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Coexpression cluster:C663: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!2.11e-89!56;UBERON:0005068!2.11e-89!56;UBERON:0006241!2.11e-89!56;UBERON:0007135!2.11e-89!56;UBERON:0000073!6.87e-86!53;UBERON:0002616!6.87e-86!53;UBERON:0000955!1.11e-70!68;UBERON:0006238!1.11e-70!68;UBERON:0002346!2.13e-69!86;UBERON:0001016!2.47e-68!89;UBERON:0001017!4.31e-67!81;UBERON:0003528!6.37e-67!34;UBERON:0002020!6.37e-67!34;UBERON:0002780!7.52e-67!41;UBERON:0001890!7.52e-67!41;UBERON:0003080!7.52e-67!41;UBERON:0006240!7.52e-67!41;UBERON:0001893!9.51e-67!34;UBERON:0003075!1.06e-66!82;UBERON:0007284!1.06e-66!82;UBERON:0001869!4.55e-62!32;UBERON:0002791!9.81e-62!32;UBERON:0007023!3.77e-54!114;UBERON:0010371!3.23e-50!104;UBERON:0002619!2.30e-49!22;UBERON:0003056!4.06e-45!61;UBERON:0001950!1.18e-43!20;UBERON:0000956!5.18e-43!25;UBERON:0000203!5.18e-43!25;UBERON:0010314!3.70e-41!132;UBERON:0004121!2.02e-38!171;UBERON:0000924!2.02e-38!171;UBERON:0006601!2.02e-38!171;UBERON:0011216!1.96e-26!223;UBERON:0000125!8.31e-26!9;UBERON:0002308!8.31e-26!9;UBERON:0000025!1.71e-24!192;UBERON:0003076!1.91e-22!15;UBERON:0003057!1.91e-22!15;UBERON:0002420!7.37e-21!9;UBERON:0007245!7.37e-21!9;UBERON:0010009!7.37e-21!9;UBERON:0010011!7.37e-21!9;UBERON:0000454!7.37e-21!9;UBERON:0009663!1.04e-20!7;UBERON:0004733!2.85e-19!12;UBERON:0002028!2.85e-19!12;UBERON:0007277!2.85e-19!12;UBERON:0000200!1.64e-18!6;UBERON:0004111!3.25e-18!240;UBERON:0004732!1.20e-17!13;UBERON:0002298!4.04e-17!6;UBERON:0001872!1.16e-15!5;UBERON:0000477!1.62e-14!373;UBERON:0000483!4.42e-14!306;UBERON:0000119!7.98e-14!309;UBERON:0000064!5.13e-13!218;UBERON:0000369!5.58e-13!4;UBERON:0002435!5.58e-13!4;UBERON:0000204!5.58e-13!4;UBERON:0010082!5.58e-13!4;UBERON:0002680!4.29e-12!9;UBERON:0001895!4.29e-12!9;UBERON:0010092!4.29e-12!9;UBERON:0000481!5.40e-12!342;UBERON:0001871!8.94e-11!6;UBERON:0000349!2.06e-10!5;UBERON:0005383!2.25e-10!3;UBERON:0005382!2.25e-10!3;UBERON:0001870!2.47e-10!3;UBERON:0002021!2.75e-10!5;UBERON:0001896!1.66e-09!3;UBERON:0005290!1.66e-09!3;UBERON:0010096!1.66e-09!3;UBERON:0000988!2.57e-09!3;UBERON:0000923!1.80e-08!560;UBERON:0010316!1.80e-08!560;UBERON:0005291!1.80e-08!560;UBERON:0006598!1.80e-08!560;UBERON:0010317!1.80e-08!560;UBERON:0002532!1.80e-08!560;UBERON:0002050!2.61e-08!564;UBERON:0000922!7.93e-08!592;UBERON:0005423!1.21e-07!581;UBERON:0002702!1.58e-07!2;UBERON:0001873!1.79e-07!2;UBERON:0010122!1.79e-07!2;UBERON:0001954!1.91e-07!2;UBERON:0003022!1.91e-07!2;UBERON:0002421!1.91e-07!2;UBERON:0002600!1.91e-07!2;UBERON:0002771!2.30e-07!2;UBERON:0001897!3.55e-07!2;UBERON:0010225!3.55e-07!2;UBERON:0001875!3.77e-07!2;UBERON:0006514!3.77e-07!2;UBERON:0002148!8.74e-07!2;UBERON:0006331!8.74e-07!2;UBERON:0009662!8.74e-07!2
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|tfbs_overrepresentation_for_novel_motifs=0.208137,0.00180775,0.202418,0.320418,0.17087,0.319017,0.385011,0.0904943,0.0889928,0.00827619,0.293498,0.423573,0.0649383,0.37489,0.506988,0.187326,0.587543,0.412009,0.0716493,0.0998348,1.1081,0.148689,0.312425,0.167123,0.238419,0.443987,0.0543847,0.310589,0.173154,0.177695,0.275306,0.622056,0.110199,0.234859,0.145955,0.0103638,0.143715,0.320003,0.799036,0.0786667,0.144976,0.261903,0.340762,0.504255,0.0138934,0.226447,0.385972,0.284438,0.312409,0.515273,0.456831,0.396393,0.0308939,0.694739,0.841347,0.377467,0.176395,0.348876,0.0468732,0.348003,0.660716,0.388062,0.62293,0.561703,0.403967,0.529794,0.927044,1.28869,0.612294,1.12869,0.251183,0.0939573,0.0300688,0.839414,0.0625815,0.0562052,0.0498505,0.546008,0.609242,1.22782,0.548433,0.560705,0.403653,1.57209,0.789807,0.00329133,2.44064,0.170958,0.480498,1.38705,1.01818,0.763867,1.54057,0.368116,0.171417,0.123575,0.0708422,0.67819,0.484706,0.0378976,0.403442,0.632556,0.672898,0.590971,0.519171,0.289709,0.576179,0.371864,0.238217,0.15924,0.211112,0.670274,0.198172,0.301413,0.971251,0.439271,0.00477951,0.274314,0.527634,0.750778,0.831412,0.478284,0.316671,0.413695,1.0796,0.546713,0.988587,0.642598,0.872646,0.784076,0.76453,0.277675,0.886589,1.86125,1.03079,0.161675,0.270369,0.836727,0.989273,1.83943,1.43902,0.95284,0.991928,0.674844,0.52079,0.341558,0.505455,1.68078,0.259186,0.112739,0.0262543,0.0123511,0.764896,0.286124,0.387634,1.15881,0.465765,0.160686,0.238466,0.21563,0.951654,0.747146,0.608503,0.21815,0.535644,0.402951,0.10496,0.383837,0.000163658
}}
}}

