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Coexpression cluster:C702: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!8.91e-89!81;UBERON:0001049!4.67e-88!56;UBERON:0005068!4.67e-88!56;UBERON:0006241!4.67e-88!56;UBERON:0007135!4.67e-88!56;UBERON:0001016!6.81e-83!89;UBERON:0000073!1.78e-82!53;UBERON:0002616!1.78e-82!53;UBERON:0000955!8.27e-68!68;UBERON:0006238!8.27e-68!68;UBERON:0002780!6.07e-66!41;UBERON:0001890!6.07e-66!41;UBERON:0003080!6.07e-66!41;UBERON:0006240!6.07e-66!41;UBERON:0003075!8.86e-66!82;UBERON:0007284!8.86e-66!82;UBERON:0002346!7.65e-62!86;UBERON:0007023!1.33e-61!114;UBERON:0003528!1.27e-55!34;UBERON:0002020!1.27e-55!34;UBERON:0001893!4.23e-55!34;UBERON:0001869!5.34e-52!32;UBERON:0002791!6.24e-52!32;UBERON:0010371!1.84e-51!104;UBERON:0003056!9.22e-47!61;UBERON:0004121!5.31e-41!171;UBERON:0000924!5.31e-41!171;UBERON:0006601!5.31e-41!171;UBERON:0000956!3.28e-40!25;UBERON:0000203!3.28e-40!25;UBERON:0011216!3.76e-40!223;UBERON:0010314!4.94e-38!132;UBERON:0002619!8.72e-36!22;UBERON:0001950!3.00e-32!20;UBERON:0003076!4.80e-22!15;UBERON:0003057!4.80e-22!15;UBERON:0000477!3.08e-21!373;UBERON:0000025!8.70e-21!192;UBERON:0004732!2.15e-18!13;UBERON:0004733!5.93e-17!12;UBERON:0002028!5.93e-17!12;UBERON:0007277!5.93e-17!12;UBERON:0000125!1.41e-16!9;UBERON:0002308!1.41e-16!9;UBERON:0002420!1.98e-16!9;UBERON:0007245!1.98e-16!9;UBERON:0010009!1.98e-16!9;UBERON:0010011!1.98e-16!9;UBERON:0000454!1.98e-16!9;UBERON:0004111!1.09e-15!240;UBERON:0000064!3.60e-13!218;UBERON:0009663!5.07e-13!7;UBERON:0000922!1.39e-12!592;UBERON:0000481!1.68e-12!342;UBERON:0002680!5.52e-12!9;UBERON:0001895!5.52e-12!9;UBERON:0010092!5.52e-12!9;UBERON:0001894!6.42e-12!7;UBERON:0006222!6.42e-12!7;UBERON:0002298!8.72e-12!6;UBERON:0000200!2.71e-11!6;UBERON:0000923!2.71e-10!560;UBERON:0010316!2.71e-10!560;UBERON:0005291!2.71e-10!560;UBERON:0006598!2.71e-10!560;UBERON:0010317!2.71e-10!560;UBERON:0002532!2.71e-10!560;UBERON:0000349!3.69e-10!5;UBERON:0000483!3.73e-10!306;UBERON:0002050!4.95e-10!564;UBERON:0002021!5.52e-10!5;UBERON:0000119!6.93e-10!309;UBERON:0001871!9.15e-10!6;UBERON:0001872!