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Coexpression cluster:C4014: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!4.68e-64!56;UBERON:0005068!4.68e-64!56;UBERON:0006241!4.68e-64!56;UBERON:0007135!4.68e-64!56;UBERON:0000073!7.78e-61!53;UBERON:0002616!7.78e-61!53;UBERON:0002780!2.25e-55!41;UBERON:0001890!2.25e-55!41;UBERON:0003080!2.25e-55!41;UBERON:0006240!2.25e-55!41;UBERON:0003528!2.93e-54!34;UBERON:0002020!2.93e-54!34;UBERON:0002346!6.73e-54!86;UBERON:0001869!1.38e-53!32;UBERON:0000955!2.70e-50!68;UBERON:0006238!2.70e-50!68;UBERON:0001893!4.28e-50!34;UBERON:0002791!1.54e-49!32;UBERON:0001017!2.42e-48!81;UBERON:0003075!3.57e-48!82;UBERON:0007284!3.57e-48!82;UBERON:0001016!3.97e-45!89;UBERON:0003056!1.07e-42!61;UBERON:0002619!6.06e-42!22;UBERON:0010371!3.46e-40!104;UBERON:0001950!6.43e-37!20;UBERON:0000956!1.75e-36!25;UBERON:0000203!1.75e-36!25;UBERON:0007023!2.06e-35!114;UBERON:0010314!7.40e-31!132;UBERON:0004121!3.21e-28!171;UBERON:0000924!3.21e-28!171;UBERON:0006601!3.21e-28!171;UBERON:0002420!6.29e-20!9;UBERON:0007245!6.29e-20!9;UBERON:0010009!6.29e-20!9;UBERON:0010011!6.29e-20!9;UBERON:0000454!6.29e-20!9;UBERON:0000125!2.70e-19!9;UBERON:0002308!2.70e-19!9;UBERON:0011216!2.38e-18!223;UBERON:0000200!3.49e-17!6;UBERON:0000025!1.54e-16!192;UBERON:0001871!2.45e-15!6;UBERON:0009663!1.43e-14!7;UBERON:0000349!1.57e-14!5;UBERON:0000483!1.23e-12!306;UBERON:0000119!2.15e-12!309;UBERON:0000369!4.52e-12!4;UBERON:0002435!4.52e-12!4;UBERON:0000204!4.52e-12!4;UBERON:0010082!4.52e-12!4;UBERON:0000064!2.05e-11!218;UBERON:0004111!3.90e-11!240;UBERON:0003076!1.38e-10!15;UBERON:0003057!1.38e-10!15;UBERON:0001872!6.07e-10!5;UBERON:0005383!7.53e-10!3;UBERON:0005382!7.53e-10!3;UBERON:0002021!1.54e-09!5;UBERON:0001870!2.48e-09!3;UBERON:0000477!2.91e-09!373;UBERON:0000988!1.36e-08!3;UBERON:0000481!4.58e-08!342;UBERON:0004733!8.31e-08!12;UBERON:0002028!8.31e-08!12;UBERON:0007277!8.31e-08!12;UBERON:0002680!1.12e-07!9;UBERON:0001895!1.12e-07!9;UBERON:0010092!1.12e-07!9;UBERON:0002771!2.15e-07!2;UBERON:0002784!2.66e-07!4;UBERON:0002298!3.14e-07!6;UBERON:0001876!3.49e-07!2;UBERON:0001873!3.71e-07!2;UBERON:0010122!3.71e-07!2;UBERON:0004732!3.74e-07!13;UBERON:0001905!4.05e-07!2;UBERON:0002757!4.05e-07!2;UBERON:0010134!4.05e-07!2;UBERON:0005408!4.05e-07!2;UBERON:0001899!4.05e-07!2;UBERON:0001894!5.46e-07!7;UBERON:0006222!5.46e-07!7;UBERON:0002702!6.32e-07!2;UBERON:0001954!8.71e-07!2;UBERON:0003022!8.71e-07!2;UBERON:0002421!8.71e-07!2;UBERON:0002600!8.71e-07!2;UBERON:0001875!9.78e-07!2;UBERON:0006514!9.78e-07!2
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,1.18351,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,1.00813,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,1.18324,0.598234,0.777097,0.259059,1.54087,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,1.34254,1.54991,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,2.36218,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.698641,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,3.92523
}}
}}

