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Coexpression cluster:C1428

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Full id: C1428_neuroblastoma_medulla_locus_spinal_hippocampus_thalamus_globus



Phase1 CAGE Peaks

Hg19::chr17:10741337..10741344,-p3@PIRT
Hg19::chr17:10741366..10741377,-p2@PIRT
Hg19::chr17:10741392..10741423,-p1@PIRT
Hg19::chr3:28617858..28617911,+p1@ENST00000443912
Hg19::chr3:28617928..28617938,+p1@ENST00000445077
Hg19::chr3:28617949..28617957,+p2@ENST00000445077


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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism3.24e-62115
neural tube7.44e-6057
neural rod7.44e-6057
future spinal cord7.44e-6057
neural keel7.44e-6057
regional part of nervous system2.69e-5894
nervous system2.69e-5894
central nervous system6.12e-5782
regional part of brain2.49e-4959
brain6.37e-4669
future brain6.37e-4669
regional part of forebrain3.16e-4541
forebrain3.16e-4541
future forebrain3.16e-4541
neurectoderm6.40e-4590
anterior neural tube8.70e-4442
neural plate1.13e-4186
presumptive neural plate1.13e-4186
gray matter2.28e-3834
brain grey matter2.28e-3834
telencephalon4.74e-3834
regional part of telencephalon5.78e-3733
cerebral hemisphere1.69e-3532
ectoderm6.21e-34173
presumptive ectoderm6.21e-34173
ectoderm-derived structure2.84e-31169
cerebral cortex4.13e-2725
pallium4.13e-2725
pre-chordal neural plate6.20e-2761
anterior region of body3.69e-26129
craniocervical region3.69e-26129
head1.42e-25123
regional part of cerebral cortex4.66e-2422
neocortex1.55e-2120
posterior neural tube1.53e-1615
chordal neural plate1.53e-1615
segmental subdivision of nervous system1.53e-1313
segmental subdivision of hindbrain1.02e-1212
hindbrain1.02e-1212
presumptive hindbrain1.02e-1212
nucleus of brain1.15e-129
neural nucleus1.15e-129
tube1.36e-12194
basal ganglion2.23e-129
nuclear complex of neuraxis2.23e-129
aggregate regional part of brain2.23e-129
collection of basal ganglia2.23e-129
cerebral subcortex2.23e-129
embryo9.36e-12612
multi-cellular organism2.09e-11659
organ part6.27e-11219
anatomical conduit7.00e-11241
organism subdivision1.17e-10365
temporal lobe1.61e-107
telencephalic nucleus4.63e-107
embryonic structure1.20e-09605
developing anatomical structure1.20e-09605
anatomical cluster2.51e-09286
germ layer3.04e-09604
embryonic tissue3.04e-09604
presumptive structure3.04e-09604
epiblast (generic)3.04e-09604
multi-tissue structure4.70e-09347
brainstem5.03e-098
regional part of metencephalon5.89e-099
metencephalon5.89e-099
future metencephalon5.89e-099
diencephalon1.89e-087
future diencephalon1.89e-087
gyrus4.50e-086
limbic system1.21e-075
anatomical system1.52e-07625
anatomical group1.80e-07626
epithelium4.03e-07309
parietal lobe6.98e-075
cell layer7.36e-07312
Disease
Ontology termp-valuen
neuroectodermal tumor3.31e-0810


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTBP2#1488331.35850016966417.81255347077474e-050.00120326688089403



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.