1.42e-09!5;UBERON:0005423!1.90e-09!581;UBERON:0000062!3.17e-09!503;UBERON:0000468!4.48e-09!656;UBERON:0000369!3.72e-08!4;UBERON:0002435!3.72e-08!4;UBERON:0000204!3.72e-08!4;UBERON:0010082!3.72e-08!4;UBERON:0002784!9.86e-08!4;UBERON:0000467!1.87e-07!624;UBERON:0000480!2.12e-07!625;UBERON:0002037!3.73e-07!6;UBERON:0006215!3.73e-07!6;UBERON:0003296!6.11e-07!4;UBERON:0010133!6.11e-07!4;UBERON:0002240!8.26e-07!3;UBERON:0005174!8.26e-07!3;UBERON:0001137!8.26e-07!3;UBERON:0001896!9.77e-07!3;UBERON:0005290!9.77e-07!3;UBERON:0010096!9.77e-07!3
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|tfbs_overrepresentation_for_novel_motifs=1.21158,1.46688,0.635061,0.345441,0.556358,0.344001,1.05908,0.340819,0.102889,1.10395,0.317729,0.451026,0.949576,0.401301,0.189126,0.207465,0.617549,0.148925,0.0839658,0.533397,0.635173,0.069487,0.337221,0.546841,2.05043,1.18915,0.231222,0.335332,1.06915,0.206722,0.809412,1.57102,0.12577,0.268295,0.163884,2.13197,2.15638,0.345014,0.14439,1.56694,0.162847,0.777985,0.20746,0.187953,0.912793,0.693545,0.412635,0.308385,0.369629,0.562381,0.484909,1.08437,0.347648,0.725869,0.873575,1.04226,0.195993,0.374657,1.20369,0.976149,2.78101,0.414771,0.688915,0.591384,0.43102,0.559038,0.959746,1.32257,0.642589,1.16217,0.752663,0.108268,1.37888,0.871629,1.39323,0.874985,0.216432,0.575479,0.639503,1.31112,0.0868483,0.590372,0.4307,0.10636,0.821696,1.76111,1.65013,1.17597,0.508983,1.42111,1.05129,0.795567,0.66846,0.130784,0.557745,0.140087,1.48453,0.709167,0.51326,0.0463096,0.875673,0.663075,0.703825,0.621018,0.54826,0.313822,0.606045,0.398205,0.260543,1.01047,0.232335,0.701175,0.21882,0.325885,1.00416,0.16034,3.93425,0.297931,0.556847,0.414358,0.863578,0.506732,0.341589,0.44095,1.11293,0.576194,0.405934,0.673222,0.905059,0.434621,0.796235,0.301402,0.919079,0.437919,1.06395,1.13627,0.293853,0.335825,1.02226,1.87395,1.47317,0.985665,0.407489,0.70579,0.549903,0.367151,0.534339,1.71519,1.40937,0.802925,1.29793,1.70437,0.796604,0.663597,0.414334,1.19239,0.494,0.179455,0.260802,0.237047,0.984474,0.778717,0.638755,1.94035,0.564971,0.429983,0.381825,1.86032,0.51183
}}
}}

