Coexpression cluster:C1022
From FANTOM5_SSTAR
Full id: C1022_Ciliary_Lens_Astrocyte_Neural_Iris_retina_Hair
Phase1 CAGE Peaks
| Hg19::chr12:97856211..97856221,+ | p@chr12:97856211..97856221 + |
| Hg19::chr2:210798666..210798677,+ | p@chr2:210798666..210798677 + |
| Hg19::chr2:45166478..45166502,- | p3@ENST00000437916 |
| Hg19::chr2:45166504..45166533,- | p2@ENST00000437916 |
| Hg19::chr3:173116225..173116242,+ | p10@NLGN1 |
| Hg19::chr3:8536114..8536125,- | p@chr3:8536114..8536125 - |
| Hg19::chr7:115723897..115723915,- | p@chr7:115723897..115723915 - |
| Hg19::chr7:115723925..115723935,- | p@chr7:115723925..115723935 - |
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:0016080 | synaptic vesicle targeting | 0.00459201695513952 |
| GO:0042043 | neurexin binding | 0.00459201695513952 |
| GO:0016079 | synaptic vesicle exocytosis | 0.00459201695513952 |
| GO:0006903 | vesicle targeting | 0.00459201695513952 |
| GO:0051650 | establishment of vesicle localization | 0.00459201695513952 |
| GO:0051648 | vesicle localization | 0.00459201695513952 |
| GO:0048489 | synaptic vesicle transport | 0.00542692912880125 |
| GO:0051656 | establishment of organelle localization | 0.00542692912880125 |
| GO:0016339 | calcium-dependent cell-cell adhesion | 0.00542692912880125 |
| GO:0007416 | synaptogenesis | 0.00542692912880125 |
| GO:0045664 | regulation of neuron differentiation | 0.00542692912880125 |
| GO:0051640 | organelle localization | 0.00631402331331684 |
| GO:0050808 | synapse organization and biogenesis | 0.00656002422162789 |
| GO:0007269 | neurotransmitter secretion | 0.00656002422162789 |
| GO:0045055 | regulated secretory pathway | 0.00811256328741317 |
| GO:0003001 | generation of a signal involved in cell-cell signaling | 0.0100450370893677 |
| GO:0001505 | regulation of neurotransmitter levels | 0.0105346271323789 |
| GO:0043062 | extracellular structure organization and biogenesis | 0.0107147062286589 |
| GO:0006887 | exocytosis | 0.0134135232110655 |
| GO:0045595 | regulation of cell differentiation | 0.0162907268170426 |
| GO:0045211 | postsynaptic membrane | 0.0162907268170426 |
| GO:0044456 | synapse part | 0.0168026074949424 |
| GO:0030182 | neuron differentiation | 0.0205790389471068 |
| GO:0006605 | protein targeting | 0.0205790389471068 |
| GO:0050793 | regulation of developmental process | 0.0205790389471068 |
| GO:0045045 | secretory pathway | 0.0205790389471068 |
| GO:0048699 | generation of neurons | 0.0205790389471068 |
| GO:0022008 | neurogenesis | 0.0214840793258313 |
| GO:0007268 | synaptic transmission | 0.0227304839279407 |
| GO:0032940 | secretion by cell | 0.0227304839279407 |
| GO:0007017 | microtubule-based process | 0.0233304087236927 |
| GO:0019226 | transmission of nerve impulse | 0.0236775874249382 |
| GO:0016337 | cell-cell adhesion | 0.0241428770217184 |
| GO:0046903 | secretion | 0.0259313898643173 |
| GO:0030054 | cell junction | 0.0281425039107837 |
| GO:0006886 | intracellular protein transport | 0.0337385690176223 |
| GO:0016192 | vesicle-mediated transport | 0.037604895605602 |
| GO:0007267 | cell-cell signaling | 0.0386696164643328 |
| GO:0007010 | cytoskeleton organization and biogenesis | 0.0403862004003297 |
| GO:0007399 | nervous system development | 0.0410985517484988 |
| GO:0015031 | protein transport | 0.0479666118900987 |
| GO:0046907 | intracellular transport | 0.0479666118900987 |
| GO:0045184 | establishment of protein localization | 0.0479666118900987 |
| GO:0022610 | biological adhesion | 0.0479666118900987 |
| GO:0007155 | cell adhesion | 0.0479666118900987 |
| GO:0008104 | protein localization | 0.0479666118900987 |
| GO:0033036 | macromolecule localization | 0.0494374591340553 |
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>cell_data<br>uberon_data<br><br>
| Ontology term | p-value | n |
|---|---|---|
| ciliated cell | 5.78e-51 | 3 |
| ciliated epithelial cell | 5.78e-51 | 3 |
| multi-ciliated epithelial cell | 5.78e-51 | 3 |
| non-pigmented ciliary epithelial cell | 5.78e-51 | 3 |
| columnar/cuboidal epithelial cell | 5.27e-22 | 27 |
| pigment cell (sensu Vertebrata) | 5.26e-18 | 1 |
| iris pigment epithelial cell | 5.26e-18 | 1 |
| crystallin accumulating cell | 1.57e-17 | 4 |
| vertebrate lens cell | 1.57e-17 | 4 |
| lens epithelial cell | 1.57e-17 | 4 |
| embryonic stem cell | 6.11e-14 | 5 |
| neurecto-epithelial cell | 1.04e-13 | 20 |
| neurectodermal cell | 1.22e-09 | 59 |
| ecto-epithelial cell | 3.48e-08 | 34 |
| ectodermal cell | 6.67e-08 | 72 |
| astrocyte of the cerebral cortex | 8.15e-07 | 3 |
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
This analysis result is provided for C0 - C305 clusters.
