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Coexpression cluster:C3155: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!1.60e-80!56;UBERON:0005068!1.60e-80!56;UBERON:0006241!1.60e-80!56;UBERON:0007135!1.60e-80!56;UBERON:0000073!7.05e-72!53;UBERON:0002616!7.05e-72!53;UBERON:0000955!1.92e-59!68;UBERON:0006238!1.92e-59!68;UBERON:0001017!1.58e-58!81;UBERON:0003075!5.20e-54!82;UBERON:0007284!5.20e-54!82;UBERON:0001016!2.16e-52!89;UBERON:0002346!2.46e-51!86;UBERON:0002780!4.07e-51!41;UBERON:0001890!4.07e-51!41;UBERON:0003080!4.07e-51!41;UBERON:0006240!4.07e-51!41;UBERON:0003528!1.18e-48!34;UBERON:0002020!1.18e-48!34;UBERON:0001893!1.43e-48!34;UBERON:0010371!8.13e-42!104;UBERON:0007023!2.05e-41!114;UBERON:0002791!2.87e-39!32;UBERON:0001869!4.77e-39!32;UBERON:0010314!6.32e-35!132;UBERON:0003056!1.50e-33!61;UBERON:0001950!9.67e-32!20;UBERON:0002298!1.51e-30!6;UBERON:0003076!2.80e-30!15;UBERON:0003057!2.80e-30!15;UBERON:0002619!7.62e-29!22;UBERON:0000125!2.13e-28!9;UBERON:0002308!2.13e-28!9;UBERON:0004121!1.12e-25!171;UBERON:0000924!1.12e-25!171;UBERON:0006601!1.12e-25!171;UBERON:0000956!2.47e-25!25;UBERON:0000203!2.47e-25!25;UBERON:0000988!2.43e-22!3;UBERON:0004733!1.50e-21!12;UBERON:0002028!1.50e-21!12;UBERON:0007277!1.50e-21!12;UBERON:0000025!8.80e-21!192;UBERON:0011216!2.26e-20!223;UBERON:0004732!7.38e-20!13;UBERON:0000200!7.34e-19!6;UBERON:0009663!9.56e-17!7;UBERON:0004111!9.30e-16!240;UBERON:0001875!1.35e-15!2;UBERON:0006514!1.35e-15!2;UBERON:0002148!1.80e-15!2;UBERON:0006331!1.80e-15!2;UBERON:0009662!1.80e-15!2;UBERON:0002771!6.14e-15!2;UBERON:0001872!1.64e-13!5;UBERON:0002680!4.27e-13!9;UBERON:0001895!4.27e-13!9;UBERON:0010092!4.27e-13!9;UBERON:0002420!4.55e-13!9;UBERON:0007245!4.55e-13!9;UBERON:0010009!4.55e-13!9;UBERON:0010011!4.55e-13!9;UBERON:0000454!4.55e-13!9;UBERON:0000483!2.14e-11!306;UBERON:0000119!3.06e-11!309;UBERON:0001896!4.59e-11!3;UBERON:0005290!4.59e-11!3;UBERON:0010096!4.59e-11!3;UBERON:0002240!6.47e-11!3;UBERON:0005174!6.47e-11!3;UBERON:0001137!6.47e-11!3;UBERON:0000477!1.91e-10!373;UBERON:0000064!1.96e-10!218;UBERON:0001871!1.45e-09!6;UBERON:0002336!8.15e-09!1;UBERON:0011215!8.15e-09!1;UBERON:0001018!8.15e-09!1;UBERON:0002473!8.15e-09!1;UBERON:0005340!8.15e-09!1;UBERON:0003544!8.15e-09!1;UBERON:0005970!8.15e-09!1;UBERON:0002316!8.15e-09!1;UBERON:0001020!8.15e-09!1;UBERON:0002437!8.15e-09!1;UBERON:0002038!1.02e-08!1;UBERON:0009661!1.02e-08!1;UBERON:0002950!1.02e-08!1;UBERON:0001891!1.02e-08!1;UBERON:0009616!1.02e-08!1;UBERON:0010286!1.02e-08!1;UBERON:0000481!1.30e-08!342;UBERON:0002581!1.59e-08!1;UBERON:0003112!1.84e-08!1;UBERON:0011158!1.84e-08!1;UBERON:0003128!1.84e-08!1;UBERON:0001703!1.84e-08!1;UBERON:0002241!1.84e-08!1;UBERON:0004761!1.84e-08!1;UBERON:0009617!1.84e-08!1;UBERON:0002902!1.98e-08!1;UBERON:0009899!1.98e-08!1;UBERON:0001882!2.64e-08!1;UBERON:0005403!2.64e-08!1;UBERON:0007190!3.53e-08!1;UBERON:0002022!4.07e-08!1
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}}
}}

