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Coexpression cluster:C3010: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!3.69e-83!82;UBERON:0005743!3.79e-81!86;UBERON:0001049!1.43e-77!57;UBERON:0005068!1.43e-77!57;UBERON:0006241!1.43e-77!57;UBERON:0007135!1.43e-77!57;UBERON:0000073!7.67e-72!94;UBERON:0001016!7.67e-72!94;UBERON:0002616!4.11e-65!59;UBERON:0000955!6.16e-61!69;UBERON:0006238!6.16e-61!69;UBERON:0002780!1.01e-60!41;UBERON:0001890!1.01e-60!41;UBERON:0006240!1.01e-60!41;UBERON:0003075!1.21e-59!86;UBERON:0007284!1.21e-59!86;UBERON:0003080!5.05e-59!42;UBERON:0002346!2.86e-56!90;UBERON:0001869!9.19e-56!32;UBERON:0002020!1.99e-55!34;UBERON:0003528!1.99e-55!34;UBERON:0001893!2.40e-55!34;UBERON:0002791!1.72e-53!33;UBERON:0003056!3.98e-46!61;UBERON:0002619!2.68e-44!22;UBERON:0000956!1.05e-41!25;UBERON:0000203!1.05e-41!25;UBERON:0001950!6.77e-41!20;UBERON:0004121!6.11e-39!169;UBERON:0000924!1.30e-37!173;UBERON:0006601!1.30e-37!173;UBERON:0000033!1.09e-36!123;UBERON:0007023!1.90e-35!115;UBERON:0000153!3.02e-34!129;UBERON:0007811!3.02e-34!129;UBERON:0003076!9.76e-19!15;UBERON:0003057!9.76e-19!15;UBERON:0001871!3.68e-16!7;UBERON:0000025!1.10e-15!194;UBERON:0002308!7.17e-15!9;UBERON:0000125!7.17e-15!9;UBERON:0002420!7.99e-15!9;UBERON:0007245!7.99e-15!9;UBERON:0010009!7.99e-15!9;UBERON:0010011!7.99e-15!9;UBERON:0000454!7.99e-15!9;UBERON:0004733!4.65e-14!12;UBERON:0002028!4.65e-14!12;UBERON:0007277!4.65e-14!12;UBERON:0004732!8.34e-13!13;UBERON:0000200!1.18e-12!6;UBERON:0009663!1.47e-11!7;UBERON:0001872!2.60e-11!5;UBERON:0002021!6.44e-11!5;UBERON:0000349!2.96e-10!5;UBERON:0000369!5.99e-10!4;UBERON:0002435!5.99e-10!4;UBERON:0000204!5.99e-10!4;UBERON:0010082!5.99e-10!4;UBERON:0004111!6.27e-10!241;UBERON:0000922!8.47e-10!612;UBERON:0002680!1.40e-09!9;UBERON:0001895!1.40e-09!9;UBERON:0010092!1.40e-09!9;UBERON:0000483!3.59e-09!309;UBERON:0000064!5.29e-09!219;UBERON:0000119!6.11e-09!312;UBERON:0000477!2.70e-08!286;UBERON:0000473!2.90e-08!8;UBERON:0002298!3.61e-08!8;UBERON:0005383!5.78e-08!3;UBERON:0005382!5.78e-08!3;UBERON:0000468!2.14e-07!659;UBERON:0001894!3.27e-07!7;UBERON:0006222!3.27e-07!7;UBERON:0002771!5.52e-07!3;UBERON:0000923!6.77e-07!604;UBERON:0005291!6.77e-07!604;UBERON:0006598!6.77e-07!604;UBERON:0002532!6.77e-07!604;UBERON:0000475!6.96e-07!365;UBERON:0002050!7.55e-07!605;UBERON:0005423!7.55e-07!605
