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Coexpression cluster:C1589: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!8.07e-109!56;UBERON:0005068!8.07e-109!56;UBERON:0006241!8.07e-109!56;UBERON:0007135!8.07e-109!56;UBERON:0000073!1.63e-98!53;UBERON:0002616!1.63e-98!53;UBERON:0001017!5.32e-87!81;UBERON:0000955!2.29e-82!68;UBERON:0006238!2.29e-82!68;UBERON:0002780!1.08e-81!41;UBERON:0001890!1.08e-81!41;UBERON:0003080!1.08e-81!41;UBERON:0006240!1.08e-81!41;UBERON:0001016!6.08e-81!89;UBERON:0001893!9.91e-81!34;UBERON:0003528!2.10e-80!34;UBERON:0002020!2.10e-80!34;UBERON:0003075!4.89e-75!82;UBERON:0007284!4.89e-75!82;UBERON:0002791!2.80e-74!32;UBERON:0001869!3.06e-74!32;UBERON:0002346!4.08e-71!86;UBERON:0002619!5.53e-66!22;UBERON:0001950!9.80e-66!20;UBERON:0000956!1.01e-57!25;UBERON:0000203!1.01e-57!25;UBERON:0010371!3.65e-57!104;UBERON:0007023!8.71e-57!114;UBERON:0003056!4.57e-56!61;UBERON:0010314!2.35e-45!132;UBERON:0004121!1.41e-39!171;UBERON:0000924!1.41e-39!171;UBERON:0006601!1.41e-39!171;UBERON:0011216!4.05e-34!223;UBERON:0003076!1.29e-26!15;UBERON:0003057!1.29e-26!15;UBERON:0000025!1.71e-26!192;UBERON:0002420!3.99e-24!9;UBERON:0007245!3.99e-24!9;UBERON:0010009!3.99e-24!9;UBERON:0010011!3.99e-24!9;UBERON:0000454!3.99e-24!9;UBERON:0000125!1.47e-23!9;UBERON:0002308!1.47e-23!9;UBERON:0000200!5.08e-22!6;UBERON:0002298!1.80e-20!6;UBERON:0004111!2.53e-20!240;UBERON:0002021!2.70e-19!5;UBERON:0001871!8.34e-19!6;UBERON:0001872!4.97e-18!5;UBERON:0009663!1.21e-17!7;UBERON:0004733!2.16e-17!12;UBERON:0002028!2.16e-17!12;UBERON:0007277!2.16e-17!12;UBERON:0000477!5.46e-17!373;UBERON:0004732!5.93e-16!13;UBERON:0000483!1.27e-14!306;UBERON:0000119!2.23e-14!309;UBERON:0000369!3.00e-14!4;UBERON:0002435!3.00e-14!4;UBERON:0000204!3.00e-14!4;UBERON:0010082!3.00e-14!4;UBERON:0000064!1.32e-13!218;UBERON:0002240!3.81e-12!3;UBERON:0005174!3.81e-12!3;UBERON:0001137!3.81e-12!3;UBERON:0000349!6.78e-12!5;UBERON:0000481!7.51e-12!342;UBERON:0001870!9.90e-12!3;UBERON:0001896!2.11e-11!3;UBERON:0005290!2.11e-11!3;UBERON:0010096!2.11e-11!3;UBERON:0005383!3.47e-11!3;UBERON:0005382!3.47e-11!3;UBERON:0000988!8.34e-11!3;UBERON:0002680!2.25e-09!9;UBERON:0001895!2.25e-09!9;UBERON:0010092!2.25e-09!9;UBERON:0002771!1.03e-08!2;UBERON:0001897!1.24e-08!2;UBERON:0010225!1.24e-08!2;UBERON:0002702!1.39e-08!2;UBERON:0001876!2.42e-08!2;UBERON:0000062!2.72e-08!503;UBERON:0000923!4.01e-08!560;UBERON:0010316!4.01e-08!560;UBERON:0005291!4.01e-08!560;UBERON:0006598!4.01e-08!560;UBERON:0010317!4.01e-08!560;UBERON:0002532!4.01e-08!560;UBERON:0001873!5.35e-08!2;UBERON:0010122!5.35e-08!2;UBERON:0002050!5.53e-08!564;UBERON:0002148!1.08e-07!2;UBERON:0006331!1.08e-07!2;UBERON:0009662!1.08e-07!2;UBERON:0005423!2.09e-07!581;UBERON:0000922!4.73e-07!592
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,1.15291,0.653236,0.733342,0.324142,0.321368,0.106358,0.621241,0.778743,0.752887,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.167776,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.757784,0.413782,0.654459,0.388123,0.815792,0.415749,0.580638,1.33238,0.451846,0.0606304,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,0.255232,1.25519,0.917983,2.26106,0.543014,0.796279,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,2.01367,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,2.05741,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,3.03743,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,1.63047,0.87256,2.09294,0.577088,0.363423,0.526389,0.126633,1.15522,0.840171,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.233587
}}
}}