Revision as of 15:57, 26 November 2012


Full id: C3155_medulla_spinal_diencephalon_corpus_locus_globus_parietal



Phase1 CAGE Peaks

Hg19::chr11:45922629..45922637,+p@chr11:45922629..45922637
+
Hg19::chr17:76492734..76492735,+p3@uc002jvt.1
Hg19::chr1:156589297..156589300,+p9@HAPLN2


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:0005540hyaluronic acid binding0.0079477216531261
GO:0005539glycosaminoglycan binding0.00841133874955846
GO:0030247polysaccharide binding0.00841133874955846
GO:0001871pattern binding0.00841133874955846
GO:0005578proteinaceous extracellular matrix0.0211056163899682
GO:0030246carbohydrate binding0.0211056163899682
GO:0044421extracellular region part0.0282585658777817
GO:0022610biological adhesion0.0282585658777817
GO:0007155cell adhesion0.0282585658777817



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 tube1.60e-8056
neural rod1.60e-8056
future spinal cord1.60e-8056
neural keel1.60e-8056
regional part of nervous system7.05e-7253
regional part of brain7.05e-7253
brain1.92e-5968
future brain1.92e-5968
central nervous system1.58e-5881
neural plate5.20e-5482
presumptive neural plate5.20e-5482
nervous system2.16e-5289
neurectoderm2.46e-5186
regional part of forebrain4.07e-5141
forebrain4.07e-5141
anterior neural tube4.07e-5141
future forebrain4.07e-5141
brain grey matter1.18e-4834
gray matter1.18e-4834
telencephalon1.43e-4834
ecto-epithelium8.13e-42104
adult organism2.05e-41114
regional part of telencephalon2.87e-3932
cerebral hemisphere4.77e-3932
structure with developmental contribution from neural crest6.32e-35132
pre-chordal neural plate1.50e-3361
neocortex9.67e-3220
brainstem1.51e-306
posterior neural tube2.80e-3015
chordal neural plate2.80e-3015
regional part of cerebral cortex7.62e-2922
neural nucleus2.13e-289
nucleus of brain2.13e-289
ectoderm-derived structure1.12e-25171
ectoderm1.12e-25171
presumptive ectoderm1.12e-25171
cerebral cortex2.47e-2525
pallium2.47e-2525
pons2.43e-223
segmental subdivision of hindbrain1.50e-2112
hindbrain1.50e-2112
presumptive hindbrain1.50e-2112
tube8.80e-21192
organ system subdivision2.26e-20223
segmental subdivision of nervous system7.38e-2013
gyrus7.34e-196
telencephalic nucleus9.56e-177
anatomical conduit9.30e-16240
globus pallidus1.35e-152
pallidum1.35e-152
locus ceruleus1.80e-152
brainstem nucleus1.80e-152
hindbrain nucleus1.80e-152
middle temporal gyrus6.14e-152
parietal lobe1.64e-135
regional part of metencephalon4.27e-139
metencephalon4.27e-139
future metencephalon4.27e-139
basal ganglion4.55e-139
nuclear complex of neuraxis4.55e-139
aggregate regional part of brain4.55e-139
collection of basal ganglia4.55e-139
cerebral subcortex4.55e-139
epithelium2.14e-11306
cell layer3.06e-11309
medulla oblongata4.59e-113
myelencephalon4.59e-113
future myelencephalon4.59e-113
spinal cord6.47e-113
dorsal region element6.47e-113
dorsum6.47e-113
anatomical cluster1.91e-10373
organ part1.96e-10218
temporal lobe1.45e-096
corpus callosum8.15e-091
central nervous system cell part cluster8.15e-091
axon tract8.15e-091
intercerebral commissure8.15e-091
dorsal telencephalic commissure8.15e-091
brain white matter8.15e-091
brain commissure8.15e-091
white matter8.15e-091
nervous system commissure8.15e-091
cerebral hemisphere white matter8.15e-091
substantia nigra1.02e-081
midbrain nucleus1.02e-081
regional part of midbrain1.02e-081
midbrain1.02e-081
presumptive midbrain1.02e-081
midbrain neural tube1.02e-081
multi-tissue structure1.30e-08342
postcentral gyrus1.59e-081
olfactory region1.84e-081
primary subdivision of skull1.84e-081
cranium1.84e-081
neurocranium1.84e-081
chondrocranium1.84e-081
cartilaginous neurocranium1.84e-081
head paraxial mesoderm1.84e-081
occipital pole1.98e-081


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.

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