|ontology_enrichment_uberon=UBERON:0001017!3.69e-83!82;UBERON:0005743!3.79e-81!86;UBERON:0001049!1.43e-77!57;UBERON:0005068!1.43e-77!57;UBERON:0006241!1.43e-77!57;UBERON:0007135!1.43e-77!57;UBERON:0000073!7.67e-72!94;UBERON:0001016!7.67e-72!94;UBERON:0002616!4.11e-65!59;UBERON:0000955!6.16e-61!69;UBERON:0006238!6.16e-61!69;UBERON:0002780!1.01e-60!41;UBERON:0001890!1.01e-60!41;UBERON:0006240!1.01e-60!41;UBERON:0003075!1.21e-59!86;UBERON:0007284!1.21e-59!86;UBERON:0003080!5.05e-59!42;UBERON:0002346!2.86e-56!90;UBERON:0001869!9.19e-56!32;UBERON:0002020!1.99e-55!34;UBERON:0003528!1.99e-55!34;UBERON:0001893!2.40e-55!34;UBERON:0002791!1.72e-53!33;UBERON:0003056!3.98e-46!61;UBERON:0002619!2.68e-44!22;UBERON:0000956!1.05e-41!25;UBERON:0000203!1.05e-41!25;UBERON:0001950!6.77e-41!20;UBERON:0004121!6.11e-39!169;UBERON:0000924!1.30e-37!173;UBERON:0006601!1.30e-37!173;UBERON:0000033!1.09e-36!123;UBERON:0007023!1.90e-35!115;UBERON:0000153!3.02e-34!129;UBERON:0007811!3.02e-34!129;UBERON:0003076!9.76e-19!15;UBERON:0003057!9.76e-19!15;UBERON:0001871!3.68e-16!7;UBERON:0000025!1.10e-15!194;UBERON:0002308!7.17e-15!9;UBERON:0000125!7.17e-15!9;UBERON:0002420!7.99e-15!9;UBERON:0007245!7.99e-15!9;UBERON:0010009!7.99e-15!9;UBERON:0010011!7.99e-15!9;UBERON:0000454!7.99e-15!9;UBERON:0004733!4.65e-14!12;UBERON:0002028!4.65e-14!12;UBERON:0007277!4.65e-14!12;UBERON:0004732!8.34e-13!13;UBERON:0000200!1.18e-12!6;UBERON:0009663!1.47e-11!7;UBERON:0001872!2.60e-11!5;UBERON:0002021!6.44e-11!5;UBERON:0000349!2.96e-10!5;UBERON:0000369!5.99e-10!4;UBERON:0002435!5.99e-10!4;UBERON:0000204!5.99e-10!4;UBERON:0010082!5.99e-10!4;UBERON:0004111!6.27e-10!241;UBERON:0000922!8.47e-10!612;UBERON:0002680!1.40e-09!9;UBERON:0001895!1.40e-09!9;UBERON:0010092!1.40e-09!9;UBERON:0000483!3.59e-09!309;UBERON:0000064!5.29e-09!219;UBERON:0000119!6.11e-09!312;UBERON:0000477!2.70e-08!286;UBERON:0000473!2.90e-08!8;UBERON:0002298!3.61e-08!8;UBERON:0005383!5.78e-08!3;UBERON:0005382!5.78e-08!3;UBERON:0000468!2.14e-07!659;UBERON:0001894!3.27e-07!7;UBERON:0006222!3.27e-07!7;UBERON:0002771!5.52e-07!3;UBERON:0000923!6.77e-07!604;UBERON:0005291!6.77e-07!604;UBERON:0006598!6.77e-07!604;UBERON:0002532!6.77e-07!604;UBERON:0000475!6.96e-07!365;UBERON:0002050!7.55e-07!605;UBERON:0005423!7.55e-07!605
|tf_chipseq_enrich=CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000128943022088346!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278171633512362!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0318897693606287!REST#5978;3:9.65002871612802:0.00111263624711459:0.00765094923705561!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.0062753406476779
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0.361435
}}
}}

