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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2868_pons_caudate_spinal_hippocampus_locus_thalamus_acute
|full_id=C2868_pons_caudate_spinal_hippocampus_locus_thalamus_acute
|id=C2868
|id=C2868

Revision as of 15:39, 12 September 2012


Full id: C2868_pons_caudate_spinal_hippocampus_locus_thalamus_acute



Phase1 CAGE Peaks

Hg19::chr6:71665655..71665669,-p7@B3GAT2
Hg19::chr6:71665679..71665708,-p4@B3GAT2
Hg19::chr6:71665711..71665727,-p5@B3GAT2
Hg19::chr6:71665738..71665769,-p3@B3GAT2


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 cell1.25e-098
neuron2.68e-076
neuroblast2.68e-076
electrically signaling cell2.68e-076
Uber Anatomy
Ontology termp-valuen
central nervous system9.83e-6182
regional part of nervous system5.74e-5894
nervous system5.74e-5894
neural tube5.42e-5757
neural rod5.42e-5757
future spinal cord5.42e-5757
neural keel5.42e-5757
regional part of brain1.05e-4659
brain3.69e-4669
future brain3.69e-4669
anterior neural tube4.90e-4542
regional part of forebrain4.20e-4441
forebrain4.20e-4441
future forebrain4.20e-4441
neural plate1.28e-4186
presumptive neural plate1.28e-4186
neurectoderm3.09e-4090
gray matter1.04e-3834
brain grey matter1.04e-3834
telencephalon1.97e-3834
regional part of telencephalon3.16e-3733
cerebral hemisphere5.92e-3632
adult organism6.11e-33115
pre-chordal neural plate1.60e-3261
ectoderm-derived structure3.70e-29169
ectoderm8.51e-29173
presumptive ectoderm8.51e-29173
cerebral cortex3.87e-2725
pallium3.87e-2725
regional part of cerebral cortex1.23e-2622
anterior region of body4.08e-24129
craniocervical region4.08e-24129
neocortex7.07e-2420
head2.22e-23123
nucleus of brain5.29e-139
neural nucleus5.29e-139
posterior neural tube9.24e-1315
chordal neural plate9.24e-1315
basal ganglion1.12e-129
nuclear complex of neuraxis1.12e-129
aggregate regional part of brain1.12e-129
collection of basal ganglia1.12e-129
cerebral subcortex1.12e-129
brainstem1.21e-118
tube1.22e-11194
telencephalic nucleus2.67e-107
segmental subdivision of nervous system6.59e-1013
segmental subdivision of hindbrain5.60e-0912
hindbrain5.60e-0912
presumptive hindbrain5.60e-0912
gyrus9.30e-096
temporal lobe1.30e-087
limbic system6.34e-085
anatomical conduit1.28e-07241
occipital lobe1.29e-075
parietal lobe2.03e-075
organ part3.60e-07219
diencephalon4.56e-077
future diencephalon4.56e-077
epithelium6.60e-07309


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#8553444.87181354697742.46312701995675e-071.28752013432064e-05
CCNT2#90546.336201576962630.0006203100587215640.00513551821029104
CTCF#1066445.360256373075030.001211145381643620.00819771954073093
CTCFL#140690419.74647435897446.5732084880439e-060.000193489098444988
E2F1#186944.907389214879320.001724022357361790.0106787955032624
E2F6#187645.017155731697390.00157802193473060.00999133269726153
EBF1#187948.9064668465690.00015887907472010.00200014123489544
EGR1#195844.988179094810140.001615011500076050.010163916002196
ELF1#199744.258097958807540.003041525565781240.0161245628713008
MAX#414946.452555509007120.0005767613195645490.00486404840552341
MYC#460945.22228187160940.001344309395272740.00889723250525281
NANOG#79923429.24477848101271.36586687657858e-065.34869781488529e-05
PAX5#507946.669565531177830.0005052774169483260.00444871591204402
RAD21#5885410.35503389545638.6948481184721e-050.00129911479634493
REST#597849.650028716128020.0001152825614219170.00157550319711379
SMC3#9126415.04493284493281.95092670935632e-050.000439596191150949
TCF7L2#6934410.77017656313737.42969445082454e-050.00115727048284812
TRIM28#10155418.59052504526258.36730015875654e-060.000230999857594601
USF1#739146.361499277207960.0006105011399140830.00508941000570617
USF2#7392412.99219738506963.50833029870167e-050.000682829869672202
YY1#752844.911170749853860.00171871838055440.0107069030090499
ZEB1#6935416.88843201754391.22862303393937e-050.000305151393677988
ZNF143#7702413.50087655222793.00867915035614e-050.000621855218254591



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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