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Coexpression cluster:C2314: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!1.36e-32!86;UBERON:0001017!1.66e-32!82;UBERON:0000073!3.11e-31!94;UBERON:0001016!3.11e-31!94;UBERON:0001049!1.54e-30!57;UBERON:0005068!1.54e-30!57;UBERON:0006241!1.54e-30!57;UBERON:0007135!1.54e-30!57;UBERON:0000955!1.57e-28!69;UBERON:0006238!1.57e-28!69;UBERON:0002616!5.40e-26!59;UBERON:0002780!1.44e-25!41;UBERON:0001890!1.44e-25!41;UBERON:0006240!1.44e-25!41;UBERON:0003075!4.83e-25!86;UBERON:0007284!4.83e-25!86;UBERON:0003080!2.04e-24!42;UBERON:0002346!1.22e-23!90;UBERON:0004121!2.10e-22!169;UBERON:0000924!1.09e-21!173;UBERON:0006601!1.09e-21!173;UBERON:0003056!3.34e-21!61;UBERON:0001893!5.53e-21!34;UBERON:0002020!5.80e-21!34;UBERON:0003528!5.80e-21!34;UBERON:0002791!3.15e-20!33;UBERON:0000153!3.37e-20!129;UBERON:0007811!3.37e-20!129;UBERON:0001869!5.05e-20!32;UBERON:0000033!6.28e-19!123;UBERON:0007023!5.38e-18!115;UBERON:0002619!1.16e-16!22;UBERON:0001950!1.07e-15!20;UBERON:0000956!1.47e-15!25;UBERON:0000203!1.47e-15!25;UBERON:0000062!3.86e-09!511;UBERON:0000064!4.81e-09!219;UBERON:0003076!2.39e-07!15;UBERON:0003057!2.39e-07!15;UBERON:0000922!3.11e-07!612;UBERON:0002308!7.19e-07!9;UBERON:0000125!7.19e-07!9;UBERON:0002420!7.24e-07!9;UBERON:0007245!7.24e-07!9;UBERON:0010009!7.24e-07!9;UBERON:0010011!7.24e-07!9;UBERON:0000454!7.24e-07!9
|ontology_enrichment_uberon=UBERON:0001049!2.57e-36!56;UBERON:0005068!2.57e-36!56;UBERON:0006241!2.57e-36!56;UBERON:0007135!2.57e-36!56;UBERON:0000073!1.35e-34!53;UBERON:0002616!1.35e-34!53;UBERON:0001017!1.90e-34!81;UBERON:0000955!3.01e-33!68;UBERON:0006238!3.01e-33!68;UBERON:0001016!4.88e-33!89;UBERON:0002780!5.01e-31!41;UBERON:0001890!5.01e-31!41;UBERON:0003080!5.01e-31!41;UBERON:0006240!5.01e-31!41;UBERON:0003075!4.83e-27!82;UBERON:0007284!4.83e-27!82;UBERON:0001893!1.55e-25!34;UBERON:0003528!1.88e-25!34;UBERON:0002020!1.88e-25!34;UBERON:0002346!2.05e-25!86;UBERON:0003056!2.89e-25!61;UBERON:0010371!8.64e-25!104;UBERON:0001869!2.16e-24!32;UBERON:0002791!4.67e-24!32;UBERON:0004121!1.53e-22!171;UBERON:0000924!1.53e-22!171;UBERON:0006601!1.53e-22!171;UBERON:0007023!7.99e-22!114;UBERON:0011216!9.50e-21!223;UBERON:0002619!5.28e-20!22;UBERON:0000956!3.87e-19!25;UBERON:0000203!3.87e-19!25;UBERON:0001950!5.48e-19!20;UBERON:0010314!2.13e-13!132;UBERON:0000064!2.06e-09!218;UBERON:0002420!8.61e-08!9;UBERON:0007245!8.61e-08!9;UBERON:0010009!8.61e-08!9;UBERON:0010011!8.61e-08!9;UBERON:0000454!8.61e-08!9;UBERON:0000125!9.60e-08!9;UBERON:0002308!9.60e-08!9;UBERON:0000062!1.86e-07!503;UBERON:0001871!4.71e-07!6;UBERON:0000922!5.90e-07!592;UBERON:0003076!6.25e-07!15;UBERON:0003057!6.25e-07!15;UBERON:0001894!7.03e-07!7;UBERON:0006222!7.03e-07!7;UBERON:0000477!9.03e-07!373
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106365294766368!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199461133365699!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00886632958212121!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00795220673347809!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00683474047520646!STAT1#6772;4:20.7065874971992:5.43610708103893e-06:0.000165041159138554!SUZ12#23512;4:50.1157809110629:1.5827390373096e-07:8.79253629348818e-06!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321677299305749!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000229905935617042!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106693550253638!ZEB1#6935;4:16.8884320175439:1.22862303393937e-05:0.000303850724701857!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248314581904049
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}}
}}

