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Coexpression cluster:C3340: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.36e-53!57;UBERON:0005068!1.36e-53!57;UBERON:0006241!1.36e-53!57;UBERON:0007135!1.36e-53!57;UBERON:0001017!4.02e-46!82;UBERON:0002616!6.69e-46!59;UBERON:0005743!3.14e-45!86;UBERON:0003075!3.22e-43!86;UBERON:0007284!3.22e-43!86;UBERON:0000955!7.02e-43!69;UBERON:0006238!7.02e-43!69;UBERON:0002346!1.40e-42!90;UBERON:0000073!1.43e-41!94;UBERON:0001016!1.43e-41!94;UBERON:0002780!8.54e-41!41;UBERON:0001890!8.54e-41!41;UBERON:0006240!8.54e-41!41;UBERON:0003080!1.35e-39!42;UBERON:0002020!3.71e-38!34;UBERON:0003528!3.71e-38!34;UBERON:0001893!5.81e-38!34;UBERON:0002791!2.29e-36!33;UBERON:0007023!8.75e-35!115;UBERON:0001869!1.69e-34!32;UBERON:0003056!5.77e-33!61;UBERON:0002619!9.06e-31!22;UBERON:0000153!9.98e-30!129;UBERON:0007811!9.98e-30!129;UBERON:0000033!3.43e-29!123;UBERON:0000956!4.79e-29!25;UBERON:0000203!4.79e-29!25;UBERON:0001950!4.92e-27!20;UBERON:0000924!1.93e-24!173;UBERON:0006601!1.93e-24!173;UBERON:0004121!2.83e-24!169;UBERON:0000064!1.17e-14!219;UBERON:0003076!1.29e-14!15;UBERON:0003057!1.29e-14!15;UBERON:0004732!2.64e-14!13;UBERON:0000025!3.63e-14!194;UBERON:0004733!1.43e-12!12;UBERON:0002028!1.43e-12!12;UBERON:0007277!1.43e-12!12;UBERON:0000200!6.92e-12!6;UBERON:0002298!6.99e-12!8;UBERON:0001871!1.03e-11!7;UBERON:0000477!1.14e-10!286;UBERON:0002420!1.50e-10!9;UBERON:0007245!1.50e-10!9;UBERON:0010009!1.50e-10!9;UBERON:0010011!1.50e-10!9;UBERON:0000454!1.50e-10!9;UBERON:0000349!1.91e-10!5;UBERON:0002308!1.92e-10!9;UBERON:0000125!1.92e-10!9;UBERON:0004111!7.84e-10!241;UBERON:0000119!1.56e-09!312;UBERON:0000483!3.15e-09!309;UBERON:0000481!1.50e-08!347;UBERON:0000062!4.35e-08!511;UBERON:0002680!5.95e-08!9;UBERON:0001895!5.95e-08!9;UBERON:0010092!5.95e-08!9;UBERON:0000475!5.98e-08!365;UBERON:0000922!6.87e-08!612;UBERON:0002050!3.00e-07!605;UBERON:0005423!3.00e-07!605;UBERON:0009663!3.31e-07!7;UBERON:0006331!4.20e-07!3;UBERON:0002021!5.12e-07!5;UBERON:0002771!5.54e-07!3;UBERON:0000923!7.97e-07!604;UBERON:0005291!7.97e-07!604;UBERON:0006598!7.97e-07!604;UBERON:0002532!7.97e-07!604;UBERON:0000988!9.18e-07!3;UBERON:0001896!9.92e-07!3;UBERON:0005290!9.92e-07!3;UBERON:0010096!9.92e-07!3
|ontology_enrichment_uberon=UBERON:0001049!1.36e-53!57;UBERON:0005068!1.36e-53!57;UBERON:0006241!1.36e-53!57;UBERON:0007135!1.36e-53!57;UBERON:0001017!4.02e-46!82;UBERON:0002616!6.69e-46!59;UBERON:0005743!3.14e-45!86;UBERON:0003075!3.22e-43!86;UBERON:0007284!3.22e-43!86;UBERON:0000955!7.02e-43!69;UBERON:0006238!7.02e-43!69;UBERON:0002346!1.40e-42!90;UBERON:0000073!1.43e-41!94;UBERON:0001016!1.43e-41!94;UBERON:0002780!8.54e-41!41;UBERON:0001890!8.54e-41!41;UBERON:0006240!8.54e-41!41;UBERON:0003080!1.35e-39!42;UBERON:0002020!3.71e-38!34;UBERON:0003528!3.71e-38!34;UBERON:0001893!5.81e-38!34;UBERON:0002791!2.29e-36!33;UBERON:0007023!8.75e-35!115;UBERON:0001869!1.69e-34!32;UBERON:0003056!5.77e-33!61;UBERON:0002619!9.06e-31!22;UBERON:0000153!9.98e-30!129;UBERON:0007811!9.98e-30!129;UBERON:0000033!3.43e-29!123;UBERON:0000956!4.79e-29!25;UBERON:0000203!4.79e-29!25;UBERON:0001950!4.92e-27!20;UBERON:0000924!1.93e-24!173;UBERON:0006601!1.93e-24!173;UBERON:0004121!2.83e-24!169;UBERON:0000064!1.17e-14!219;UBERON:0003076!1.29e-14!15;UBERON:0003057!1.29e-14!15;UBERON:0004732!2.64e-14!13;UBERON:0000025!3.63e-14!194;UBERON:0004733!1.43e-12!12;UBERON:0002028!1.43e-12!12;UBERON:0007277!1.43e-12!12;UBERON:0000200!6.92e-12!6;UBERON:0002298!6.99e-12!8;UBERON:0001871!1.03e-11!7;UBERON:0000477!1.14e-10!286;UBERON:0002420!1.50e-10!9;UBERON:0007245!1.50e-10!9;UBERON:0010009!1.50e-10!9;UBERON:0010011!1.50e-10!9;UBERON:0000454!1.50e-10!9;UBERON:0000349!1.91e-10!5;UBERON:0002308!1.92e-10!9;UBERON:0000125!1.92e-10!9;UBERON:0004111!7.84e-10!241;UBERON:0000119!1.56e-09!312;UBERON:0000483!3.15e-09!309;UBERON:0000481!1.50e-08!347;UBERON:0000062!4.35e-08!511;UBERON:0002680!5.95e-08!9;UBERON:0001895!5.95e-08!9;UBERON:0010092!5.95e-08!9;UBERON:0000475!5.98e-08!365;UBERON:0000922!6.87e-08!612;UBERON:0002050!3.00e-07!605;UBERON:0005423!3.00e-07!605;UBERON:0009663!3.31e-07!7;UBERON:0006331!4.20e-07!3;UBERON:0002021!5.12e-07!5;UBERON:0002771!5.54e-07!3;UBERON:0000923!7.97e-07!604;UBERON:0005291!7.97e-07!604;UBERON:0006598!7.97e-07!604;UBERON:0002532!7.97e-07!604;UBERON:0000988!9.18e-07!3;UBERON:0001896!9.92e-07!3;UBERON:0005290!9.92e-07!3;UBERON:0010096!9.92e-07!3
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}}
}}