Revision as of 14:24, 26 November 2012


Full id: C702_spinal_parietal_Neural_occipital_locus_temporal_globus



Phase1 CAGE Peaks

Hg19::chr15:93632421..93632446,-p1@RGMA
Hg19::chr16:72459838..72459857,+p1@uc002fch.1
Hg19::chr17:49124054..49124065,-p8@SPAG9
Hg19::chr17:54230819..54230848,+p1@ANKFN1
Hg19::chr19:51814892..51814930,+p1@IGLON5
Hg19::chr6:123154483..123154508,-p@chr6:123154483..123154508
-
Hg19::chr7:103969251..103969288,+p1@LHFPL3
Hg19::chr7:121513146..121513153,+p3@PTPRZ1
Hg19::chr7:121513171..121513202,+p2@PTPRZ1
Hg19::chr7:121513207..121513221,+p1@PTPRZ1
Hg19::chr8:63161180..63161204,+p4@NKAIN3
Hg19::chr8:85618155..85618173,+p3@RALYL


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:0001843neural tube closure0.0357467999751478
GO:0014020primary neural tube formation0.0357467999751478
GO:0001839neural plate morphogenesis0.0357467999751478
GO:0001841neural tube formation0.0357467999751478
GO:0001840neural plate development0.0357467999751478
GO:0001838embryonic epithelial tube formation0.0357467999751478
GO:0019198transmembrane receptor protein phosphatase activity0.0357467999751478
GO:0021915neural tube development0.0357467999751478
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.0357467999751478
GO:0016331morphogenesis of embryonic epithelium0.0369304705862911
GO:0001669acrosome0.0369304705862911



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 cell1.69e-138
neuron4.85e-106
neuroblast4.85e-106
electrically signaling cell4.85e-106
neural cell2.35e-0925
embryonic stem cell1.90e-075
Uber Anatomy
Ontology termp-valuen
central nervous system8.91e-8981
neural tube4.67e-8856
neural rod4.67e-8856
future spinal cord4.67e-8856
neural keel4.67e-8856
nervous system6.81e-8389
regional part of nervous system1.78e-8253
regional part of brain1.78e-8253
brain8.27e-6868
future brain8.27e-6868
regional part of forebrain6.07e-6641
forebrain6.07e-6641
anterior neural tube6.07e-6641
future forebrain6.07e-6641
neural plate8.86e-6682
presumptive neural plate8.86e-6682
neurectoderm7.65e-6286
adult organism1.33e-61114
brain grey matter1.27e-5534
gray matter1.27e-5534
telencephalon4.23e-5534
cerebral hemisphere5.34e-5232
regional part of telencephalon6.24e-5232
ecto-epithelium1.84e-51104
pre-chordal neural plate9.22e-4761
ectoderm-derived structure5.31e-41171
ectoderm5.31e-41171
presumptive ectoderm5.31e-41171
cerebral cortex3.28e-4025
pallium3.28e-4025
organ system subdivision3.76e-40223
structure with developmental contribution from neural crest4.94e-38132
regional part of cerebral cortex8.72e-3622
neocortex3.00e-3220
posterior neural tube4.80e-2215
chordal neural plate4.80e-2215
anatomical cluster3.08e-21373
tube8.70e-21192
segmental subdivision of nervous system2.15e-1813
segmental subdivision of hindbrain5.93e-1712
hindbrain5.93e-1712
presumptive hindbrain5.93e-1712
neural nucleus1.41e-169
nucleus of brain1.41e-169
basal ganglion1.98e-169
nuclear complex of neuraxis1.98e-169
aggregate regional part of brain1.98e-169
collection of basal ganglia1.98e-169
cerebral subcortex1.98e-169
anatomical conduit1.09e-15240
organ part3.60e-13218
telencephalic nucleus5.07e-137
embryo1.39e-12592
multi-tissue structure1.68e-12342
regional part of metencephalon5.52e-129
metencephalon5.52e-129
future metencephalon5.52e-129
diencephalon6.42e-127
future diencephalon6.42e-127
brainstem8.72e-126
gyrus2.71e-116
germ layer2.71e-10560
germ layer / neural crest2.71e-10560
embryonic tissue2.71e-10560
presumptive structure2.71e-10560
germ layer / neural crest derived structure2.71e-10560
epiblast (generic)2.71e-10560
limbic system3.69e-105
epithelium3.73e-10306
embryonic structure4.95e-10564
occipital lobe5.52e-105
cell layer6.93e-10309
temporal lobe9.15e-106
parietal lobe1.42e-095
developing anatomical structure1.90e-09581
organ3.17e-09503
multi-cellular organism4.48e-09656
corpus striatum3.72e-084
striatum3.72e-084
ventral part of telencephalon3.72e-084
future corpus striatum3.72e-084
regional part of diencephalon9.86e-084
anatomical system1.87e-07624
anatomical group2.12e-07625
cerebellum3.73e-076
rhombic lip3.73e-076
gland of diencephalon6.11e-074
neuroendocrine gland6.11e-074
spinal cord8.26e-073
dorsal region element8.26e-073
dorsum8.26e-073
medulla oblongata9.77e-073
myelencephalon9.77e-073
future myelencephalon9.77e-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.

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