Coexpression cluster:C89
From FANTOM5_SSTAR
Full id: C89_small_retinoblastoma_medulloblastoma_iPS_acantholytic_eye_bronchogenic
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 |
|---|---|---|---|---|
| 7.83036217125079e-05 | 0.0495661925440175 | 2 | 21 | {POU2F1,21} (Static Module):NA |
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:0043565 | sequence-specific DNA binding | 0.00984692052000621 |
| GO:0032501 | multicellular organismal process | 0.0184043811554295 |
| GO:0007275 | multicellular organismal development | 0.0208285303637392 |
| GO:0042706 | eye photoreceptor cell fate commitment | 0.0208285303637392 |
| GO:0046552 | photoreceptor cell fate commitment | 0.0208285303637392 |
| GO:0003700 | transcription factor activity | 0.0208285303637392 |
| GO:0040036 | regulation of fibroblast growth factor receptor signaling pathway | 0.0434788203863315 |
| GO:0007389 | pattern specification process | 0.0434788203863315 |
| GO:0003828 | alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity | 0.0434788203863315 |
| GO:0031301 | integral to organelle membrane | 0.0434788203863315 |
| GO:0043231 | intracellular membrane-bound organelle | 0.0434788203863315 |
| GO:0043227 | membrane-bound organelle | 0.0434788203863315 |
| GO:0031300 | intrinsic to organelle membrane | 0.0434788203863315 |
| GO:0008190 | eukaryotic initiation factor 4E binding | 0.0434788203863315 |
| GO:0031369 | translation initiation factor binding | 0.0434788203863315 |
| GO:0006349 | genetic imprinting | 0.0434788203863315 |
| GO:0032502 | developmental process | 0.0434788203863315 |
| GO:0008589 | regulation of smoothened signaling pathway | 0.0434788203863315 |
| GO:0001754 | eye photoreceptor cell differentiation | 0.0434788203863315 |
| GO:0043229 | intracellular organelle | 0.0434788203863315 |
| GO:0043226 | organelle | 0.0434788203863315 |
| GO:0030901 | midbrain development | 0.0434788203863315 |
| GO:0007399 | nervous system development | 0.0434788203863315 |
| GO:0030182 | neuron differentiation | 0.0434788203863315 |
| GO:0016564 | transcription repressor activity | 0.0434788203863315 |
| GO:0006688 | glycosphingolipid biosynthetic process | 0.0434788203863315 |
| GO:0046530 | photoreceptor cell differentiation | 0.0434788203863315 |
| GO:0004887 | thyroid hormone receptor activity | 0.0434788203863315 |
| GO:0009790 | embryonic development | 0.0459553101092688 |
| GO:0044424 | intracellular part | 0.0459553101092688 |
| GO:0005720 | nuclear heterochromatin | 0.0459553101092688 |
| GO:0048699 | generation of neurons | 0.0459553101092688 |
| GO:0010468 | regulation of gene expression | 0.0472670367834421 |
| GO:0007224 | smoothened signaling pathway | 0.0472670367834421 |
| GO:0048663 | neuron fate commitment | 0.0472670367834421 |
| GO:0022008 | neurogenesis | 0.0472670367834421 |
| GO:0009247 | glycolipid biosynthetic process | 0.0472670367834421 |
| GO:0001708 | cell fate specification | 0.0472670367834421 |
| GO:0006643 | membrane lipid metabolic process | 0.0472670367834421 |
| GO:0008543 | fibroblast growth factor receptor signaling pathway | 0.048631848475914 |
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>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| regional part of nervous system | 3.11e-25 | 94 |
| nervous system | 3.11e-25 | 94 |
| central nervous system | 5.04e-22 | 82 |
| neurectoderm | 8.48e-18 | 90 |
| neural tube | 4.29e-17 | 57 |
| neural rod | 4.29e-17 | 57 |
| future spinal cord | 4.29e-17 | 57 |
| neural keel | 4.29e-17 | 57 |
| neural plate | 6.20e-17 | 86 |
| presumptive neural plate | 6.20e-17 | 86 |
| brain | 1.80e-16 | 69 |
| future brain | 1.80e-16 | 69 |
| regional part of brain | 1.52e-14 | 59 |
| regional part of forebrain | 2.53e-14 | 41 |
| forebrain | 2.53e-14 | 41 |
| future forebrain | 2.53e-14 | 41 |
| ectoderm | 3.99e-14 | 173 |
| presumptive ectoderm | 3.99e-14 | 173 |
| ectoderm-derived structure | 2.39e-13 | 169 |
| pre-chordal neural plate | 2.73e-13 | 61 |
| anterior neural tube | 3.22e-13 | 42 |
| adult organism | 8.30e-12 | 115 |
| gray matter | 2.63e-11 | 34 |
| brain grey matter | 2.63e-11 | 34 |
| telencephalon | 5.08e-11 | 34 |
| regional part of telencephalon | 9.37e-11 | 33 |
| cerebral hemisphere | 2.39e-10 | 32 |
| anterior region of body | 3.34e-10 | 129 |
| craniocervical region | 3.34e-10 | 129 |
| head | 6.87e-10 | 123 |
| regional part of cerebral cortex | 2.63e-08 | 22 |
| cerebral cortex | 3.66e-08 | 25 |
| pallium | 3.66e-08 | 25 |
| neocortex | 1.51e-07 | 20 |
| Ontology term | p-value | n |
|---|---|---|
| cancer | 4.26e-15 | 235 |
| disease of cellular proliferation | 2.84e-13 | 239 |
| cell type cancer | 5.88e-09 | 143 |
| germ cell and embryonal cancer | 9.14e-08 | 22 |
| germ cell cancer | 9.14e-08 | 22 |
| hematologic cancer | 9.64e-07 | 51 |
| immune system cancer | 9.64e-07 | 51 |
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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