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Coexpression cluster:C1596: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.47e-51!115;UBERON:0005743!4.64e-27!86;UBERON:0001049!2.73e-26!57;UBERON:0005068!2.73e-26!57;UBERON:0006241!2.73e-26!57;UBERON:0007135!2.73e-26!57;UBERON:0001017!5.87e-26!82;UBERON:0000073!1.23e-25!94;UBERON:0001016!1.23e-25!94;UBERON:0003075!6.63e-24!86;UBERON:0007284!6.63e-24!86;UBERON:0000955!8.55e-24!69;UBERON:0006238!8.55e-24!69;UBERON:0002616!3.17e-22!59;UBERON:0002346!8.33e-21!90;UBERON:0003080!1.62e-20!42;UBERON:0002780!5.33e-20!41;UBERON:0001890!5.33e-20!41;UBERON:0006240!5.33e-20!41;UBERON:0000033!4.86e-18!123;UBERON:0000153!1.30e-17!129;UBERON:0007811!1.30e-17!129;UBERON:0004121!1.34e-17!169;UBERON:0003056!1.30e-16!61;UBERON:0001893!3.51e-16!34;UBERON:0002020!3.71e-16!34;UBERON:0003528!3.71e-16!34;UBERON:0000924!7.32e-16!173;UBERON:0006601!7.32e-16!173;UBERON:0002791!1.42e-15!33;UBERON:0001869!7.51e-15!32;UBERON:0004111!2.85e-14!241;UBERON:0000025!1.96e-13!194;UBERON:0000475!4.11e-13!365;UBERON:0000477!6.76e-13!286;UBERON:0000956!7.93e-11!25;UBERON:0000203!7.93e-11!25;UBERON:0002619!1.36e-10!22;UBERON:0000468!2.21e-10!659;UBERON:0000483!4.52e-10!309;UBERON:0000119!5.22e-10!312;UBERON:0001950!1.70e-09!20;UBERON:0000480!9.57e-09!626;UBERON:0000467!1.41e-08!625;UBERON:0000481!2.46e-08!347;UBERON:0000062!9.69e-08!511;UBERON:0002308!4.87e-07!9;UBERON:0000125!4.87e-07!9;UBERON:0003076!5.50e-07!15;UBERON:0003057!5.50e-07!15;UBERON:0002420!7.58e-07!9;UBERON:0007245!7.58e-07!9;UBERON:0010009!7.58e-07!9;UBERON:0010011!7.58e-07!9;UBERON:0000454!7.58e-07!9
|ontology_enrichment_uberon=UBERON:0007023!1.91e-86!114;UBERON:0001049!2.19e-47!56;UBERON:0005068!2.19e-47!56;UBERON:0006241!2.19e-47!56;UBERON:0007135!2.19e-47!56;UBERON:0000073!1.44e-43!53;UBERON:0002616!1.44e-43!53;UBERON:0003075!6.24e-41!82;UBERON:0007284!6.24e-41!82;UBERON:0001017!2.69e-40!81;UBERON:0000955!2.03e-39!68;UBERON:0006238!2.03e-39!68;UBERON:0001016!1.13e-38!89;UBERON:0002346!4.28e-38!86;UBERON:0002780!1.56e-35!41;UBERON:0001890!1.56e-35!41;UBERON:0003080!1.56e-35!41;UBERON:0006240!1.56e-35!41;UBERON:0010314!2.00e-33!132;UBERON:0010371!1.59e-30!104;UBERON:0003528!1.06e-27!34;UBERON:0002020!1.06e-27!34;UBERON:0001893!1.25e-27!34;UBERON:0003056!3.97e-27!61;UBERON:0002791!3.71e-25!32;UBERON:0001869!5.57e-25!32;UBERON:0004121!7.95e-24!171;UBERON:0000924!7.95e-24!171;UBERON:0006601!7.95e-24!171;UBERON:0011216!6.41e-19!223;UBERON:0002619!1.70e-18!22;UBERON:0000956!4.01e-17!25;UBERON:0000203!4.01e-17!25;UBERON:0001950!3.04e-16!20;UBERON:0000025!1.77e-15!192;UBERON:0000481!4.32e-15!342;UBERON:0000119!5.78e-15!309;UBERON:0000483!7.47e-15!306;UBERON:0000477!1.41e-14!373;UBERON:0004111!2.76e-13!240;UBERON:0000125!9.40e-13!9;UBERON:0002308!9.40e-13!9;UBERON:0003076!1.22e-12!15;UBERON:0003057!1.22e-12!15;UBERON:0002420!2.56e-12!9;UBERON:0007245!2.56e-12!9;UBERON:0010009!2.56e-12!9;UBERON:0010011!2.56e-12!9;UBERON:0000454!2.56e-12!9;UBERON:0004732!2.06e-10!13;UBERON:0000064!3.38e-10!218;UBERON:0009663!4.17e-10!7;UBERON:0002298!1.53e-09!6;UBERON:0001894!1.80e-09!7;UBERON:0006222!1.80e-09!7;UBERON:0004733!3.88e-09!12;UBERON:0002028!3.88e-09!12;UBERON:0007277!3.88e-09!12;UBERON:0000200!9.19e-09!6;UBERON:0000922!1.45e-08!592;UBERON:0000062!1.63e-08!503;UBERON:0000923!2.36e-08!560;UBERON:0010316!2.36e-08!560;UBERON:0005291!2.36e-08!560;UBERON:0006598!2.36e-08!560;UBERON:0010317!2.36e-08!560;UBERON:0002532!2.36e-08!560;UBERON:0002050!4.61e-08!564;UBERON:0005423!5.10e-08!581;UBERON:0000468!8.70e-08!656;UBERON:0000349!2.26e-07!5
|tf_chipseq_enrich=SETDB1#9869;2:16.1280104712042:0.0058505784665934:0.0262661120436981
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}}
}}

