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Coexpression cluster:C1480

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Full id: C1480_optic_neuroectodermal_corpus_cerebellum_diencephalon_occipital_Astrocyte



Phase1 CAGE Peaks

Hg19::chr20:24449821..24449843,+p4@SYNDIG1
Hg19::chr20:24449953..24450011,+p2@SYNDIG1
Hg19::chr20:24450118..24450148,+p3@SYNDIG1
Hg19::chr20:24450259..24450346,+p1@SYNDIG1
Hg19::chr20:24450356..24450367,+p5@SYNDIG1
Hg19::chr20:24450498..24450540,+p@chr20:24450498..24450540
+


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


No GOStat results

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>


Cell Type
Ontology termp-valuen
neurectodermal cell2.13e-0859
ectodermal cell1.67e-0771
neural cell6.59e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system1.52e-4282
regional part of nervous system1.33e-4194
nervous system1.33e-4194
neurectoderm1.18e-3590
brain2.64e-3569
future brain2.64e-3569
neural tube2.72e-3557
neural rod2.72e-3557
future spinal cord2.72e-3557
neural keel2.72e-3557
neural plate8.76e-3486
presumptive neural plate8.76e-3486
regional part of brain1.80e-3359
adult organism3.24e-32115
ectoderm1.07e-30173
presumptive ectoderm1.07e-30173
ectoderm-derived structure5.81e-29169
regional part of forebrain1.48e-2541
forebrain1.48e-2541
future forebrain1.48e-2541
telencephalon1.01e-2434
head1.19e-24123
anterior region of body1.25e-24129
craniocervical region1.25e-24129
gray matter2.02e-2434
brain grey matter2.02e-2434
anterior neural tube2.02e-2442
regional part of telencephalon6.15e-2433
pre-chordal neural plate3.60e-2361
cerebral hemisphere3.88e-2332
cerebral cortex1.22e-1825
pallium1.22e-1825
regional part of cerebral cortex3.11e-1722
neocortex6.10e-1620
organism subdivision3.89e-15365
posterior neural tube5.72e-1215
chordal neural plate5.72e-1215
segmental subdivision of nervous system1.23e-1013
cell layer1.45e-10312
tube1.89e-10194
multi-cellular organism2.01e-10659
epithelium4.94e-10309
segmental subdivision of hindbrain7.69e-1012
hindbrain7.69e-1012
presumptive hindbrain7.69e-1012
anatomical conduit2.57e-08241
anatomical cluster2.61e-08286
regional part of metencephalon8.07e-089
metencephalon8.07e-089
future metencephalon8.07e-089
organ part1.18e-07219
embryo2.62e-07612
nucleus of brain3.23e-079
neural nucleus3.23e-079
basal ganglion3.30e-079
nuclear complex of neuraxis3.30e-079
aggregate regional part of brain3.30e-079
collection of basal ganglia3.30e-079
cerebral subcortex3.30e-079
multi-tissue structure5.09e-07347


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


This analysis result is provided for C0 - C305 clusters.