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Coexpression cluster:C708: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001016!2.47e-57!89;UBERON:0001017!4.87e-54!81;UBERON:0001049!8.31e-53!56;UBERON:0005068!8.31e-53!56;UBERON:0006241!8.31e-53!56;UBERON:0007135!8.31e-53!56;UBERON:0000073!8.26e-47!53;UBERON:0002616!8.26e-47!53;UBERON:0000955!1.05e-40!68;UBERON:0006238!1.05e-40!68;UBERON:0002346!1.74e-37!86;UBERON:0002780!1.29e-35!41;UBERON:0001890!1.29e-35!41;UBERON:0003080!1.29e-35!41;UBERON:0006240!1.29e-35!41;UBERON:0003075!7.55e-33!82;UBERON:0007284!7.55e-33!82;UBERON:0003528!4.40e-31!34;UBERON:0002020!4.40e-31!34;UBERON:0001869!8.21e-30!32;UBERON:0011216!1.87e-28!223;UBERON:0004121!3.80e-28!171;UBERON:0000924!3.80e-28!171;UBERON:0006601!3.80e-28!171;UBERON:0001893!9.37e-28!34;UBERON:0002791!5.44e-27!32;UBERON:0010371!9.59e-24!104;UBERON:0002619!9.41e-23!22;UBERON:0007023!1.49e-22!114;UBERON:0001950!5.59e-22!20;UBERON:0003056!1.20e-21!61;UBERON:0000956!1.20e-19!25;UBERON:0000203!1.20e-19!25;UBERON:0010314!5.64e-19!132;UBERON:0003076!4.98e-18!15;UBERON:0003057!4.98e-18!15;UBERON:0002298!5.01e-15!6;UBERON:0000200!5.21e-14!6;UBERON:0000125!1.79e-13!9;UBERON:0002308!1.79e-13!9;UBERON:0011135!1.32e-12!5;UBERON:0002216!1.32e-12!5;UBERON:0011134!1.32e-12!5;UBERON:0002209!1.32e-12!5;UBERON:0002213!1.32e-12!5;UBERON:0005856!1.32e-12!5;UBERON:0005866!1.32e-12!5;UBERON:0005863!1.32e-12!5;UBERON:0007844!1.32e-12!5;UBERON:0011138!1.32e-12!5;UBERON:0001130!1.32e-12!5;UBERON:0001066!1.32e-12!5;UBERON:0001468!1.32e-12!5;UBERON:0004733!4.00e-12!12;UBERON:0002028!4.00e-12!12;UBERON:0007277!4.00e-12!12;UBERON:0000025!1.31e-11!192;UBERON:0004732!4.45e-11!13;UBERON:0000477!5.67e-11!373;UBERON:0000369!6.45e-11!4;UBERON:0002435!6.45e-11!4;UBERON:0000204!6.45e-11!4;UBERON:0010082!6.45e-11!4;UBERON:0002420!1.12e-09!9;UBERON:0007245!1.12e-09!9;UBERON:0010009!1.12e-09!9;UBERON:0010011!1.12e-09!9;UBERON:0000454!1.12e-09!9;UBERON:0001894!2.04e-09!7;UBERON:0006222!2.04e-09!7;UBERON:0005383!4.71e-09!3;UBERON:0005382!4.71e-09!3;UBERON:0009663!5.07e-09!7;UBERON:0000988!1.20e-08!3;UBERON:0002242!1.47e-08!3;UBERON:0003068!1.47e-08!3;UBERON:0002328!1.47e-08!3;UBERON:0004880!1.47e-08!3;UBERON:0002240!2.77e-08!3;UBERON:0005174!2.77e-08!3;UBERON:0001137!2.77e-08!3;UBERON:0000013!4.32e-08!5;UBERON:0002410!4.32e-08!5;UBERON:0001896!4.56e-08!3;UBERON:0005290!4.56e-08!3;UBERON:0010096!4.56e-08!3;UBERON:0001870!6.58e-08!3;UBERON:0001872!8.70e-08!5;UBERON:0004905!1.01e-07!8;UBERON:0000982!1.01e-07!8;UBERON:0004770!1.01e-07!8;UBERON:0004111!2.55e-07!240;UBERON:0003296!7.84e-07!4;UBERON:0010133!7.84e-07!4;UBERON:0002680!8.50e-07!9;UBERON:0001895!8.50e-07!9;UBERON:0010092!8.50e-07!9
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|tfbs_overrepresentation_for_novel_motifs=0.22923,0.00275938,0.223258,0.345441,0.190185,2.46597,0.411652,0.104517,0.687431,0.0552668,0.317729,0.451026,0.0765797,0.401301,0.189126,0.597712,0.617549,0.148925,0.0839658,0.120925,0.223306,0.069487,0.337221,1.64894,0.260754,0.471832,0.0648754,0.335332,0.192587,0.0565237,0.298956,0.65246,0.12577,0.566765,0.163884,0.0497783,0.161511,0.345014,0.14439,0.0916487,0.162847,0.285097,0.658594,2.35487,0.143066,0.24831,0.412635,0.308385,0.0729507,0.192687,0.484909,1.08437,0.150575,0.725869,0.873575,0.403938,1.70369,0.374657,0.20655,0.373762,0.691524,0.414771,0.103208,0.591384,0.43102,0.559038,0.959746,1.32257,0.642589,1.16217,0.273995,1.17358,0.0373297,0.871629,0.0739759,0.237079,0.817785,0.575479,1.54395,0.255642,0.293113,0.590372,0.4307,0.345708,0.821696,0.00480132,0.527748,0.0540708,0.508983,1.42111,1.05129,0.795567,0.66846,3.30365,0.190761,0.140087,0.59259,0.709167,0.51326,0.0463096,0.145361,0.663075,0.703825,0.621018,0.54826,0.313822,0.606045,0.398205,0.260543,0.177931,0.232335,0.701175,0.21882,0.325885,1.00416,0.938502,0.104888,0.297931,0.556847,1.33199,3.32193,0.506732,0.341589,0.44095,1.11293,0.576194,0.405934,0.673222,0.905059,0.140769,0.796235,0.301402,0.919079,0.437919,1.06395,0.189287,0.293853,0.892152,1.02226,1.87395,1.47317,0.985665,0.407489,0.70579,0.549903,0.367151,0.534339,1.71519,0.282284,0.128495,0.0329025,0.0163338,0.796604,0.0978005,0.414334,1.19239,0.494,0.179455,0.260802,0.237047,0.984474,0.778717,0.638755,0.673477,0.564971,0.429983,0.120139,0.410452,0.000300182
}}
}}

