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Coexpression cluster:C2676: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.81e-52!82;UBERON:0001049!2.57e-51!57;UBERON:0005068!2.57e-51!57;UBERON:0006241!2.57e-51!57;UBERON:0007135!2.57e-51!57;UBERON:0005743!1.42e-50!86;UBERON:0000073!6.24e-50!94;UBERON:0001016!6.24e-50!94;UBERON:0007023!1.12e-49!115;UBERON:0000955!2.85e-45!69;UBERON:0006238!2.85e-45!69;UBERON:0002616!1.86e-44!59;UBERON:0002780!1.19e-37!41;UBERON:0001890!1.19e-37!41;UBERON:0006240!1.19e-37!41;UBERON:0003075!2.99e-37!86;UBERON:0007284!2.99e-37!86;UBERON:0003080!2.16e-36!42;UBERON:0002346!4.05e-36!90;UBERON:0001893!4.90e-34!34;UBERON:0002020!7.86e-34!34;UBERON:0003528!7.86e-34!34;UBERON:0002791!7.80e-33!33;UBERON:0001869!6.47e-32!32;UBERON:0002619!5.41e-27!22;UBERON:0004121!6.05e-27!169;UBERON:0000924!1.13e-26!173;UBERON:0006601!1.13e-26!173;UBERON:0003056!5.92e-25!61;UBERON:0001950!8.94e-25!20;UBERON:0000956!1.03e-24!25;UBERON:0000203!1.03e-24!25;UBERON:0000153!6.13e-24!129;UBERON:0007811!6.13e-24!129;UBERON:0000033!1.90e-23!123;UBERON:0003076!1.28e-15!15;UBERON:0003057!1.28e-15!15;UBERON:0004732!6.48e-14!13;UBERON:0000025!7.38e-14!194;UBERON:0000477!4.50e-13!286;UBERON:0004733!8.22e-13!12;UBERON:0002028!8.22e-13!12;UBERON:0007277!8.22e-13!12;UBERON:0004111!6.06e-12!241;UBERON:0000064!4.20e-11!219;UBERON:0002420!8.70e-11!9;UBERON:0007245!8.70e-11!9;UBERON:0010009!8.70e-11!9;UBERON:0010011!8.70e-11!9;UBERON:0000454!8.70e-11!9;UBERON:0002308!1.70e-10!9;UBERON:0000125!1.70e-10!9;UBERON:0001871!2.97e-10!7;UBERON:0002680!6.50e-10!9;UBERON:0001895!6.50e-10!9;UBERON:0010092!6.50e-10!9;UBERON:0000483!1.92e-09!309;UBERON:0000119!4.15e-09!312;UBERON:0000468!4.27e-09!659;UBERON:0000200!1.22e-08!6;UBERON:0009663!1.55e-08!7;UBERON:0000475!3.49e-08!365;UBERON:0000467!5.67e-08!625;UBERON:0000480!6.85e-08!626;UBERON:0000922!8.63e-08!612;UBERON:0000481!1.35e-07!347;UBERON:0000062!2.00e-07!511;UBERON:0002298!2.90e-07!8;UBERON:0001872!3.05e-07!5;UBERON:0000349!3.57e-07!5;UBERON:0002021!5.63e-07!5;UBERON:0002037!6.33e-07!6;UBERON:0006215!6.33e-07!6;UBERON:0002050!9.25e-07!605;UBERON:0005423!9.25e-07!605
|ontology_enrichment_uberon=UBERON:0001049!6.40e-68!56;UBERON:0005068!6.40e-68!56;UBERON:0006241!6.40e-68!56;UBERON:0007135!6.40e-68!56;UBERON:0001016!1.58e-66!89;UBERON:0001017!4.21e-66!81;UBERON:0000073!1.62e-63!53;UBERON:0002616!1.62e-63!53;UBERON:0000955!8.45e-55!68;UBERON:0006238!8.45e-55!68;UBERON:0007023!7.15e-52!114;UBERON:0003075!6.94e-49!82;UBERON:0007284!6.94e-49!82;UBERON:0002780!3.65e-48!41;UBERON:0001890!3.65e-48!41;UBERON:0003080!3.65e-48!41;UBERON:0006240!3.65e-48!41;UBERON:0002346!7.41e-48!86;UBERON:0001893!3.97e-47!34;UBERON:0003528!7.60e-47!34;UBERON:0002020!7.60e-47!34;UBERON:0001869!5.32e-44!32;UBERON:0002791!7.28e-44!32;UBERON:0010371!2.67e-36!104;UBERON:0002619!7.61e-36!22;UBERON:0003056!4.56e-34!61;UBERON:0000956!1.78e-33!25;UBERON:0000203!1.78e-33!25;UBERON:0011216!1.00e-32!223;UBERON:0001950!1.50e-32!20;UBERON:0010314!4.04e-31!132;UBERON:0004121!1.03e-30!171;UBERON:0000924!1.03e-30!171;UBERON:0006601!1.03e-30!171;UBERON:0000477!7.68e-21!373;UBERON:0003076!4.41e-20!15;UBERON:0003057!4.41e-20!15;UBERON:0000025!9.93e-18!192;UBERON:0004732!1.27e-17!13;UBERON:0004733!5.46e-16!12;UBERON:0002028!5.46e-16!12;UBERON:0007277!5.46e-16!12;UBERON:0002420!4.08e-15!9;UBERON:0007245!4.08e-15!9;UBERON:0010009!4.08e-15!9;UBERON:0010011!4.08e-15!9;UBERON:0000454!4.08e-15!9;UBERON:0000125!1.16e-14!9;UBERON:0002308!1.16e-14!9;UBERON:0000064!5.29e-12!218;UBERON:0004111!6.54e-12!240;UBERON:0000200!6.55e-12!6;UBERON:0009663!8.64e-12!7;UBERON:0002680!9.75e-12!9;UBERON:0001895!9.75e-12!9;UBERON:0010092!9.75e-12!9;UBERON:0000481!5.56e-11!342;UBERON:0000483!1.52e-10!306;UBERON:0002298!2.40e-10!6;UBERON:0000119!2.89e-10!309;UBERON:0000349!6.91e-10!5;UBERON:0001872!7.54e-10!5;UBERON:0001871!1.00e-09!6;UBERON:0002021!1.69e-09!5;UBERON:0000922!3.11e-08!592;UBERON:0000468!8.42e-08!656;UBERON:0000062!1.31e-07!503;UBERON:0002037!1.98e-07!6;UBERON:0006215!1.98e-07!6;UBERON:0000923!2.18e-07!560;UBERON:0010316!2.18e-07!560;UBERON:0005291!2.18e-07!560;UBERON:0006598!2.18e-07!560;UBERON:0010317!2.18e-07!560;UBERON:0002532!2.18e-07!560;UBERON:0000369!2.46e-07!4;UBERON:0002435!2.46e-07!4;UBERON:0000204!2.46e-07!4;UBERON:0010082!2.46e-07!4;UBERON:0000467!3.17e-07!624;UBERON:0000480!3.60e-07!625;UBERON:0002050!3.68e-07!564;UBERON:0005423!4.56e-07!581;UBERON:0001870!7.36e-07!3
|tf_chipseq_enrich=NR3C1#2908;3:11.2297674983798:0.00113167206806385:0.00775529521761948!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.00499439019940564
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}}
}}

