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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4878_spleen_H9_HES3GFP_iPS_hippocampus_spinal_Neural
|full_id=C4878_spleen_H9_HES3GFP_iPS_hippocampus_spinal_Neural
|id=C4878
|id=C4878

Revision as of 18:01, 12 September 2012


Full id: C4878_spleen_H9_HES3GFP_iPS_hippocampus_spinal_Neural



Phase1 CAGE Peaks

Hg19::chrX:69642952..69642968,+p3@GDPD2
Hg19::chrX:69643029..69643035,+p6@GDPD2
Hg19::chrX:69643047..69643060,+p2@GDPD2


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
neuronal stem cell2.39e-168
neural cell6.12e-1325
neuron1.57e-126
neuroblast1.57e-126
electrically signaling cell1.57e-126
oligodendrocyte5.41e-127
macroglial cell5.41e-127
astrocyte5.41e-127
oligodendrocyte precursor cell5.41e-127
embryonic stem cell8.68e-125
ectodermal cell6.26e-0871
neurectodermal cell8.79e-0859
Uber Anatomy
Ontology termp-valuen
central nervous system1.16e-8882
neural tube1.80e-8757
neural rod1.80e-8757
future spinal cord1.80e-8757
neural keel1.80e-8757
regional part of nervous system1.01e-7694
nervous system1.01e-7694
regional part of brain7.53e-7459
neural plate2.43e-6986
presumptive neural plate2.43e-6986
brain7.06e-6869
future brain7.06e-6869
neurectoderm1.72e-6590
regional part of forebrain1.30e-6241
forebrain1.30e-6241
future forebrain1.30e-6241
anterior neural tube7.31e-6142
gray matter1.28e-5434
brain grey matter1.28e-5434
telencephalon1.78e-5434
regional part of telencephalon7.49e-5333
pre-chordal neural plate1.72e-5261
cerebral hemisphere8.42e-5132
ectoderm-derived structure6.53e-46169
head9.18e-46123
anterior region of body1.89e-44129
craniocervical region1.89e-44129
ectoderm2.13e-44173
presumptive ectoderm2.13e-44173
cerebral cortex2.78e-3825
pallium2.78e-3825
regional part of cerebral cortex2.61e-3322
adult organism1.11e-32115
neocortex8.00e-3020
posterior neural tube1.50e-2615
chordal neural plate1.50e-2615
segmental subdivision of hindbrain1.65e-2112
hindbrain1.65e-2112
presumptive hindbrain1.65e-2112
segmental subdivision of nervous system1.30e-1913
nucleus of brain1.30e-179
neural nucleus1.30e-179
basal ganglion1.69e-179
nuclear complex of neuraxis1.69e-179
aggregate regional part of brain1.69e-179
collection of basal ganglia1.69e-179
cerebral subcortex1.69e-179
organ part1.52e-16219
tube1.64e-16194
regional part of metencephalon8.01e-169
metencephalon8.01e-169
future metencephalon8.01e-169
telencephalic nucleus6.09e-147
anatomical conduit2.62e-12241
brainstem2.94e-128
temporal lobe5.73e-127
anatomical cluster1.01e-11286
gyrus1.65e-116
epithelium3.37e-11309
cell layer6.21e-11312
cerebellum1.32e-106
rhombic lip1.32e-106
limbic system1.68e-105
parietal lobe8.61e-105
organism subdivision1.15e-09365
diencephalon1.97e-097
future diencephalon1.97e-097
embryo3.66e-09612
corpus striatum1.21e-084
striatum1.21e-084
ventral part of telencephalon1.21e-084
future corpus striatum1.21e-084
organ1.88e-07511
medulla oblongata2.19e-073
myelencephalon2.19e-073
future myelencephalon2.19e-073
multi-cellular organism2.39e-07659
brainstem nucleus6.48e-073
pons6.75e-073
caudate-putamen7.61e-073
dorsal striatum7.61e-073
middle temporal gyrus9.46e-073


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
CTCF#1066435.360256373075030.0064925092527670.028186023770617
RAD21#5885310.35503389545630.0009004912073565420.00669893875668565
SMC3#9126315.04493284493280.0002935825420371870.00311252330807245
ZNF263#1012738.221841637010680.001799043925565870.0110335515028583



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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