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Coexpression cluster:C4147: Difference between revisions

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|full_id=C4147_extraskeletal_occipital_small_brain_medial_temporal_insula
|full_id=C4147_extraskeletal_occipital_small_brain_medial_temporal_insula
|id=C4147
|id=C4147
|ontology_enrichment_celltype=CL:0002319!1.19e-07!25
|ontology_enrichment_celltype=CL:0002319!1.58e-07!25
|ontology_enrichment_disease=DOID:0050687!1.50e-09!143;DOID:305!2.40e-08!106
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!8.60e-33!86;UBERON:0000073!5.47e-32!94;UBERON:0001016!5.47e-32!94;UBERON:0001017!1.94e-31!82;UBERON:0001049!2.06e-26!57;UBERON:0005068!2.06e-26!57;UBERON:0006241!2.06e-26!57;UBERON:0007135!2.06e-26!57;UBERON:0002346!4.70e-26!90;UBERON:0003075!7.85e-26!86;UBERON:0007284!7.85e-26!86;UBERON:0000955!9.52e-26!69;UBERON:0006238!9.52e-26!69;UBERON:0007023!2.64e-25!115;UBERON:0003080!3.23e-25!42;UBERON:0002780!1.01e-24!41;UBERON:0001890!1.01e-24!41;UBERON:0006240!1.01e-24!41;UBERON:0001893!1.30e-23!34;UBERON:0002020!2.70e-23!34;UBERON:0003528!2.70e-23!34;UBERON:0001869!3.67e-23!32;UBERON:0002791!7.34e-23!33;UBERON:0002616!9.03e-23!59;UBERON:0003056!1.58e-22!61;UBERON:0000477!1.12e-20!286;UBERON:0000956!7.81e-19!25;UBERON:0000203!7.81e-19!25;UBERON:0000033!8.59e-19!123;UBERON:0000924!1.69e-18!173;UBERON:0006601!1.69e-18!173;UBERON:0000153!3.01e-18!129;UBERON:0007811!3.01e-18!129;UBERON:0004111!4.63e-18!241;UBERON:0004121!4.83e-18!169;UBERON:0002619!4.35e-17!22;UBERON:0000025!2.09e-16!194;UBERON:0001950!7.40e-16!20;UBERON:0000119!2.27e-14!312;UBERON:0000483!3.42e-14!309;UBERON:0000064!5.98e-14!219;UBERON:0000481!6.77e-14!347;UBERON:0000475!4.91e-13!365;UBERON:0000468!8.28e-12!659;UBERON:0000480!9.68e-10!626;UBERON:0000467!1.38e-09!625;UBERON:0000922!4.28e-09!612;UBERON:0002050!2.51e-07!605;UBERON:0005423!2.51e-07!605;UBERON:0000923!3.80e-07!604;UBERON:0005291!3.80e-07!604;UBERON:0006598!3.80e-07!604;UBERON:0002532!3.80e-07!604;UBERON:0000062!8.60e-07!511
|ontology_enrichment_uberon=UBERON:0001017!3.92e-36!81;UBERON:0001016!2.15e-35!89;UBERON:0001049!3.25e-33!56;UBERON:0005068!3.25e-33!56;UBERON:0006241!3.25e-33!56;UBERON:0007135!3.25e-33!56;UBERON:0000955!9.29e-32!68;UBERON:0006238!9.29e-32!68;UBERON:0007023!9.97e-32!114;UBERON:0002780!2.06e-31!41;UBERON:0001890!2.06e-31!41;UBERON:0003080!2.06e-31!41;UBERON:0006240!2.06e-31!41;UBERON:0000073!2.15e-31!53;UBERON:0002616!2.15e-31!53;UBERON:0001893!9.16e-31!34;UBERON:0003528!1.97e-30!34;UBERON:0002020!1.97e-30!34;UBERON:0001869!1.05e-29!32;UBERON:0002791!2.87e-29!32;UBERON:0002346!1.02e-25!86;UBERON:0003075!3.91e-25!82;UBERON:0007284!3.91e-25!82;UBERON:0011216!1.44e-24!223;UBERON:0000956!7.25e-24!25;UBERON:0000203!7.25e-24!25;UBERON:0003056!2.14e-23!61;UBERON:0000477!2.38e-22!373;UBERON:0002619!8.53e-22!22;UBERON:0001950!3.11e-20!20;UBERON:0004121!5.73e-20!171;UBERON:0000924!5.73e-20!171;UBERON:0006601!5.73e-20!171;UBERON:0010314!9.11e-19!132;UBERON:0010371!1.16e-17!104;UBERON:0004111!3.76e-15!240;UBERON:0000025!7.37e-15!192;UBERON:0000481!5.33e-14!342;UBERON:0000064!1.18e-13!218;UBERON:0000468!5.10e-11!656;UBERON:0000119!3.79e-10!309;UBERON:0000483!5.62e-10!306;UBERON:0002420!1.53e-08!9;UBERON:0007245!1.53e-08!9;UBERON:0010009!1.53e-08!9;UBERON:0010011!1.53e-08!9;UBERON:0000454!1.53e-08!9;UBERON:0000467!2.12e-08!624;UBERON:0000922!2.41e-08!592;UBERON:0000480!2.73e-08!625;UBERON:0000125!5.30e-08!9;UBERON:0002308!5.30e-08!9;UBERON:0001871!1.22e-07!6;UBERON:0000062!1.66e-07!503;UBERON:0000200!4.45e-07!6;UBERON:0005423!6.40e-07!581;UBERON:0009663!7.26e-07!7
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280113675321078!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326180963670715!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323077346596606!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108899624435329!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295117886583654!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000738442039317454!SREBF1#6720;3:47.0058494404883:9.62099323994382e-06:0.000254962424000632!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00544213658394299!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00616935603361499!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330057711970017!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109640163705534
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280113675321078!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326180963670715!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323077346596606!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108899624435329!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295117886583654!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000738442039317454!SREBF1#6720;3:47.0058494404883:9.62099323994382e-06:0.000254962424000632!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00544213658394299!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00616935603361499!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330057711970017!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109640163705534
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6,0.205954,0.361435
}}
}}

