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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3681_neuroblastoma_optic_teratocarcinoma_substantia_diencephalon_corpus_globus
|full_id=C3681_neuroblastoma_optic_teratocarcinoma_substantia_diencephalon_corpus_globus
|id=C3681
|id=C3681

Revision as of 16:38, 12 September 2012


Full id: C3681_neuroblastoma_optic_teratocarcinoma_substantia_diencephalon_corpus_globus



Phase1 CAGE Peaks

Hg19::chr17:74540323..74540336,+p6@PRCD
Hg19::chr17:74540344..74540355,+p8@PRCD
Hg19::chr17:74540357..74540388,+p1@PRCD


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
neural tube3.59e-5657
neural rod3.59e-5657
future spinal cord3.59e-5657
neural keel3.59e-5657
neurectoderm1.24e-5390
regional part of nervous system6.61e-5394
nervous system6.61e-5394
neural plate1.66e-5086
presumptive neural plate1.66e-5086
regional part of brain7.04e-4859
central nervous system2.10e-4782
brain6.26e-4569
future brain6.26e-4569
regional part of forebrain5.61e-3941
forebrain5.61e-3941
future forebrain5.61e-3941
anterior neural tube8.17e-3842
adult organism2.28e-37115
pre-chordal neural plate3.01e-3561
gray matter1.47e-3334
brain grey matter1.47e-3334
telencephalon1.68e-3334
ectoderm6.80e-33173
presumptive ectoderm6.80e-33173
regional part of telencephalon6.31e-3233
ectoderm-derived structure2.03e-30169
cerebral hemisphere4.26e-3032
head1.56e-28123
anterior region of body1.83e-26129
craniocervical region1.83e-26129
regional part of cerebral cortex7.76e-2322
neocortex8.48e-2020
cerebral cortex1.53e-1925
pallium1.53e-1925
posterior neural tube3.64e-1915
chordal neural plate3.64e-1915
nucleus of brain7.96e-179
neural nucleus7.96e-179
tube3.10e-16194
segmental subdivision of nervous system5.67e-1613
segmental subdivision of hindbrain3.28e-1412
hindbrain3.28e-1412
presumptive hindbrain3.28e-1412
cell layer5.10e-14312
epithelium1.07e-13309
telencephalic nucleus2.77e-137
basal ganglion6.18e-139
nuclear complex of neuraxis6.18e-139
aggregate regional part of brain6.18e-139
collection of basal ganglia6.18e-139
cerebral subcortex6.18e-139
brainstem4.34e-128
gyrus2.48e-116
anatomical conduit3.63e-11241
anatomical cluster1.49e-10286
organism subdivision9.21e-10365
regional part of metencephalon2.55e-099
metencephalon2.55e-099
future metencephalon2.55e-099
organ part5.15e-09219
corpus striatum7.73e-084
striatum7.73e-084
ventral part of telencephalon7.73e-084
future corpus striatum7.73e-084
organ2.31e-07511
embryo2.49e-07612
brainstem nucleus5.00e-073
pons5.51e-073
medulla oblongata6.92e-073
myelencephalon6.92e-073
future myelencephalon6.92e-073
germ layer7.05e-07604
embryonic tissue7.05e-07604
presumptive structure7.05e-07604
epiblast (generic)7.05e-07604
diencephalon7.69e-077
future diencephalon7.69e-077
embryonic structure7.95e-07605
developing anatomical structure7.95e-07605
spinal cord8.68e-073
multi-tissue structure9.98e-07347
Disease
Ontology termp-valuen
neuroectodermal tumor3.48e-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
EP300#203336.77394172622320.003216880500103790.0167356305130929
GATA2#2624312.7449317335540.0004829527704283790.00436777835043034
RAD21#5885310.35503389545630.0009004912073565420.00663513483879708
YY1#752834.911170749853860.008441455341808260.0329010730871441



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.

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