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Difference between revisions of "Coexpression cluster:C1442"

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|ontology_enrichment_celltype=
 
|ontology_enrichment_celltype=
 
|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!2.29e-46!94;UBERON:0001016!2.29e-46!94;UBERON:0001017!4.04e-45!82;UBERON:0005743!4.71e-43!86;UBERON:0001049!2.20e-40!57;UBERON:0005068!2.20e-40!57;UBERON:0006241!2.20e-40!57;UBERON:0007135!2.20e-40!57;UBERON:0000955!3.99e-38!69;UBERON:0006238!3.99e-38!69;UBERON:0002616!2.34e-37!59;UBERON:0002780!8.01e-34!41;UBERON:0001890!8.01e-34!41;UBERON:0006240!8.01e-34!41;UBERON:0003080!1.35e-32!42;UBERON:0002346!6.59e-31!90;UBERON:0002020!2.96e-28!34;UBERON:0003528!2.96e-28!34;UBERON:0001893!3.79e-28!34;UBERON:0003075!5.70e-28!86;UBERON:0007284!5.70e-28!86;UBERON:0002791!3.01e-27!33;UBERON:0000924!7.15e-27!173;UBERON:0006601!7.15e-27!173;UBERON:0001869!1.26e-26!32;UBERON:0007023!8.91e-26!115;UBERON:0004121!1.90e-24!169;UBERON:0003056!4.42e-23!61;UBERON:0002619!1.28e-22!22;UBERON:0000153!2.17e-21!129;UBERON:0007811!2.17e-21!129;UBERON:0001950!1.32e-20!20;UBERON:0000956!5.03e-20!25;UBERON:0000203!5.03e-20!25;UBERON:0000033!5.79e-20!123;UBERON:0002420!6.80e-10!9;UBERON:0007245!6.80e-10!9;UBERON:0010009!6.80e-10!9;UBERON:0010011!6.80e-10!9;UBERON:0000454!6.80e-10!9;UBERON:0002308!1.02e-09!9;UBERON:0000125!1.02e-09!9;UBERON:0003076!5.96e-09!15;UBERON:0003057!5.96e-09!15;UBERON:0001871!9.13e-09!7;UBERON:0000475!1.94e-08!365;UBERON:0009663!5.45e-08!7;UBERON:0000025!8.87e-08!194;UBERON:0004732!2.51e-07!13;UBERON:0000200!4.90e-07!6;UBERON:0001894!4.92e-07!7;UBERON:0006222!4.92e-07!7;UBERON:0000477!4.93e-07!286
+
|ontology_enrichment_uberon=UBERON:0001016!1.64e-73!89;UBERON:0001017!2.60e-73!81;UBERON:0001049!9.16e-70!56;UBERON:0005068!9.16e-70!56;UBERON:0006241!9.16e-70!56;UBERON:0007135!9.16e-70!56;UBERON:0000073!7.79e-65!53;UBERON:0002616!7.79e-65!53;UBERON:0000955!2.03e-61!68;UBERON:0006238!2.03e-61!68;UBERON:0002780!1.88e-56!41;UBERON:0001890!1.88e-56!41;UBERON:0003080!1.88e-56!41;UBERON:0006240!1.88e-56!41;UBERON:0002346!1.18e-48!86;UBERON:0001893!2.66e-48!34;UBERON:0003528!2.80e-48!34;UBERON:0002020!2.80e-48!34;UBERON:0001869!2.12e-45!32;UBERON:0002791!4.76e-45!32;UBERON:0003075!1.31e-44!82;UBERON:0007284!1.31e-44!82;UBERON:0004121!1.86e-41!171;UBERON:0000924!1.86e-41!171;UBERON:0006601!1.86e-41!171;UBERON:0002619!3.04e-38!22;UBERON:0010371!9.37e-37!104;UBERON:0003056!5.76e-36!61;UBERON:0001950!1.88e-34!20;UBERON:0007023!5.88e-33!114;UBERON:0000956!5.95e-33!25;UBERON:0000203!5.95e-33!25;UBERON:0011216!1.20e-32!223;UBERON:0010314!8.04e-28!132;UBERON:0002420!3.11e-17!9;UBERON:0007245!3.11e-17!9;UBERON:0010009!3.11e-17!9;UBERON:0010011!3.11e-17!9;UBERON:0000454!3.11e-17!9;UBERON:0000125!8.50e-17!9;UBERON:0002308!8.50e-17!9;UBERON:0000477!2.35e-16!373;UBERON:0000025!8.35e-16!192;UBERON:0003076!3.24e-14!15;UBERON:0003057!3.24e-14!15;UBERON:0009663!1.11e-13!7;UBERON:0000200!6.66e-12!6;UBERON:0004111!2.37e-11!240;UBERON:0000349!7.79e-11!5;UBERON:0001872!2.07e-10!5;UBERON:0001871!2.16e-10!6;UBERON:0002298!2.69e-10!6;UBERON:0002021!3.93e-10!5;UBERON:0004733!5.92e-10!12;UBERON:0002028!5.92e-10!12;UBERON:0007277!5.92e-10!12;UBERON:0000483!1.52e-09!306;UBERON:0001894!2.20e-09!7;UBERON:0006222!2.20e-09!7;UBERON:0000119!2.72e-09!309;UBERON:0000369!3.80e-09!4;UBERON:0002435!3.80e-09!4;UBERON:0000204!3.80e-09!4;UBERON:0010082!3.80e-09!4;UBERON:0000064!4.25e-09!218;UBERON:0000922!4.46e-09!592;UBERON:0004732!4.79e-09!13;UBERON:0000481!6.08e-09!342;UBERON:0002784!3.40e-08!4;UBERON:0000923!5.84e-08!560;UBERON:0010316!5.84e-08!560;UBERON:0005291!5.84e-08!560;UBERON:0006598!5.84e-08!560;UBERON:0010317!5.84e-08!560;UBERON:0002532!5.84e-08!560;UBERON:0002050!9.77e-08!564;UBERON:0005383!2.73e-07!3;UBERON:0005382!2.73e-07!3;UBERON:0005423!2.79e-07!581;UBERON:0000468!4.77e-07!656;UBERON:0001870!8.42e-07!3
 
