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Coexpression cluster:C4487: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!7.77e-57!82;UBERON:0005743!2.90e-56!86;UBERON:0001049!1.05e-52!57;UBERON:0005068!1.05e-52!57;UBERON:0006241!1.05e-52!57;UBERON:0007135!1.05e-52!57;UBERON:0000073!7.69e-50!94;UBERON:0001016!7.69e-50!94;UBERON:0003075!1.95e-45!86;UBERON:0007284!1.95e-45!86;UBERON:0002616!3.80e-45!59;UBERON:0000955!1.28e-43!69;UBERON:0006238!1.28e-43!69;UBERON:0002346!1.45e-43!90;UBERON:0002780!1.43e-42!41;UBERON:0001890!1.43e-42!41;UBERON:0006240!1.43e-42!41;UBERON:0003080!3.64e-41!42;UBERON:0003056!5.48e-36!61;UBERON:0001893!1.09e-35!34;UBERON:0002020!1.92e-35!34;UBERON:0003528!1.92e-35!34;UBERON:0002791!1.42e-34!33;UBERON:0000153!2.42e-34!129;UBERON:0007811!2.42e-34!129;UBERON:0001869!1.10e-33!32;UBERON:0000033!1.46e-32!123;UBERON:0007023!1.89e-32!115;UBERON:0004121!4.58e-32!169;UBERON:0000924!1.95e-31!173;UBERON:0006601!1.95e-31!173;UBERON:0000956!6.64e-26!25;UBERON:0000203!6.64e-26!25;UBERON:0002619!3.03e-23!22;UBERON:0001950!3.95e-21!20;UBERON:0000025!7.48e-20!194;UBERON:0004111!2.06e-19!241;UBERON:0000477!1.39e-18!286;UBERON:0000483!1.24e-14!309;UBERON:0000119!3.48e-14!312;UBERON:0000922!1.28e-12!612;UBERON:0000468!1.52e-12!659;UBERON:0003076!2.42e-12!15;UBERON:0003057!2.42e-12!15;UBERON:0002420!4.06e-11!9;UBERON:0007245!4.06e-11!9;UBERON:0010009!4.06e-11!9;UBERON:0010011!4.06e-11!9;UBERON:0000454!4.06e-11!9;UBERON:0002308!6.66e-11!9;UBERON:0000125!6.66e-11!9;UBERON:0000064!5.12e-10!219;UBERON:0000467!9.58e-10!625;UBERON:0002050!1.18e-09!605;UBERON:0005423!1.18e-09!605;UBERON:0000480!1.18e-09!626;UBERON:0004733!1.63e-09!12;UBERON:0002028!1.63e-09!12;UBERON:0007277!1.63e-09!12;UBERON:0000923!2.75e-09!604;UBERON:0005291!2.75e-09!604;UBERON:0006598!2.75e-09!604;UBERON:0002532!2.75e-09!604;UBERON:0009663!5.38e-09!7;UBERON:0000475!7.48e-09!365;UBERON:0004732!1.57e-08!13;UBERON:0001894!3.58e-08!7;UBERON:0006222!3.58e-08!7;UBERON:0000200!4.16e-08!6;UBERON:0001871!1.14e-07!7;UBERON:0000481!1.45e-07!347;UBERON:0001872!5.60e-07!5;UBERON:0000349!5.67e-07!5;UBERON:0002680!8.01e-07!9;UBERON:0001895!8.01e-07!9;UBERON:0010092!8.01e-07!9;UBERON:0000062!8.09e-07!511;UBERON:0002298!8.76e-07!8
|ontology_enrichment_uberon=UBERON:0001017!7.77e-57!82;UBERON:0005743!2.90e-56!86;UBERON:0001049!1.05e-52!57;UBERON:0005068!1.05e-52!57;UBERON:0006241!1.05e-52!57;UBERON:0007135!1.05e-52!57;UBERON:0000073!7.69e-50!94;UBERON:0001016!7.69e-50!94;UBERON:0003075!1.95e-45!86;UBERON:0007284!1.95e-45!86;UBERON:0002616!3.80e-45!59;UBERON:0000955!1.28e-43!69;UBERON:0006238!1.28e-43!69;UBERON:0002346!1.45e-43!90;UBERON:0002780!1.43e-42!41;UBERON:0001890!1.43e-42!41;UBERON:0006240!1.43e-42!41;UBERON:0003080!3.64e-41!42;UBERON:0003056!5.48e-36!61;UBERON:0001893!1.09e-35!34;UBERON:0002020!1.92e-35!34;UBERON:0003528!1.92e-35!34;UBERON:0002791!1.42e-34!33;UBERON:0000153!2.42e-34!129;UBERON:0007811!2.42e-34!129;UBERON:0001869!1.10e-33!32;UBERON:0000033!1.46e-32!123;UBERON:0007023!1.89e-32!115;UBERON:0004121!4.58e-32!169;UBERON:0000924!1.95e-31!173;UBERON:0006601!1.95e-31!173;UBERON:0000956!6.64e-26!25;UBERON:0000203!6.64e-26!25;UBERON:0002619!3.03e-23!22;UBERON:0001950!3.95e-21!20;UBERON:0000025!7.48e-20!194;UBERON:0004111!2.06e-19!241;UBERON:0000477!1.39e-18!286;UBERON:0000483!1.24e-14!309;UBERON:0000119!3.48e-14!312;UBERON:0000922!1.28e-12!612;UBERON:0000468!1.52e-12!659;UBERON:0003076!2.42e-12!15;UBERON:0003057!2.42e-12!15;UBERON:0002420!4.06e-11!9;UBERON:0007245!4.06e-11!9;UBERON:0010009!4.06e-11!9;UBERON:0010011!4.06e-11!9;UBERON:0000454!4.06e-11!9;UBERON:0002308!6.66e-11!9;UBERON:0000125!6.66e-11!9;UBERON:0000064!5.12e-10!219;UBERON:0000467!9.58e-10!625;UBERON:0002050!1.18e-09!605;UBERON:0005423!1.18e-09!605;UBERON:0000480!1.18e-09!626;UBERON:0004733!1.63e-09!12;UBERON:0002028!1.63e-09!12;UBERON:0007277!1.63e-09!12;UBERON:0000923!2.75e-09!604;UBERON:0005291!2.75e-09!604;UBERON:0006598!2.75e-09!604;UBERON:0002532!2.75e-09!604;UBERON:0009663!5.38e-09!7;UBERON:0000475!7.48e-09!365;UBERON:0004732!1.57e-08!13;UBERON:0001894!3.58e-08!7;UBERON:0006222!3.58e-08!7;UBERON:0000200!4.16e-08!6;UBERON:0001871!1.14e-07!7;UBERON:0000481!1.45e-07!347;UBERON:0001872!5.60e-07!5;UBERON:0000349!5.67e-07!5;UBERON:0002680!8.01e-07!9;UBERON:0001895!8.01e-07!9;UBERON:0010092!8.01e-07!9;UBERON:0000062!8.09e-07!511;UBERON:0002298!8.76e-07!8
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.016813521296684!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00583286000598155!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187223272775674!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247591340471207
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0.157274,0.215705,0.252796,4.48768e-06,0.361435
}}
}}