Revision as of 13:52, 19 October 2012


Full id: C2314_salivary_pituitary_cerebellum_breast_small_occipital_brain



Phase1 CAGE Peaks

Hg19::chr14:77648077..77648103,+p3@TMEM63C
Hg19::chr14:77648123..77648162,+p1@TMEM63C
Hg19::chr14:77648167..77648183,+p2@TMEM63C
Hg19::chr14:77648188..77648205,+p4@TMEM63C


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 tube2.57e-3656
neural rod2.57e-3656
future spinal cord2.57e-3656
neural keel2.57e-3656
regional part of nervous system1.35e-3453
regional part of brain1.35e-3453
central nervous system1.90e-3481
brain3.01e-3368
future brain3.01e-3368
nervous system4.88e-3389
regional part of forebrain5.01e-3141
forebrain5.01e-3141
anterior neural tube5.01e-3141
future forebrain5.01e-3141
neural plate4.83e-2782
presumptive neural plate4.83e-2782
telencephalon1.55e-2534
brain grey matter1.88e-2534
gray matter1.88e-2534
neurectoderm2.05e-2586
pre-chordal neural plate2.89e-2561
ecto-epithelium8.64e-25104
cerebral hemisphere2.16e-2432
regional part of telencephalon4.67e-2432
ectoderm-derived structure1.53e-22171
ectoderm1.53e-22171
presumptive ectoderm1.53e-22171
adult organism7.99e-22114
organ system subdivision9.50e-21223
regional part of cerebral cortex5.28e-2022
cerebral cortex3.87e-1925
pallium3.87e-1925
neocortex5.48e-1920
structure with developmental contribution from neural crest2.13e-13132
organ part2.06e-09218
basal ganglion8.61e-089
nuclear complex of neuraxis8.61e-089
aggregate regional part of brain8.61e-089
collection of basal ganglia8.61e-089
cerebral subcortex8.61e-089
neural nucleus9.60e-089
nucleus of brain9.60e-089
organ1.86e-07503
temporal lobe4.71e-076
embryo5.90e-07592
posterior neural tube6.25e-0715
chordal neural plate6.25e-0715
diencephalon7.03e-077
future diencephalon7.03e-077
anatomical cluster9.03e-07373


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#186944.907389214879320.001724022357361790.0106365294766368
EBF1#187948.9064668465690.00015887907472010.00199461133365699
MYC#460945.22228187160940.001344309395272740.00886632958212121
SIN3A#2594245.408884726815140.001168172384885160.00795220673347809
SP1#666745.69838137814090.0009482606065333980.00683474047520646
STAT1#6772420.70658749719925.43610708103893e-060.000165041159138554
SUZ12#23512450.11578091106291.5827390373096e-078.79253629348818e-06
TAF1#687243.343046285745290.008005664898701650.0321677299305749
TRIM28#10155418.59052504526258.36730015875654e-060.000229905935617042
YY1#752844.911170749853860.00171871838055440.0106693550253638
ZEB1#6935416.88843201754391.22862303393937e-050.000303850724701857
ZNF263#1012748.221841637010680.0002187871180958320.00248314581904049



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.