|tf_chipseq_enrich=CTCF#10664;4:3.57350424871668:0.0131663500723851:0.0466081562963031!RAD21#5885;4:6.90335593030422:0.0011108515162536:0.00771333166052857!SMC3#9126;4:10.0299552299552:0.000262388182106552:0.00281033323259421!SUZ12#23512;2:16.7052603036876:0.00566023468207957:0.0255621054208124
 
|tf_chipseq_enrich=CTCF#10664;4:3.57350424871668:0.0131663500723851:0.0466081562963031!RAD21#5885;4:6.90335593030422:0.0011108515162536:0.00771333166052857!SMC3#9126;4:10.0299552299552:0.000262388182106552:0.00281033323259421!SUZ12#23512;2:16.7052603036876:0.00566023468207957:0.0255621054208124
 
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}}
 
}}

Revision as of 02:17, 19 October 2012


Full id: C1442_neuroectodermal_parietal_small_caudate_hippocampus_occipital_pineal



Phase1 CAGE Peaks

Hg19::chr18:49866447..49866458,+p6@DCC
Hg19::chr18:49866496..49866548,+p2@DCC
Hg19::chr18:49866551..49866576,+p1@DCC
Hg19::chr18:49866586..49866594,+p10@DCC
Hg19::chr18:49867060..49867094,+p3@DCC
Hg19::chr6:130088699..130088729,-p@chr6:130088699..130088729
-


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 system1.64e-7389
central nervous system2.60e-7381
neural tube9.16e-7056
neural rod9.16e-7056
future spinal cord9.16e-7056
neural keel9.16e-7056
regional part of nervous system7.79e-6553
regional part of brain7.79e-6553
brain2.03e-6168
future brain2.03e-6168
regional part of forebrain1.88e-5641
forebrain1.88e-5641
anterior neural tube1.88e-5641
future forebrain1.88e-5641
neurectoderm1.18e-4886
telencephalon2.66e-4834
brain grey matter2.80e-4834
gray matter2.80e-4834
cerebral hemisphere2.12e-4532
regional part of telencephalon4.76e-4532
neural plate1.31e-4482
presumptive neural plate1.31e-4482
ectoderm-derived structure1.86e-41171
ectoderm1.86e-41171
presumptive ectoderm1.86e-41171
regional part of cerebral cortex3.04e-3822
ecto-epithelium9.37e-37104
pre-chordal neural plate5.76e-3661
neocortex1.88e-3420
adult organism5.88e-33114
cerebral cortex5.95e-3325
pallium5.95e-3325
organ system subdivision1.20e-32223
structure with developmental contribution from neural crest8.04e-28132
basal ganglion3.11e-179
nuclear complex of neuraxis3.11e-179
aggregate regional part of brain3.11e-179
collection of basal ganglia3.11e-179
cerebral subcortex3.11e-179
neural nucleus8.50e-179
nucleus of brain8.50e-179
anatomical cluster2.35e-16373
tube8.35e-16192
posterior neural tube3.24e-1415
chordal neural plate3.24e-1415
telencephalic nucleus1.11e-137
gyrus6.66e-126
anatomical conduit2.37e-11240
limbic system7.79e-115
parietal lobe2.07e-105
temporal lobe2.16e-106
brainstem2.69e-106
occipital lobe3.93e-105
segmental subdivision of hindbrain5.92e-1012
hindbrain5.92e-1012
presumptive hindbrain5.92e-1012
epithelium1.52e-09306
diencephalon2.20e-097
future diencephalon2.20e-097
cell layer2.72e-09309
corpus striatum3.80e-094
striatum3.80e-094
ventral part of telencephalon3.80e-094
future corpus striatum3.80e-094
organ part4.25e-09218
embryo4.46e-09592
segmental subdivision of nervous system4.79e-0913
multi-tissue structure6.08e-09342
regional part of diencephalon3.40e-084
germ layer5.84e-08560
germ layer / neural crest5.84e-08560
embryonic tissue5.84e-08560
presumptive structure5.84e-08560
germ layer / neural crest derived structure5.84e-08560
epiblast (generic)5.84e-08560
embryonic structure9.77e-08564
caudate-putamen2.73e-073
dorsal striatum2.73e-073
developing anatomical structure2.79e-07581
multi-cellular organism4.77e-07656
frontal cortex8.42e-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#1066443.573504248716680.01316635007238510.0466081562963031
RAD21#588546.903355930304220.00111085151625360.00771333166052857
SMC3#9126410.02995522995520.0002623881821065520.00281033323259421
SUZ12#23512216.70526030368760.005660234682079570.0255621054208124



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.