO:0002020 | protease binding | 0.0395216162600166 |
| GO:0051147 | regulation of muscle cell differentiation | 0.0395216162600166 |
| GO:0009889 | regulation of biosynthetic process | 0.0432103641869052 |
| GO:0006968 | cellular defense response | 0.0432572368752746 |
| GO:0006950 | response to stress | 0.0441881006096219 |
| GO:0009611 | response to wounding | 0.0446582024972014 |
| GO:0030054 | cell junction | 0.0450637409087457 |
| GO:0051249 | regulation of lymphocyte activation | 0.0450637409087457 |
| GO:0035035 | histone acetyltransferase binding | 0.0450637409087457 |
| GO:0008504 | monoamine transmembrane transporter activity | 0.0450637409087457 |
| GO:0032274 | gonadotropin secretion | 0.0450637409087457 |
| GO:0046884 | follicle-stimulating hormone secretion | 0.0450637409087457 |
| GO:0048038 | quinone binding | 0.0450637409087457 |
| GO:0042787 | protein ubiquitination during ubiquitin-dependent protein catabolic process | 0.0450637409087457 |
| GO:0046479 | glycosphingolipid catabolic process | 0.0450637409087457 |
| GO:0048265 | response to pain | 0.0450637409087457 |
| GO:0045649 | regulation of macrophage differentiation | 0.0450637409087457 |
| GO:0020027 | hemoglobin metabolic process | 0.0450637409087457 |
| GO:0051093 | negative regulation of developmental process | 0.0452260905183779 |
| GO:0048522 | positive regulation of cellular process | 0.0457252457367973 |
| GO:0006836 | neurotransmitter transport | 0.0458636190680978 |
| GO:0022610 | biological adhesion | 0.0463177294120716 |
| GO:0007155 | cell adhesion | 0.0463177294120716 |
| GO:0016477 | cell migration | 0.0466077736484723 |
| GO:0050865 | regulation of cell activation | 0.0469535460708043 |
| GO:0007417 | central nervous system development | 0.0469535460708043 |
| GO:0009790 | embryonic development | 0.0469535460708043 |
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 |
|---|---|---|
| multi-cellular organism | 1.27e-11 | 659 |
| organ component layer | 1.46e-10 | 57 |
| anatomical system | 1.71e-10 | 625 |
| anatomical group | 3.19e-10 | 626 |
| organ | 6.81e-09 | 511 |
| extraembryonic membrane | 5.97e-08 | 14 |
| membranous layer | 5.97e-08 | 14 |
| mesoderm | 7.26e-07 | 448 |
| mesoderm-derived structure | 7.26e-07 | 448 |
| presumptive mesoderm | 7.26e-07 | 448 |
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) |
|---|---|
|
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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
No analysis results for this cluster
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
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