Revision as of 15:43, 19 October 2012


Full id: C4147_extraskeletal_occipital_small_brain_medial_temporal_insula



Phase1 CAGE Peaks

Hg19::chr2:175869890..175869933,-p6@CHN1
Hg19::chr2:175869936..175869949,-p14@CHN1
Hg19::chr2:175869984..175869996,-p9@CHN1


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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
neural cell1.58e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system3.92e-3681
nervous system2.15e-3589
neural tube3.25e-3356
neural rod3.25e-3356
future spinal cord3.25e-3356
neural keel3.25e-3356
brain9.29e-3268
future brain9.29e-3268
adult organism9.97e-32114
regional part of forebrain2.06e-3141
forebrain2.06e-3141
anterior neural tube2.06e-3141
future forebrain2.06e-3141
regional part of nervous system2.15e-3153
regional part of brain2.15e-3153
telencephalon9.16e-3134
brain grey matter1.97e-3034
gray matter1.97e-3034
cerebral hemisphere1.05e-2932
regional part of telencephalon2.87e-2932
neurectoderm1.02e-2586
neural plate3.91e-2582
presumptive neural plate3.91e-2582
organ system subdivision1.44e-24223
cerebral cortex7.25e-2425
pallium7.25e-2425
pre-chordal neural plate2.14e-2361
anatomical cluster2.38e-22373
regional part of cerebral cortex8.53e-2222
neocortex3.11e-2020
ectoderm-derived structure5.73e-20171
ectoderm5.73e-20171
presumptive ectoderm5.73e-20171
structure with developmental contribution from neural crest9.11e-19132
ecto-epithelium1.16e-17104
anatomical conduit3.76e-15240
tube7.37e-15192
multi-tissue structure5.33e-14342
organ part1.18e-13218
multi-cellular organism5.10e-11656
cell layer3.79e-10309
epithelium5.62e-10306
basal ganglion1.53e-089
nuclear complex of neuraxis1.53e-089
aggregate regional part of brain1.53e-089
collection of basal ganglia1.53e-089
cerebral subcortex1.53e-089
anatomical system2.12e-08624
embryo2.41e-08592
anatomical group2.73e-08625
neural nucleus5.30e-089
nucleus of brain5.30e-089
temporal lobe1.22e-076
organ1.66e-07503
gyrus4.45e-076
developing anatomical structure6.40e-07581
telencephalic nucleus7.26e-077


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#1066435.360256373075030.0064925092527670.0280113675321078
E2F1#186934.907389214879320.008460985347239390.0326180963670715
E2F6#187635.017155731697390.00791769806886330.0323077346596606
HMGN3#932438.178547723350590.001827766942164210.0108899624435329
MYC#460935.22228187160940.007020843755740150.0295117886583654
NANOG#79923329.24477848101273.99627955670032e-050.000738442039317454
SREBF1#6720347.00584944048839.62099323994382e-060.000254962424000632
TAF7#6879311.43306940492390.0006690181981945830.00544213658394299
TFAP2C#7022310.80922860986020.0007916746575753130.00616935603361499
YY1#752834.911170749853860.008441455341808260.0330057711970017
ZNF263#1012738.221841637010680.001799043925565870.0109640163705534



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.