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Coexpression cluster:C4320: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280507663033026!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326687437125341!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157239436501365!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.0047244625104203!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666475807562255!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247330935012103
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280507663033026!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326687437125341!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157239436501365!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.0047244625104203!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666475807562255!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247330935012103
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}}
}}

Revision as of 16:40, 26 November 2012


Full id: C4320_cerebellum_occipital_aorta_parietal_rectum_extraskeletal_brain



Phase1 CAGE Peaks

Hg19::chr3:2140514..2140525,+p7@CNTN4
Hg19::chr3:2140530..2140557,+p2@CNTN4
Hg19::chr3:2140565..2140621,+p1@CNTN4


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
adult organism1.76e-54114
neurectoderm1.85e-3986
neural tube5.63e-3756
neural rod5.63e-3756
future spinal cord5.63e-3756
neural keel5.63e-3756
neural plate2.06e-3682
presumptive neural plate2.06e-3682
regional part of nervous system1.51e-3453
regional part of brain1.51e-3453
brain8.73e-3168
future brain8.73e-3168
ecto-epithelium4.99e-30104
central nervous system1.53e-2981
nervous system5.40e-2989
regional part of forebrain2.04e-2741
forebrain2.04e-2741
anterior neural tube2.04e-2741
future forebrain2.04e-2741
ectoderm-derived structure5.98e-27171
ectoderm5.98e-27171
presumptive ectoderm5.98e-27171
pre-chordal neural plate8.83e-2761
organ system subdivision2.42e-26223
regional part of cerebral cortex3.74e-2622
telencephalon1.08e-2534
brain grey matter1.76e-2534
gray matter1.76e-2534
cerebral hemisphere9.93e-2532
neocortex1.21e-2420
structure with developmental contribution from neural crest3.75e-24132
regional part of telencephalon5.51e-2432
cerebral cortex4.10e-2225
pallium4.10e-2225
anatomical cluster6.86e-17373
organ part8.57e-14218
multi-tissue structure2.81e-13342
organ1.24e-12503
posterior neural tube1.56e-1015
chordal neural plate1.56e-1015
embryo4.16e-10592
multi-cellular organism4.52e-10656
intestine5.26e-1017
embryonic structure5.24e-09564
gastrointestinal system5.65e-0925
temporal lobe6.03e-096
epithelium6.51e-09306
developing anatomical structure7.01e-09581
germ layer7.37e-09560
germ layer / neural crest7.37e-09560
embryonic tissue7.37e-09560
presumptive structure7.37e-09560
germ layer / neural crest derived structure7.37e-09560
epiblast (generic)7.37e-09560
tube1.26e-08192
cell layer1.32e-08309
gyrus1.53e-086
segmental subdivision of hindbrain2.83e-0812
hindbrain2.83e-0812
presumptive hindbrain2.83e-0812
anatomical conduit3.70e-08240
regional part of metencephalon7.91e-089
metencephalon7.91e-089
future metencephalon7.91e-089
segmental subdivision of nervous system1.94e-0713
occipital lobe4.83e-075
parietal lobe5.02e-075
anatomical system6.39e-07624
anatomical group7.53e-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#1066435.360256373075030.0064925092527670.0280507663033026
E2F1#186934.907389214879320.008460985347239390.0326687437125341
JUND#372736.994663941871030.002921845042734990.0157239436501365
NRF1#4899312.21027944771090.0005492172401020010.0047244625104203
RAD21#5885310.35503389545630.0009004912073565420.00666475807562255
SP1#666735.69838137814090.005403962701712170.0247330935012103



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.