Revision as of 19:05, 8 August 2012


Full id: C3340_occipital_temporal_brain_hippocampus_cerebellum_substantia_parietal



Phase1 CAGE Peaks

Hg19::chr12:86578513..86578516,-p@chr12:86578513..86578516
-
Hg19::chr6:124231666..124231669,+p@chr6:124231666..124231669
+
Hg19::chr9:8339833..8339834,-p@chr9:8339833..8339834
-


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
neural tube1.36e-5357
neural rod1.36e-5357
future spinal cord1.36e-5357
neural keel1.36e-5357
central nervous system4.02e-4682
regional part of brain6.69e-4659
neural plate3.22e-4386
presumptive neural plate3.22e-4386
brain7.02e-4369
future brain7.02e-4369
neurectoderm1.40e-4290
regional part of nervous system1.43e-4194
nervous system1.43e-4194
regional part of forebrain8.54e-4141
forebrain8.54e-4141
future forebrain8.54e-4141
anterior neural tube1.35e-3942
gray matter3.71e-3834
brain grey matter3.71e-3834
telencephalon5.81e-3834
regional part of telencephalon2.29e-3633
adult organism8.75e-35115
cerebral hemisphere1.69e-3432
pre-chordal neural plate5.77e-3361
regional part of cerebral cortex9.06e-3122
anterior region of body9.98e-30129
craniocervical region9.98e-30129
head3.43e-29123
cerebral cortex4.79e-2925
pallium4.79e-2925
neocortex4.92e-2720
ectoderm1.93e-24173
presumptive ectoderm1.93e-24173
ectoderm-derived structure2.83e-24169
organ part1.17e-14219
posterior neural tube1.29e-1415
chordal neural plate1.29e-1415
segmental subdivision of nervous system2.64e-1413
tube3.63e-14194
segmental subdivision of hindbrain1.43e-1212
hindbrain1.43e-1212
presumptive hindbrain1.43e-1212
gyrus6.92e-126
brainstem6.99e-128
temporal lobe1.03e-117
anatomical cluster1.14e-10286
basal ganglion1.50e-109
nuclear complex of neuraxis1.50e-109
aggregate regional part of brain1.50e-109
collection of basal ganglia1.50e-109
cerebral subcortex1.50e-109
limbic system1.91e-105
nucleus of brain1.92e-109
neural nucleus1.92e-109
anatomical conduit7.84e-10241
cell layer1.56e-09312
epithelium3.15e-09309
multi-tissue structure1.50e-08347
organ4.35e-08511
regional part of metencephalon5.95e-089
metencephalon5.95e-089
future metencephalon5.95e-089
organism subdivision5.98e-08365
embryo6.87e-08612
embryonic structure3.00e-07605
developing anatomical structure3.00e-07605
telencephalic nucleus3.31e-077
brainstem nucleus4.20e-073
occipital lobe5.12e-075
middle temporal gyrus5.54e-073
germ layer7.97e-07604
embryonic tissue7.97e-07604
presumptive structure7.97e-07604
epiblast (generic)7.97e-07604
pons9.18e-073
medulla oblongata9.92e-073
myelencephalon9.92e-073
future myelencephalon9.92e-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


No analysis results for this cluster

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.