Revision as of 14:59, 26 November 2012


Full id: C1589_medial_thalamus_occipital_temporal_spinal_amygdala_duodenum



Phase1 CAGE Peaks

Hg19::chr10:61005374..61005392,+p@chr10:61005374..61005392
+
Hg19::chr19:19367894..19367904,-p8@HAPLN4
Hg19::chr3:11060284..11060322,+p@chr3:11060284..11060322
+
Hg19::chr7:128434397..128434413,+p@chr7:128434397..128434413
+
Hg19::chr7:30198187..30198200,+p@chr7:30198187..30198200
+


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 tube8.07e-10956
neural rod8.07e-10956
future spinal cord8.07e-10956
neural keel8.07e-10956
regional part of nervous system1.63e-9853
regional part of brain1.63e-9853
central nervous system5.32e-8781
brain2.29e-8268
future brain2.29e-8268
regional part of forebrain1.08e-8141
forebrain1.08e-8141
anterior neural tube1.08e-8141
future forebrain1.08e-8141
nervous system6.08e-8189
telencephalon9.91e-8134
brain grey matter2.10e-8034
gray matter2.10e-8034
neural plate4.89e-7582
presumptive neural plate4.89e-7582
regional part of telencephalon2.80e-7432
cerebral hemisphere3.06e-7432
neurectoderm4.08e-7186
regional part of cerebral cortex5.53e-6622
neocortex9.80e-6620
cerebral cortex1.01e-5725
pallium1.01e-5725
ecto-epithelium3.65e-57104
adult organism8.71e-57114
pre-chordal neural plate4.57e-5661
structure with developmental contribution from neural crest2.35e-45132
ectoderm-derived structure1.41e-39171
ectoderm1.41e-39171
presumptive ectoderm1.41e-39171
organ system subdivision4.05e-34223
posterior neural tube1.29e-2615
chordal neural plate1.29e-2615
tube1.71e-26192
basal ganglion3.99e-249
nuclear complex of neuraxis3.99e-249
aggregate regional part of brain3.99e-249
collection of basal ganglia3.99e-249
cerebral subcortex3.99e-249
neural nucleus1.47e-239
nucleus of brain1.47e-239
gyrus5.08e-226
brainstem1.80e-206
anatomical conduit2.53e-20240
occipital lobe2.70e-195
temporal lobe8.34e-196
parietal lobe4.97e-185
telencephalic nucleus1.21e-177
segmental subdivision of hindbrain2.16e-1712
hindbrain2.16e-1712
presumptive hindbrain2.16e-1712
anatomical cluster5.46e-17373
segmental subdivision of nervous system5.93e-1613
epithelium1.27e-14306
cell layer2.23e-14309
corpus striatum3.00e-144
striatum3.00e-144
ventral part of telencephalon3.00e-144
future corpus striatum3.00e-144
organ part1.32e-13218
spinal cord3.81e-123
dorsal region element3.81e-123
dorsum3.81e-123
limbic system6.78e-125
multi-tissue structure7.51e-12342
frontal cortex9.90e-123
medulla oblongata2.11e-113
myelencephalon2.11e-113
future myelencephalon2.11e-113
caudate-putamen3.47e-113
dorsal striatum3.47e-113
pons8.34e-113
regional part of metencephalon2.25e-099
metencephalon2.25e-099
future metencephalon2.25e-099
middle temporal gyrus1.03e-082
dorsal plus ventral thalamus1.24e-082
thalamic complex1.24e-082
middle frontal gyrus1.39e-082
amygdala2.42e-082
organ2.72e-08503
germ layer4.01e-08560
germ layer / neural crest4.01e-08560
embryonic tissue4.01e-08560
presumptive structure4.01e-08560
germ layer / neural crest derived structure4.01e-08560
epiblast (generic)4.01e-08560
caudate nucleus5.35e-082
future caudate nucleus5.35e-082
embryonic structure5.53e-08564
locus ceruleus1.08e-072
brainstem nucleus1.08e-072
hindbrain nucleus1.08e-072
developing anatomical structure2.09e-07581
embryo4.73e-07592


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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