Revision as of 16:29, 26 November 2012


Full id: C4014_neuroectodermal_neuroblastoma_smallcell_gastrointestinal_peripheral_thyroid_pineal



Phase1 CAGE Peaks

Hg19::chr20:17207665..17207699,+p1@PCSK2
Hg19::chr20:17349884..17349887,+p@chr20:17349884..17349887
+
Hg19::chr20:17402931..17402956,+p@chr20:17402931..17402956
+


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><br>

Cell Type
Ontology termp-valuen
Merkel cell3.39e-072
Uber Anatomy
Ontology termp-valuen
neural tube4.68e-6456
neural rod4.68e-6456
future spinal cord4.68e-6456
neural keel4.68e-6456
regional part of nervous system7.78e-6153
regional part of brain7.78e-6153
regional part of forebrain2.25e-5541
forebrain2.25e-5541
anterior neural tube2.25e-5541
future forebrain2.25e-5541
brain grey matter2.93e-5434
gray matter2.93e-5434
neurectoderm6.73e-5486
cerebral hemisphere1.38e-5332
brain2.70e-5068
future brain2.70e-5068
telencephalon4.28e-5034
regional part of telencephalon1.54e-4932
central nervous system2.42e-4881
neural plate3.57e-4882
presumptive neural plate3.57e-4882
nervous system3.97e-4589
pre-chordal neural plate1.07e-4261
regional part of cerebral cortex6.06e-4222
ecto-epithelium3.46e-40104
neocortex6.43e-3720
cerebral cortex1.75e-3625
pallium1.75e-3625
adult organism2.06e-35114
structure with developmental contribution from neural crest7.40e-31132
ectoderm-derived structure3.21e-28171
ectoderm3.21e-28171
presumptive ectoderm3.21e-28171
basal ganglion6.29e-209
nuclear complex of neuraxis6.29e-209
aggregate regional part of brain6.29e-209
collection of basal ganglia6.29e-209
cerebral subcortex6.29e-209
neural nucleus2.70e-199
nucleus of brain2.70e-199
organ system subdivision2.38e-18223
gyrus3.49e-176
tube1.54e-16192
temporal lobe2.45e-156
telencephalic nucleus1.43e-147
limbic system1.57e-145
epithelium1.23e-12306
cell layer2.15e-12309
corpus striatum4.52e-124
striatum4.52e-124
ventral part of telencephalon4.52e-124
future corpus striatum4.52e-124
organ part2.05e-11218
anatomical conduit3.90e-11240
posterior neural tube1.38e-1015
chordal neural plate1.38e-1015
parietal lobe6.07e-105
caudate-putamen7.53e-103
dorsal striatum7.53e-103
occipital lobe1.54e-095
frontal cortex2.48e-093
anatomical cluster2.91e-09373
pons1.36e-083
multi-tissue structure4.58e-08342
segmental subdivision of hindbrain8.31e-0812
hindbrain8.31e-0812
presumptive hindbrain8.31e-0812
regional part of metencephalon1.12e-079
metencephalon1.12e-079
future metencephalon1.12e-079
middle temporal gyrus2.15e-072
regional part of diencephalon2.66e-074
brainstem3.14e-076
amygdala3.49e-072
caudate nucleus3.71e-072
future caudate nucleus3.71e-072
segmental subdivision of nervous system3.74e-0713
pineal body4.05e-072
regional part of epithalamus4.05e-072
secretory circumventricular organ4.05e-072
circumventricular organ4.05e-072
epithalamus4.05e-072
diencephalon5.46e-077
future diencephalon5.46e-077
middle frontal gyrus6.32e-072
Ammon's horn8.71e-072
lobe parts of cerebral cortex8.71e-072
hippocampal formation8.71e-072
limbic lobe8.71e-072
globus pallidus9.78e-072
pallidum9.78e-072


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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