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Coexpression cluster:C4460: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327050167911594!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323798444911118!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464325453009846!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154647082801156!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.027051654354324!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173488009125779!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00240190589164147!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330775955593409!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.014071281098309!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00390246746556112
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327050167911594!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323798444911118!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464325453009846!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154647082801156!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.027051654354324!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173488009125779!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00240190589164147!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330775955593409!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.014071281098309!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00390246746556112
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}}
}}

Revision as of 16:45, 26 November 2012


Full id: C4460_brain_occipital_diencephalon_temporal_postcentral_olfactory_amygdala



Phase1 CAGE Peaks

Hg19::chr5:132113042..132113061,-p4@SEPT8
Hg19::chr5:132113063..132113082,-p3@SEPT8
Hg19::chr5:132113083..132113109,-p2@SEPT8


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
nervous system4.32e-3589
neural plate1.47e-3382
presumptive neural plate1.47e-3382
neurectoderm2.63e-3386
central nervous system1.71e-3281
neural tube2.22e-3156
neural rod2.22e-3156
future spinal cord2.22e-3156
neural keel2.22e-3156
ectoderm-derived structure4.85e-31171
ectoderm4.85e-31171
presumptive ectoderm4.85e-31171
brain7.14e-3168
future brain7.14e-3168
regional part of nervous system1.51e-2953
regional part of brain1.51e-2953
structure with developmental contribution from neural crest3.32e-28132
anatomical cluster9.72e-28373
ecto-epithelium5.38e-27104
pre-chordal neural plate6.25e-2761
cell layer3.97e-25309
epithelium9.31e-25306
regional part of forebrain1.42e-2341
forebrain1.42e-2341
anterior neural tube1.42e-2341
future forebrain1.42e-2341
organ part6.81e-22218
telencephalon3.43e-2134
brain grey matter3.56e-2134
gray matter3.56e-2134
tube3.17e-20192
cerebral hemisphere5.43e-2032
regional part of telencephalon6.36e-2032
multi-tissue structure3.08e-19342
anatomical conduit9.66e-18240
organ system subdivision6.02e-17223
adult organism2.07e-16114
cerebral cortex1.39e-1525
pallium1.39e-1525
regional part of cerebral cortex1.98e-1422
neocortex2.99e-1320
multi-cellular organism1.31e-11656
anatomical group6.00e-10625
anatomical system6.03e-10624
embryo1.32e-09592
posterior neural tube6.77e-0915
chordal neural plate6.77e-0915
developing anatomical structure2.76e-08581
segmental subdivision of nervous system9.75e-0813
segmental subdivision of hindbrain3.41e-0712
hindbrain3.41e-0712
presumptive hindbrain3.41e-0712
basal ganglion4.48e-079
nuclear complex of neuraxis4.48e-079
aggregate regional part of brain4.48e-079
collection of basal ganglia4.48e-079
cerebral subcortex4.48e-079
neural nucleus4.61e-079
nucleus of brain4.61e-079
germ layer7.39e-07560
germ layer / neural crest7.39e-07560
embryonic tissue7.39e-07560
presumptive structure7.39e-07560
germ layer / neural crest derived structure7.39e-07560
epiblast (generic)7.39e-07560
organ8.38e-07503


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
E2F1#186934.907389214879320.008460985347239390.0327050167911594
E2F6#187635.017155731697390.00791769806886330.0323798444911118
ELF1#199734.258097958807540.01295179875054610.0464325453009846
GABPB1#255337.067683836182170.002832212825417420.0154647082801156
NFKB1#479035.488063424193840.006049381815655430.027051654354324
PAX5#507936.669565531177830.003370290999677260.0173488009125779
SIX5#147912317.0867153554590.0002004060546325010.00240190589164147
YY1#752834.911170749853860.008441455341808260.0330775955593409
ZBTB7A#5134137.35190930787590.002516255860282270.014071281098309
ZNF143#7702313.50087655222790.0004062804962997170.00390246746556112



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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