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Coexpression cluster:C3442: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278892433615651!REST#5978;3:9.65002871612802:0.00111263624711459:0.00766356374150238
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278892433615651!REST#5978;3:9.65002871612802:0.00111263624711459:0.00766356374150238
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}}
}}

Revision as of 16:08, 26 November 2012


Full id: C3442_amniotic_epitheloid_occipital_brain_retina_frontal_medial



Phase1 CAGE Peaks

Hg19::chr14:63512137..63512153,-p2@KCNH5
Hg19::chr14:63512154..63512187,-p1@KCNH5
Hg19::chr14:63512678..63512708,-p@chr14:63512678..63512708
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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
embryonic stem cell4.24e-095
Uber Anatomy
Ontology termp-valuen
neural tube5.28e-5956
neural rod5.28e-5956
future spinal cord5.28e-5956
neural keel5.28e-5956
central nervous system4.42e-5481
regional part of nervous system7.78e-5453
regional part of brain7.78e-5453
nervous system1.55e-5189
regional part of forebrain3.28e-5141
forebrain3.28e-5141
anterior neural tube3.28e-5141
future forebrain3.28e-5141
cerebral hemisphere2.22e-4932
telencephalon2.70e-4934
brain grey matter3.18e-4934
gray matter3.18e-4934
brain1.41e-4868
future brain1.41e-4868
regional part of telencephalon1.41e-4532
cerebral cortex1.56e-4025
pallium1.56e-4025
neocortex7.44e-4020
regional part of cerebral cortex1.56e-3922
neural plate1.70e-3882
presumptive neural plate1.70e-3882
neurectoderm7.38e-3886
pre-chordal neural plate1.63e-3361
ecto-epithelium2.72e-32104
adult organism5.04e-28114
organ system subdivision9.13e-28223
ectoderm-derived structure9.57e-27171
ectoderm9.57e-27171
presumptive ectoderm9.57e-27171
structure with developmental contribution from neural crest1.61e-22132
larynx1.30e-179
gyrus4.85e-146
organ part4.89e-13218
occipital lobe2.02e-125
brainstem2.12e-126
parietal lobe1.17e-115
anatomical cluster2.91e-11373
temporal lobe6.30e-116
tube1.01e-10192
neural nucleus2.66e-109
nucleus of brain2.66e-109
basal ganglion3.81e-109
nuclear complex of neuraxis3.81e-109
aggregate regional part of brain3.81e-109
collection of basal ganglia3.81e-109
cerebral subcortex3.81e-109
posterior neural tube9.70e-1015
chordal neural plate9.70e-1015
corpus striatum1.65e-084
striatum1.65e-084
ventral part of telencephalon1.65e-084
future corpus striatum1.65e-084
frontal cortex4.20e-083
pons2.42e-073
upper respiratory tract2.50e-0719
anatomical conduit2.57e-07240
telencephalic nucleus5.02e-077
multi-tissue structure5.67e-07342
limbic system5.99e-075
spinal cord8.24e-073
dorsal region element8.24e-073
dorsum8.24e-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#1066435.360256373075030.0064925092527670.0278892433615651
REST#597839.650028716128020.001112636247114590.00766356374150238



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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