Revision as of 11:31, 5 September 2012


Full id: C3010_caudate_putamen_argyrophil_temporal_parietal_globus_duodenum



Phase1 CAGE Peaks

Hg19::chr10:26505179..26505186,+p13@GAD2
Hg19::chr10:26505290..26505312,+p4@GAD2
Hg19::chr10:26505329..26505346,+p6@GAD2


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
neuronal stem cell2.07e-158
neuron6.68e-126
neuroblast6.68e-126
electrically signaling cell6.68e-126
embryonic stem cell1.88e-105
Uber Anatomy
Ontology termp-valuen
central nervous system3.69e-8382
neural tube1.43e-7757
neural rod1.43e-7757
future spinal cord1.43e-7757
neural keel1.43e-7757
regional part of nervous system7.67e-7294
nervous system7.67e-7294
regional part of brain4.11e-6559
brain6.16e-6169
future brain6.16e-6169
regional part of forebrain1.01e-6041
forebrain1.01e-6041
future forebrain1.01e-6041
neural plate1.21e-5986
presumptive neural plate1.21e-5986
anterior neural tube5.05e-5942
neurectoderm2.86e-5690
cerebral hemisphere9.19e-5632
gray matter1.99e-5534
brain grey matter1.99e-5534
telencephalon2.40e-5534
regional part of telencephalon1.72e-5333
pre-chordal neural plate3.98e-4661
regional part of cerebral cortex2.68e-4422
cerebral cortex1.05e-4125
pallium1.05e-4125
neocortex6.77e-4120
ectoderm-derived structure6.11e-39169
ectoderm1.30e-37173
presumptive ectoderm1.30e-37173
head1.09e-36123
adult organism1.90e-35115
anterior region of body3.02e-34129
craniocervical region3.02e-34129
posterior neural tube9.76e-1915
chordal neural plate9.76e-1915
temporal lobe3.68e-167
tube1.10e-15194
nucleus of brain7.17e-159
neural nucleus7.17e-159
basal ganglion7.99e-159
nuclear complex of neuraxis7.99e-159
aggregate regional part of brain7.99e-159
collection of basal ganglia7.99e-159
cerebral subcortex7.99e-159
segmental subdivision of hindbrain4.65e-1412
hindbrain4.65e-1412
presumptive hindbrain4.65e-1412
segmental subdivision of nervous system8.34e-1313
gyrus1.18e-126
telencephalic nucleus1.47e-117
parietal lobe2.60e-115
occipital lobe6.44e-115
limbic system2.96e-105
corpus striatum5.99e-104
striatum5.99e-104
ventral part of telencephalon5.99e-104
future corpus striatum5.99e-104
anatomical conduit6.27e-10241
embryo8.47e-10612
regional part of metencephalon1.40e-099
metencephalon1.40e-099
future metencephalon1.40e-099
epithelium3.59e-09309
organ part5.29e-09219
cell layer6.11e-09312
anatomical cluster2.70e-08286
testis2.90e-088
brainstem3.61e-088
caudate-putamen5.78e-083
dorsal striatum5.78e-083
multi-cellular organism2.14e-07659
diencephalon3.27e-077
future diencephalon3.27e-077
middle temporal gyrus5.52e-073
germ layer6.77e-07604
embryonic tissue6.77e-07604
presumptive structure6.77e-07604
epiblast (generic)6.77e-07604
organism subdivision6.96e-07365
embryonic structure7.55e-07605
developing anatomical structure7.55e-07605


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
CTBP2#1488362.71700033932814.049570681927e-060.000128943022088346
CTCF#1066435.360256373075030.0064925092527670.0278171633512362
EGR1#195834.988179094810140.008056488137383440.0318897693606287
REST#597839.650028716128020.001112636247114590.00765094923705561
TCF12#6938310.63446490218640.0008313523990202070.0062753406476779



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.

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