Revision as of 14:23, 26 November 2012


Full id: C663_cerebellum_neuroectodermal_neuroblastoma_occipital_parietal_middle_olfactory



Phase1 CAGE Peaks

Hg19::chr13:102598711..102598714,-p@chr13:102598711..102598714
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Hg19::chr13:102630287..102630291,-p@chr13:102630287..102630291
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Hg19::chr13:102789008..102789010,-p@chr13:102789008..102789010
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Hg19::chr13:102858331..102858333,-p@chr13:102858331..102858333
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Hg19::chr13:102859969..102859975,-p@chr13:102859969..102859975
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Hg19::chr13:102935198..102935205,-p@chr13:102935198..102935205
-
Hg19::chr13:102961261..102961267,-p@chr13:102961261..102961267
-
Hg19::chr13:102964569..102964573,-p@chr13:102964569..102964573
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Hg19::chr13:102976572..102976580,-p@chr13:102976572..102976580
-
Hg19::chr13:103012200..103012204,-p@chr13:103012200..103012204
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Hg19::chr13:103023283..103023286,-p@chr13:103023283..103023286
-
Hg19::chr7:70664362..70664387,+p@chr7:70664362..70664387
+
Hg19::chr7:70681484..70681504,+p@chr7:70681484..70681504
+