Revision as of 14:17, 19 October 2012


Full id: C2676_small_cerebellum_medial_carcinoid_frontal_amygdala_occipital



Phase1 CAGE Peaks

Hg19::chr2:183387244..183387259,-p3@PDE1A
Hg19::chr2:183387381..183387407,-p2@PDE1A
Hg19::chr2:183387430..183387463,-p4@PDE1A
Hg19::chr6:35026025..35026047,+p2@ANKS1A


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:0004117calmodulin-dependent cyclic-nucleotide phosphodiesterase activity0.00264916256568538
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0138255559698253
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0138255559698253
GO:0008081phosphoric diester hydrolase activity0.024851546815114
GO:0005516calmodulin binding0.024851546815114



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 tube6.40e-6856
neural rod6.40e-6856
future spinal cord6.40e-6856
neural keel6.40e-6856
nervous system1.58e-6689
central nervous system4.21e-6681
regional part of nervous system1.62e-6353
regional part of brain1.62e-6353
brain8.45e-5568
future brain8.45e-5568
adult organism7.15e-52114
neural plate6.94e-4982
presumptive neural plate6.94e-4982
regional part of forebrain3.65e-4841
forebrain3.65e-4841
anterior neural tube3.65e-4841
future forebrain3.65e-4841
neurectoderm7.41e-4886
telencephalon3.97e-4734
brain grey matter7.60e-4734
gray matter7.60e-4734
cerebral hemisphere5.32e-4432
regional part of telencephalon7.28e-4432
ecto-epithelium2.67e-36104
regional part of cerebral cortex7.61e-3622
pre-chordal neural plate4.56e-3461
cerebral cortex1.78e-3325
pallium1.78e-3325
organ system subdivision1.00e-32223
neocortex1.50e-3220
structure with developmental contribution from neural crest4.04e-31132
ectoderm-derived structure1.03e-30171
ectoderm1.03e-30171
presumptive ectoderm1.03e-30171
anatomical cluster7.68e-21373
posterior neural tube4.41e-2015
chordal neural plate4.41e-2015
tube9.93e-18192
segmental subdivision of nervous system1.27e-1713
segmental subdivision of hindbrain5.46e-1612
hindbrain5.46e-1612
presumptive hindbrain5.46e-1612
basal ganglion4.08e-159
nuclear complex of neuraxis4.08e-159
aggregate regional part of brain4.08e-159
collection of basal ganglia4.08e-159
cerebral subcortex4.08e-159
neural nucleus1.16e-149
nucleus of brain1.16e-149
organ part5.29e-12218
anatomical conduit6.54e-12240
gyrus6.55e-126
telencephalic nucleus8.64e-127
regional part of metencephalon9.75e-129
metencephalon9.75e-129
future metencephalon9.75e-129
multi-tissue structure5.56e-11342
epithelium1.52e-10306
brainstem2.40e-106
cell layer2.89e-10309
limbic system6.91e-105
parietal lobe7.54e-105
temporal lobe1.00e-096
occipital lobe1.69e-095
embryo3.11e-08592
multi-cellular organism8.42e-08656
organ1.31e-07503
cerebellum1.98e-076
rhombic lip1.98e-076
germ layer2.18e-07560
germ layer / neural crest2.18e-07560
embryonic tissue2.18e-07560
presumptive structure2.18e-07560
germ layer / neural crest derived structure2.18e-07560
epiblast (generic)2.18e-07560
corpus striatum2.46e-074
striatum2.46e-074
ventral part of telencephalon2.46e-074
future corpus striatum2.46e-074
anatomical system3.17e-07624
anatomical group3.60e-07625
embryonic structure3.68e-07564
developing anatomical structure4.56e-07581
frontal cortex7.36e-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
NR3C1#2908311.22976749837980.001131672068063850.00775529521761948
TRIM28#10155313.94289378394690.0005972858184258420.00499439019940564



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.