Revision as of 13:24, 5 September 2012


Full id: C4487_Neural_testicular_hippocampus_amygdala_maxillary_parietal_caudate



Phase1 CAGE Peaks

Hg19::chr5:16742010..16742025,-p3@MYO10
Hg19::chr5:16742041..16742054,-p11@MYO10
Hg19::chr5:16742330..16742344,-p6@MYO10


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 cell1.72e-098
neuron3.48e-076
neuroblast3.48e-076
electrically signaling cell3.48e-076
Uber Anatomy
Ontology termp-valuen
central nervous system7.77e-5782
neural tube1.05e-5257
neural rod1.05e-5257
future spinal cord1.05e-5257
neural keel1.05e-5257
regional part of nervous system7.69e-5094
nervous system7.69e-5094
neural plate1.95e-4586
presumptive neural plate1.95e-4586
regional part of brain3.80e-4559
brain1.28e-4369
future brain1.28e-4369
neurectoderm1.45e-4390
regional part of forebrain1.43e-4241
forebrain1.43e-4241
future forebrain1.43e-4241
anterior neural tube3.64e-4142
pre-chordal neural plate5.48e-3661
telencephalon1.09e-3534
gray matter1.92e-3534
brain grey matter1.92e-3534
regional part of telencephalon1.42e-3433
anterior region of body2.42e-34129
craniocervical region2.42e-34129
cerebral hemisphere1.10e-3332
head1.46e-32123
adult organism1.89e-32115
ectoderm-derived structure4.58e-32169
ectoderm1.95e-31173
presumptive ectoderm1.95e-31173
cerebral cortex6.64e-2625
pallium6.64e-2625
regional part of cerebral cortex3.03e-2322
neocortex3.95e-2120
tube7.48e-20194
anatomical conduit2.06e-19241
anatomical cluster1.39e-18286
epithelium1.24e-14309
cell layer3.48e-14312
embryo1.28e-12612
multi-cellular organism1.52e-12659
posterior neural tube2.42e-1215
chordal neural plate2.42e-1215
basal ganglion4.06e-119
nuclear complex of neuraxis4.06e-119
aggregate regional part of brain4.06e-119
collection of basal ganglia4.06e-119
cerebral subcortex4.06e-119
nucleus of brain6.66e-119
neural nucleus6.66e-119
organ part5.12e-10219
anatomical system9.58e-10625
embryonic structure1.18e-09605
developing anatomical structure1.18e-09605
anatomical group1.18e-09626
segmental subdivision of hindbrain1.63e-0912
hindbrain1.63e-0912
presumptive hindbrain1.63e-0912
germ layer2.75e-09604
embryonic tissue2.75e-09604
presumptive structure2.75e-09604
epiblast (generic)2.75e-09604
telencephalic nucleus5.38e-097
organism subdivision7.48e-09365
segmental subdivision of nervous system1.57e-0813
diencephalon3.58e-087
future diencephalon3.58e-087
gyrus4.16e-086
temporal lobe1.14e-077
multi-tissue structure1.45e-07347
parietal lobe5.60e-075
limbic system5.67e-075
regional part of metencephalon8.01e-079
metencephalon8.01e-079
future metencephalon8.01e-079
organ8.09e-07511
brainstem8.76e-078


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
EP300#203336.77394172622320.003216880500103790.016813521296684
FOXA1#3169311.08141974938550.000734755275698670.00583286000598155
MAX#414936.452555509007120.003721913834265510.0187223272775674
SP1#666735.69838137814090.005403962701712170.0247591340471207



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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