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Coexpression cluster:C1093: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;7:4.69022432644065:5.26249365325459e-05:0.00089411025647024
|tf_chipseq_enrich=CTCF#10664;7:4.69022432644065:5.26249365325459e-05:0.00089411025647024
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}}
}}

Revision as of 14:40, 26 November 2012


Full id: C1093_neuroblastoma_thyroid_cerebellum_pons_peripheral_testis_thalamus



Phase1 CAGE Peaks

Hg19::chr7:153584120..153584136,+p13@DPP6
Hg19::chr7:153584146..153584162,+p19@DPP6
Hg19::chr7:153584166..153584196,+p8@DPP6
Hg19::chr7:153584214..153584226,+p21@DPP6
Hg19::chr7:153584257..153584277,+p20@DPP6
Hg19::chr7:153584378..153584393,+p5@DPP6
Hg19::chr7:153584403..153584435,+p2@DPP6
Hg19::chr7:153585814..153585818,+p@chr7:153585814..153585818
+


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube1.94e-7656
neural rod1.94e-7656
future spinal cord1.94e-7656
neural keel1.94e-7656
regional part of nervous system3.04e-7053
regional part of brain3.04e-7053
central nervous system2.12e-6581
adult organism2.48e-65114
nervous system1.45e-6289
brain1.92e-5968
future brain1.92e-5968
regional part of forebrain1.79e-5541
forebrain1.79e-5541
anterior neural tube1.79e-5541
future forebrain1.79e-5541
neurectoderm9.26e-5286
neural plate3.81e-5082
presumptive neural plate3.81e-5082
brain grey matter2.87e-4934
gray matter2.87e-4934
telencephalon6.41e-4934
cerebral hemisphere4.82e-4532
regional part of telencephalon4.91e-4532
ecto-epithelium3.50e-42104
regional part of cerebral cortex7.03e-3722
pre-chordal neural plate3.57e-3661
ectoderm-derived structure3.48e-33171
ectoderm3.48e-33171
presumptive ectoderm3.48e-33171
neocortex3.96e-3320
cerebral cortex6.90e-3225
pallium6.90e-3225
structure with developmental contribution from neural crest7.19e-32132
organ system subdivision2.47e-27223
posterior neural tube4.45e-2115
chordal neural plate4.45e-2115
neural nucleus3.06e-199
nucleus of brain3.06e-199
basal ganglion5.03e-199
nuclear complex of neuraxis5.03e-199
aggregate regional part of brain5.03e-199
collection of basal ganglia5.03e-199
cerebral subcortex5.03e-199
tube2.47e-16192
segmental subdivision of hindbrain2.48e-1512
hindbrain2.48e-1512
presumptive hindbrain2.48e-1512
telencephalic nucleus5.67e-157
anatomical cluster8.39e-15373
brainstem1.48e-146
segmental subdivision of nervous system5.52e-1413
gyrus5.88e-136
limbic system2.43e-115
anatomical conduit4.42e-11240
temporal lobe6.72e-116
organ part1.19e-10218
occipital lobe1.20e-105
embryo3.14e-10592
organ5.79e-10503
epithelium9.55e-10306
developing anatomical structure1.31e-09581
regional part of metencephalon1.47e-099
metencephalon1.47e-099
future metencephalon1.47e-099
cell layer1.63e-09309
corpus striatum1.80e-094
striatum1.80e-094
ventral part of telencephalon1.80e-094
future corpus striatum1.80e-094
embryonic structure2.54e-09564
germ layer5.53e-09560
germ layer / neural crest5.53e-09560
embryonic tissue5.53e-09560
presumptive structure5.53e-09560
germ layer / neural crest derived structure5.53e-09560
epiblast (generic)5.53e-09560
multi-tissue structure1.75e-08342
pons3.34e-083
multi-cellular organism3.34e-08656
medulla oblongata4.94e-083
myelencephalon4.94e-083
future myelencephalon4.94e-083
diencephalon5.42e-087
future diencephalon5.42e-087
frontal cortex1.09e-073
spinal cord1.09e-073
dorsal region element1.09e-073
dorsum1.09e-073
caudate-putamen1.39e-073
dorsal striatum1.39e-073
parietal lobe3.19e-075
anatomical system6.19e-07624
anatomical group6.86e-07625


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#1066474.690224326440655.26249365325459e-050.00089411025647024



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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