Coexpression cluster:C141
From FANTOM5_SSTAR
Full id: C141_Hodgkin_acute_thymus_chronic_vein_CD4_B
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 |
|---|---|---|---|---|
| 1.63118747922973e-06 | 0.00103254167435242 | 4 | 88 | Hematopoietic cell lineage (KEGG):04640 |
| 8.45420275641347e-06 | 0.00267575517240486 | 4 | 133 | T Cell Receptor Signaling Pathway (Wikipathways):WP69 |
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:0042101 | T cell receptor complex | 0.00668629716819874 |
| GO:0001772 | immunological synapse | 0.00687743094890173 |
| GO:0044242 | cellular lipid catabolic process | 0.023972953605579 |
| GO:0030290 | sphingolipid activator protein activity | 0.023972953605579 |
| GO:0032428 | beta-N-acetylgalactosaminidase activity | 0.023972953605579 |
| GO:0043395 | heparan sulfate proteoglycan binding | 0.023972953605579 |
| GO:0043394 | proteoglycan binding | 0.023972953605579 |
| GO:0044248 | cellular catabolic process | 0.023972953605579 |
| GO:0005889 | hydrogen:potassium-exchanging ATPase complex | 0.023972953605579 |
| GO:0051371 | muscle alpha-actinin binding | 0.023972953605579 |
| GO:0043368 | positive T cell selection | 0.023972953605579 |
| GO:0016004 | phospholipase activator activity | 0.023972953605579 |
| GO:0046337 | phosphatidylethanolamine metabolic process | 0.023972953605579 |
| GO:0045179 | apical cortex | 0.023972953605579 |
| GO:0009313 | oligosaccharide catabolic process | 0.023972953605579 |
| GO:0045059 | positive thymic T cell selection | 0.023972953605579 |
| GO:0005319 | lipid transporter activity | 0.0244925688648456 |
| GO:0042110 | T cell activation | 0.0244925688648456 |
| GO:0046982 | protein heterodimerization activity | 0.0244925688648456 |
| GO:0019898 | extrinsic to membrane | 0.0244925688648456 |
| GO:0051393 | alpha-actinin binding | 0.0244925688648456 |
| GO:0046461 | neutral lipid catabolic process | 0.0244925688648456 |
| GO:0042608 | T cell receptor binding | 0.0244925688648456 |
| GO:0043235 | receptor complex | 0.0244925688648456 |
| GO:0009056 | catabolic process | 0.0252198311256358 |
| GO:0008480 | sarcosine dehydrogenase activity | 0.0264389011852018 |
| GO:0004563 | beta-N-acetylhexosaminidase activity | 0.0264389011852018 |
| GO:0006689 | ganglioside catabolic process | 0.0264389011852018 |
| GO:0046473 | phosphatidic acid metabolic process | 0.0264389011852018 |
| GO:0006869 | lipid transport | 0.0290350396039018 |
| GO:0046479 | glycosphingolipid catabolic process | 0.0290350396039018 |
| GO:0045061 | thymic T cell selection | 0.0290350396039018 |
| GO:0042805 | actinin binding | 0.0290350396039018 |
| GO:0016042 | lipid catabolic process | 0.0301622994414704 |
| GO:0001948 | glycoprotein binding | 0.0311582336324494 |
| GO:0009898 | internal side of plasma membrane | 0.0311582336324494 |
| GO:0046649 | lymphocyte activation | 0.0311582336324494 |
| GO:0046470 | phosphatidylcholine metabolic process | 0.0343771378066479 |
| GO:0019377 | glycolipid catabolic process | 0.0343771378066479 |
| GO:0008092 | cytoskeletal protein binding | 0.0350739049383545 |
| GO:0019915 | sequestering of lipid | 0.0350739049383545 |
| GO:0001573 | ganglioside metabolic process | 0.0350739049383545 |
| GO:0006658 | phosphatidylserine metabolic process | 0.0350739049383545 |
| GO:0045321 | leukocyte activation | 0.0350739049383545 |
| GO:0045058 | T cell selection | 0.0366564909979633 |
| GO:0033077 | T cell differentiation in the thymus | 0.0366564909979633 |
| GO:0015012 | heparan sulfate proteoglycan biosynthetic process | 0.0366564909979633 |
| GO:0005768 | endosome | 0.036817275616302 |
| GO:0001775 | cell activation | 0.0420860864985067 |
| GO:0002376 | immune system process | 0.043307848271674 |
| GO:0004047 | aminomethyltransferase activity | 0.043307848271674 |
| GO:0000209 | protein polyubiquitination | 0.043307848271674 |
| GO:0030201 | heparan sulfate proteoglycan metabolic process | 0.043307848271674 |
| GO:0044459 | plasma membrane part | 0.0456633991087196 |
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 |
|---|---|---|
| thymus | 8.36e-34 | 4 |
| hemolymphoid system gland | 8.36e-34 | 4 |
| thymic region | 8.36e-34 | 4 |
| pharyngeal gland | 8.36e-34 | 4 |
| thymus primordium | 8.36e-34 | 4 |
| pharyngeal epithelium | 6.07e-23 | 6 |
| hemopoietic organ | 7.84e-20 | 7 |
| immune organ | 7.84e-20 | 7 |
| neck | 3.25e-14 | 10 |
| gland of gut | 3.25e-14 | 10 |
| chordate pharynx | 3.25e-14 | 10 |
| pharyngeal region of foregut | 3.25e-14 | 10 |
| pharynx | 5.10e-13 | 11 |
| entire pharyngeal arch endoderm | 5.10e-13 | 11 |
| early pharyngeal endoderm | 5.10e-13 | 11 |
| pharyngeal arch system | 2.42e-08 | 18 |
| upper respiratory tract | 5.94e-08 | 19 |
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) |
|---|---|
|
{{{tfbs_overrepresentation_jaspar}}} |
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