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
neural tube2.11e-8956
neural rod2.11e-8956
future spinal cord2.11e-8956
neural keel2.11e-8956
regional part of nervous system6.87e-8653
regional part of brain6.87e-8653
brain1.11e-7068
future brain1.11e-7068
neurectoderm2.13e-6986
nervous system2.47e-6889
central nervous system4.31e-6781
brain grey matter6.37e-6734
gray matter6.37e-6734
regional part of forebrain7.52e-6741
forebrain7.52e-6741
anterior neural tube7.52e-6741
future forebrain7.52e-6741
telencephalon9.51e-6734
neural plate1.06e-6682
presumptive neural plate1.06e-6682
cerebral hemisphere4.55e-6232
regional part of telencephalon9.81e-6232
adult organism3.77e-54114
ecto-epithelium3.23e-50104
regional part of cerebral cortex2.30e-4922
pre-chordal neural plate4.06e-4561
neocortex1.18e-4320
cerebral cortex5.18e-4325
pallium5.18e-4325
structure with developmental contribution from neural crest3.70e-41132
ectoderm-derived structure2.02e-38171
ectoderm2.02e-38171
presumptive ectoderm2.02e-38171
organ system subdivision1.96e-26223
neural nucleus8.31e-269
nucleus of brain8.31e-269
tube1.71e-24192
posterior neural tube1.91e-2215
chordal neural plate1.91e-2215
basal ganglion7.37e-219
nuclear complex of neuraxis7.37e-219
aggregate regional part of brain7.37e-219
collection of basal ganglia7.37e-219
cerebral subcortex7.37e-219
telencephalic nucleus1.04e-207
segmental subdivision of hindbrain2.85e-1912
hindbrain2.85e-1912
presumptive hindbrain2.85e-1912
gyrus1.64e-186
anatomical conduit3.25e-18240
segmental subdivision of nervous system1.20e-1713
brainstem4.04e-176
parietal lobe1.16e-155
anatomical cluster1.62e-14373
epithelium4.42e-14306
cell layer7.98e-14309
organ part5.13e-13218
corpus striatum5.58e-134
striatum5.58e-134
ventral part of telencephalon5.58e-134
future corpus striatum5.58e-134
regional part of metencephalon4.29e-129
metencephalon4.29e-129
future metencephalon4.29e-129
multi-tissue structure5.40e-12342
temporal lobe8.94e-116
limbic system2.06e-105
caudate-putamen2.25e-103
dorsal striatum2.25e-103
frontal cortex2.47e-103
occipital lobe2.75e-105
medulla oblongata1.66e-093
myelencephalon1.66e-093
future myelencephalon1.66e-093
pons2.57e-093
germ layer1.80e-08560
germ layer / neural crest1.80e-08560
embryonic tissue1.80e-08560
presumptive structure1.80e-08560
germ layer / neural crest derived structure1.80e-08560
epiblast (generic)1.80e-08560
embryonic structure2.61e-08564
embryo7.93e-08592
developing anatomical structure1.21e-07581
middle frontal gyrus1.58e-072
caudate nucleus1.79e-072
future caudate nucleus1.79e-072
Ammon's horn1.91e-072
lobe parts of cerebral cortex1.91e-072
hippocampal formation1.91e-072
limbic lobe1.91e-072
middle temporal gyrus2.30e-072
dorsal plus ventral thalamus3.55e-072
thalamic complex3.55e-072
globus pallidus3.77e-072
pallidum3.77e-072
locus ceruleus8.74e-072
brainstem nucleus8.74e-072
hindbrain nucleus8.74e-072
Disease
Ontology termp-valuen
neuroectodermal tumor2.91e-0710


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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