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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4126_salivary_astrocytoma_spinal_hippocampus_medulla_thalamus_amygdala
|full_id=C4126_salivary_astrocytoma_spinal_hippocampus_medulla_thalamus_amygdala
|id=C4126
|id=C4126

Revision as of 17:10, 12 September 2012


Full id: C4126_salivary_astrocytoma_spinal_hippocampus_medulla_thalamus_amygdala



Phase1 CAGE Peaks

Hg19::chr2:131594446..131594472,+p3@ARHGEF4
Hg19::chr2:131594478..131594502,+p2@ARHGEF4
Hg19::chr2:131594505..131594522,+p5@ARHGEF4


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell5.22e-19254
endo-epithelial cell9.35e-1443
endodermal cell2.07e-1059
respiratory epithelial cell3.88e-0713
epithelial cell of alimentary canal6.84e-0721
Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.62e-3394
nervous system2.62e-3394
central nervous system4.39e-3382
neural tube6.75e-3357
neural rod6.75e-3357
future spinal cord6.75e-3357
neural keel6.75e-3357
ectoderm2.80e-32173
presumptive ectoderm2.80e-32173
ectoderm-derived structure1.61e-31169
head6.13e-28123
brain9.51e-2869
future brain9.51e-2869
anterior region of body9.82e-28129
craniocervical region9.82e-28129
regional part of brain1.44e-2559
regional part of forebrain7.58e-2541
forebrain7.58e-2541
future forebrain7.58e-2541
neurectoderm1.11e-2490
neural plate4.12e-2486
presumptive neural plate4.12e-2486
anterior neural tube9.15e-2442
gray matter1.49e-2134
brain grey matter1.49e-2134
telencephalon1.85e-2134
regional part of telencephalon7.32e-2133
cerebral hemisphere6.28e-2032
adult organism5.72e-19115
pre-chordal neural plate5.40e-1861
organ part2.73e-15219
cerebral cortex3.22e-1525
pallium3.22e-1525
embryo5.60e-15612
organ5.71e-15511
regional part of cerebral cortex5.95e-1422
embryonic structure1.27e-12605
developing anatomical structure1.27e-12605
neocortex1.87e-1220
germ layer2.65e-12604
embryonic tissue2.65e-12604
presumptive structure2.65e-12604
epiblast (generic)2.65e-12604
respiratory system2.79e-1272
organism subdivision3.16e-12365
endoderm-derived structure7.20e-12169
endoderm7.20e-12169
presumptive endoderm7.20e-12169
multi-tissue structure1.39e-11347
multi-cellular organism2.01e-11659
digestive system8.35e-11155
digestive tract8.35e-11155
primitive gut8.35e-11155
anatomical cluster1.45e-10286
anatomical conduit2.75e-10241
posterior neural tube3.46e-1015
chordal neural plate3.46e-1015
anatomical system3.66e-10625
anatomical group5.16e-10626
foregut8.30e-1098
anatomical space2.31e-09104
respiratory tract2.32e-0953
subdivision of digestive tract3.21e-09129
endodermal part of digestive tract3.21e-09129
segment of respiratory tract5.15e-0946
mixed endoderm/mesoderm-derived structure1.65e-08130
respiratory primordium3.23e-0838
endoderm of foregut3.23e-0838
segmental subdivision of nervous system3.79e-0813
nucleus of brain7.07e-089
neural nucleus7.07e-089
segmental subdivision of hindbrain8.30e-0812
hindbrain8.30e-0812
presumptive hindbrain8.30e-0812
basal ganglion1.01e-079
nuclear complex of neuraxis1.01e-079
aggregate regional part of brain1.01e-079
collection of basal ganglia1.01e-079
cerebral subcortex1.01e-079
organ segment1.26e-0797
primordium1.83e-07168
immaterial anatomical entity3.62e-07126
tube7.30e-07194
Disease
Ontology termp-valuen
carcinoma2.32e-18106
cell type cancer1.56e-15143
cancer2.86e-08235
disease of cellular proliferation4.15e-08239
squamous cell carcinoma2.80e-0714


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
BHLHE40#8553344.87181354697741.10603738662898e-050.000284936947760592
E2F1#186934.907389214879320.008460985347239390.0326084670534092
EGR1#195834.988179094810140.008056488137383440.032128434250265
GABPB1#255337.067683836182170.002832212825417420.015442102598474
TCF7L2#6934310.77017656313730.0008003181298398380.00614862624410349
USF1#739136.361499277207960.00388404057290560.0190703452302989



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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