Revision as of 14:25, 26 November 2012


Full id: C708_smallcell_peripheral_gastrointestinal_neuroectodermal_Neurons_pituitary_putamen



Phase1 CAGE Peaks

Hg19::chr2:224462615..224462628,-p@chr2:224462615..224462628
-
Hg19::chr2:224463129..224463140,+p@chr2:224463129..224463140
+
Hg19::chr2:224463169..224463200,+p@chr2:224463169..224463200
+
Hg19::chr2:224463254..224463266,-p@chr2:224463254..224463266
-
Hg19::chr2:224463327..224463342,-p@chr2:224463327..224463342
-
Hg19::chr2:224463365..224463374,-p@chr2:224463365..224463374
-
Hg19::chr2:224463376..224463387,-p@chr2:224463376..224463387
-
Hg19::chr2:224463424..224463445,-p@chr2:224463424..224463445
-
Hg19::chr2:224463466..224463480,-p@chr2:224463466..224463480
-
Hg19::chr2:224463513..224463539,+p@chr2:224463513..224463539
+
Hg19::chr2:224463625..224463640,-p@chr2:224463625..224463640
-
Hg19::chr2:224463819..224463838,-p@chr2:224463819..224463838
-


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>disease_data<br>

Cell Type
Ontology termp-valuen
nucleus pulposus cell of intervertebral disc1.47e-083
Uber Anatomy
Ontology termp-valuen
nervous system2.47e-5789
central nervous system4.87e-5481
neural tube8.31e-5356
neural rod8.31e-5356
future spinal cord8.31e-5356
neural keel8.31e-5356
regional part of nervous system8.26e-4753
regional part of brain8.26e-4753
brain1.05e-4068
future brain1.05e-4068
neurectoderm1.74e-3786
regional part of forebrain1.29e-3541
forebrain1.29e-3541
anterior neural tube1.29e-3541
future forebrain1.29e-3541
neural plate7.55e-3382
presumptive neural plate7.55e-3382
brain grey matter4.40e-3134
gray matter4.40e-3134
cerebral hemisphere8.21e-3032
organ system subdivision1.87e-28223
ectoderm-derived structure3.80e-28171
ectoderm3.80e-28171
presumptive ectoderm3.80e-28171
telencephalon9.37e-2834
regional part of telencephalon5.44e-2732
ecto-epithelium9.59e-24104
regional part of cerebral cortex9.41e-2322
adult organism1.49e-22114
neocortex5.59e-2220
pre-chordal neural plate1.20e-2161
cerebral cortex1.20e-1925
pallium1.20e-1925
structure with developmental contribution from neural crest5.64e-19132
posterior neural tube4.98e-1815
chordal neural plate4.98e-1815
brainstem5.01e-156
gyrus5.21e-146
neural nucleus1.79e-139
nucleus of brain1.79e-139
intervertebral cartilage1.32e-125
symphysis1.32e-125
nonsynovial joint1.32e-125
fibrous joint1.32e-125
cartilaginous joint1.32e-125
developing mesenchymal condensation1.32e-125
pre-cartilage condensation1.32e-125
cartilaginous condensation1.32e-125
cartilage element1.32e-125
post-cranial axial skeletal system1.32e-125
vertebral column1.32e-125
intervertebral disk1.32e-125
intervertebral joint1.32e-125
segmental subdivision of hindbrain4.00e-1212
hindbrain4.00e-1212
presumptive hindbrain4.00e-1212
tube1.31e-11192
segmental subdivision of nervous system4.45e-1113
anatomical cluster5.67e-11373
corpus striatum6.45e-114
striatum6.45e-114
ventral part of telencephalon6.45e-114
future corpus striatum6.45e-114
basal ganglion1.12e-099
nuclear complex of neuraxis1.12e-099
aggregate regional part of brain1.12e-099
collection of basal ganglia1.12e-099
cerebral subcortex1.12e-099
diencephalon2.04e-097
future diencephalon2.04e-097
caudate-putamen4.71e-093
dorsal striatum4.71e-093
telencephalic nucleus5.07e-097
pons1.20e-083
nucleus pulposus1.47e-083
axial mesoderm1.47e-083
notochord1.47e-083
chordamesoderm1.47e-083
spinal cord2.77e-083
dorsal region element2.77e-083
dorsum2.77e-083
sympathetic nervous system4.32e-085
autonomic nervous system4.32e-085
medulla oblongata4.56e-083
myelencephalon4.56e-083
future myelencephalon4.56e-083
frontal cortex6.58e-083
parietal lobe8.70e-085
articulation1.01e-078
skeletal joint1.01e-078
articular system1.01e-078
anatomical conduit2.55e-07240
gland of diencephalon7.84e-074
neuroendocrine gland7.84e-074
regional part of metencephalon8.50e-079
metencephalon8.50e-079
future metencephalon8.50e-079
Disease
Ontology termp-valuen
neuroectodermal tumor6.84e-1610
neuroendocrine tumor1.87e-106


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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C708&oldid=2557042"