Revision as of 11:28, 19 October 2012


Full id: C1596_heart_optic_left_corpus_substantia_spinal_medulla



Phase1 CAGE Peaks

Hg19::chr10:88426533..88426556,+p2@LDB3
Hg19::chr11:111781454..111781513,-p4@CRYAB
Hg19::chr20:44036838..44036847,+p22@DBNDD2
Hg19::chrX:10124977..10125036,+p2@CLCN4
Hg19::chrX:10125040..10125059,+p3@CLCN4


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


GO IDGO nameFDR corrected p-value
GO:0032387negative regulation of intracellular transport0.0240187203952639



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 organism1.91e-86114
neural tube2.19e-4756
neural rod2.19e-4756
future spinal cord2.19e-4756
neural keel2.19e-4756
regional part of nervous system1.44e-4353
regional part of brain1.44e-4353
neural plate6.24e-4182
presumptive neural plate6.24e-4182
central nervous system2.69e-4081
brain2.03e-3968
future brain2.03e-3968
nervous system1.13e-3889
neurectoderm4.28e-3886
regional part of forebrain1.56e-3541
forebrain1.56e-3541
anterior neural tube1.56e-3541
future forebrain1.56e-3541
structure with developmental contribution from neural crest2.00e-33132
ecto-epithelium1.59e-30104
brain grey matter1.06e-2734
gray matter1.06e-2734
telencephalon1.25e-2734
pre-chordal neural plate3.97e-2761
regional part of telencephalon3.71e-2532
cerebral hemisphere5.57e-2532
ectoderm-derived structure7.95e-24171
ectoderm7.95e-24171
presumptive ectoderm7.95e-24171
organ system subdivision6.41e-19223
regional part of cerebral cortex1.70e-1822
cerebral cortex4.01e-1725
pallium4.01e-1725
neocortex3.04e-1620
tube1.77e-15192
multi-tissue structure4.32e-15342
cell layer5.78e-15309
epithelium7.47e-15306
anatomical cluster1.41e-14373
anatomical conduit2.76e-13240
neural nucleus9.40e-139
nucleus of brain9.40e-139
posterior neural tube1.22e-1215
chordal neural plate1.22e-1215
basal ganglion2.56e-129
nuclear complex of neuraxis2.56e-129
aggregate regional part of brain2.56e-129
collection of basal ganglia2.56e-129
cerebral subcortex2.56e-129
segmental subdivision of nervous system2.06e-1013
organ part3.38e-10218
telencephalic nucleus4.17e-107
brainstem1.53e-096
diencephalon1.80e-097
future diencephalon1.80e-097
segmental subdivision of hindbrain3.88e-0912
hindbrain3.88e-0912
presumptive hindbrain3.88e-0912
gyrus9.19e-096
embryo1.45e-08592
organ1.63e-08503
germ layer2.36e-08560
germ layer / neural crest2.36e-08560
embryonic tissue2.36e-08560
presumptive structure2.36e-08560
germ layer / neural crest derived structure2.36e-08560
epiblast (generic)2.36e-08560
embryonic structure4.61e-08564
developing anatomical structure5.10e-08581
multi-cellular organism8.70e-08656
limbic system2.26e-075


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
SETDB1#9869216.12801047120420.00585057846659340.0262661120436981



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.