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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4285_medial_medulla_trachea_caudate_middle_insula_putamen
|full_id=C4285_medial_medulla_trachea_caudate_middle_insula_putamen
|id=C4285
|id=C4285

Revision as of 17:20, 12 September 2012


Full id: C4285_medial_medulla_trachea_caudate_middle_insula_putamen



Phase1 CAGE Peaks

Hg19::chr3:138048631..138048651,-p3@NME9
Hg19::chr3:138048653..138048677,-p1@NME9
Hg19::chr3:138048682..138048698,-p2@NME9


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
mature alpha-beta T cell8.50e-0818
alpha-beta T cell8.50e-0818
immature T cell8.50e-0818
mature T cell8.50e-0818
immature alpha-beta T cell8.50e-0818
T cell7.07e-0725
pro-T cell7.07e-0725
CD8-positive, alpha-beta T cell9.09e-0711
Uber Anatomy
Ontology termp-valuen
neural tube1.46e-4257
neural rod1.46e-4257
future spinal cord1.46e-4257
neural keel1.46e-4257
adult organism1.26e-40115
central nervous system5.76e-4082
brain4.88e-3969
future brain4.88e-3969
regional part of brain4.55e-3659
regional part of nervous system2.06e-3594
nervous system2.06e-3594
regional part of forebrain2.75e-3441
forebrain2.75e-3441
future forebrain2.75e-3441
anterior neural tube4.69e-3342
neural plate2.06e-3186
presumptive neural plate2.06e-3186
gray matter6.66e-2934
brain grey matter6.66e-2934
neurectoderm6.98e-2990
telencephalon7.37e-2934
regional part of telencephalon6.61e-2833
cerebral hemisphere3.78e-2732
anterior region of body8.37e-26129
craniocervical region8.37e-26129
head2.97e-24123
pre-chordal neural plate3.62e-2461
regional part of cerebral cortex8.02e-2122
cerebral cortex2.04e-2025
pallium2.04e-2025
neocortex5.68e-1920
ectoderm-derived structure5.19e-17169
ectoderm5.50e-16173
presumptive ectoderm5.50e-16173
posterior neural tube1.86e-1015
chordal neural plate1.86e-1015
nucleus of brain5.60e-109
neural nucleus5.60e-109
basal ganglion6.85e-109
nuclear complex of neuraxis6.85e-109
aggregate regional part of brain6.85e-109
collection of basal ganglia6.85e-109
cerebral subcortex6.85e-109
anatomical conduit5.23e-09241
tube1.18e-08194
telencephalic nucleus4.07e-087
organism subdivision4.47e-08365
segmental subdivision of hindbrain5.01e-0812
hindbrain5.01e-0812
presumptive hindbrain5.01e-0812
anatomical cluster1.26e-07286
gyrus1.26e-076
segmental subdivision of nervous system3.84e-0713
temporal lobe7.07e-077
brainstem8.47e-078
diencephalon8.73e-077
future diencephalon8.73e-077


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
MAX#414936.452555509007120.003721913834265510.0187052095152714
SP1#666735.69838137814090.005403962701712170.0247255086569753
SREBF1#6720347.00584944048839.62099323994382e-060.000255221466341502
STAT3#6774310.51946499715420.0008589184530415310.00644244357348495
TCF7L2#6934310.77017656313730.0008003181298398380.00615813933267095
USF1#739136.361499277207960.00388404057290560.0190838028506628



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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