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Coexpression cluster:C3350: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!3.00e-72!53;UBERON:0002616!3.00e-72!53;UBERON:0001049!5.52e-72!56;UBERON:0005068!5.52e-72!56;UBERON:0006241!5.52e-72!56;UBERON:0007135!5.52e-72!56;UBERON:0000955!2.42e-63!68;UBERON:0006238!2.42e-63!68;UBERON:0002780!1.14e-58!41;UBERON:0001890!1.14e-58!41;UBERON:0003080!1.14e-58!41;UBERON:0006240!1.14e-58!41;UBERON:0003528!4.39e-57!34;UBERON:0002020!4.39e-57!34;UBERON:0001869!1.77e-56!32;UBERON:0001017!1.07e-54!81;UBERON:0001893!7.89e-53!34;UBERON:0002791!5.20e-52!32;UBERON:0003075!9.85e-49!82;UBERON:0007284!9.85e-49!82;UBERON:0002619!1.37e-48!22;UBERON:0001016!2.91e-48!89;UBERON:0002346!5.30e-46!86;UBERON:0001950!3.95e-43!20;UBERON:0000956!2.43e-42!25;UBERON:0000203!2.43e-42!25;UBERON:0007023!2.10e-40!114;UBERON:0003056!1.12e-39!61;UBERON:0010371!2.31e-38!104;UBERON:0010314!3.94e-28!132;UBERON:0011216!1.55e-25!223;UBERON:0004121!6.71e-23!171;UBERON:0000924!6.71e-23!171;UBERON:0006601!6.71e-23!171;UBERON:0000025!4.96e-22!192;UBERON:0001871!5.79e-21!6;UBERON:0002298!3.47e-17!6;UBERON:0002420!1.82e-16!9;UBERON:0007245!1.82e-16!9;UBERON:0010009!1.82e-16!9;UBERON:0010011!1.82e-16!9;UBERON:0000454!1.82e-16!9;UBERON:0000349!5.73e-16!5;UBERON:0000064!5.94e-16!218;UBERON:0000125!7.31e-16!9;UBERON:0002308!7.31e-16!9;UBERON:0004111!2.21e-15!240;UBERON:0001872!3.55e-15!5;UBERON:0003076!2.77e-14!15;UBERON:0003057!2.77e-14!15;UBERON:0004733!2.85e-14!12;UBERON:0002028!2.85e-14!12;UBERON:0007277!2.85e-14!12;UBERON:0000369!3.37e-13!4;UBERON:0002435!3.37e-13!4;UBERON:0000204!3.37e-13!4;UBERON:0010082!3.37e-13!4;UBERON:0004732!4.54e-13!13;UBERON:0000477!1.77e-12!373;UBERON:0000200!2.23e-12!6;UBERON:0000483!6.07e-12!306;UBERON:0000119!1.02e-11!309;UBERON:0009663!5.23e-11!7;UBERON:0000481!7.40e-11!342;UBERON:0005383!2.35e-10!3;UBERON:0005382!2.35e-10!3;UBERON:0001896!1.80e-09!3;UBERON:0005290!1.80e-09!3;UBERON:0010096!1.80e-09!3;UBERON:0000988!2.03e-09!3;UBERON:0000007!6.07e-08!2;UBERON:0002680!7.93e-08!9;UBERON:0001895!7.93e-08!9;UBERON:0010092!7.93e-08!9;UBERON:0001876!1.20e-07!2;UBERON:0001894!1.69e-07!7;UBERON:0006222!1.69e-07!7;UBERON:0001873!1.93e-07!2;UBERON:0010122!1.93e-07!2;UBERON:0003127!2.72e-07!2;UBERON:0001954!3.70e-07!2;UBERON:0003022!3.70e-07!2;UBERON:0002421!3.70e-07!2;UBERON:0002600!3.70e-07!2;UBERON:0000062!3.84e-07!503;UBERON:0002148!7.67e-07!2;UBERON:0006331!7.67e-07!2;UBERON:0009662!7.67e-07!2;UBERON:0002771!9.73e-07!2
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|tfbs_overrepresentation_for_novel_motifs=0.699513,1.40091,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.85641,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,1.95911,0.599922,0.843849,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,2.64731,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,2.50498,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,1.96632,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,3.854,0.624795,0.744018,0.710709,5.47603,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
}}
}}

Revision as of 16:05, 26 November 2012


Full id: C3350_small_smallcell_nonsmall_pituitary_rhabdomyosarcoma_occipital_argyrophil



Phase1 CAGE Peaks

Hg19::chr13:102569851..102569860,-p@chr13:102569851..102569860
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Hg19::chr13:102569895..102569908,-p@chr13:102569895..102569908
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Hg19::chr13:102569922..102569927,-p@chr13:102569922..102569927
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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
regional part of nervous system3.00e-7253
regional part of brain3.00e-7253
neural tube5.52e-7256
neural rod5.52e-7256
future spinal cord5.52e-7256
neural keel5.52e-7256
brain2.42e-6368
future brain2.42e-6368
regional part of forebrain1.14e-5841
forebrain1.14e-5841
anterior neural tube1.14e-5841
future forebrain1.14e-5841
brain grey matter4.39e-5734
gray matter4.39e-5734
cerebral hemisphere1.77e-5632
central nervous system1.07e-5481
telencephalon7.89e-5334
regional part of telencephalon5.20e-5232
neural plate9.85e-4982
presumptive neural plate9.85e-4982
regional part of cerebral cortex1.37e-4822
nervous system2.91e-4889
neurectoderm5.30e-4686
neocortex3.95e-4320
cerebral cortex2.43e-4225
pallium2.43e-4225
adult organism2.10e-40114
pre-chordal neural plate1.12e-3961
ecto-epithelium2.31e-38104
structure with developmental contribution from neural crest3.94e-28132
organ system subdivision1.55e-25223
ectoderm-derived structure6.71e-23171
ectoderm6.71e-23171
presumptive ectoderm6.71e-23171
tube4.96e-22192
temporal lobe5.79e-216
brainstem3.47e-176
basal ganglion1.82e-169
nuclear complex of neuraxis1.82e-169
aggregate regional part of brain1.82e-169
collection of basal ganglia1.82e-169
cerebral subcortex1.82e-169
limbic system5.73e-165
organ part5.94e-16218
neural nucleus7.31e-169
nucleus of brain7.31e-169
anatomical conduit2.21e-15240
parietal lobe3.55e-155
posterior neural tube2.77e-1415
chordal neural plate2.77e-1415
segmental subdivision of hindbrain2.85e-1412
hindbrain2.85e-1412
presumptive hindbrain2.85e-1412
corpus striatum3.37e-134
striatum3.37e-134
ventral part of telencephalon3.37e-134
future corpus striatum3.37e-134
segmental subdivision of nervous system4.54e-1313
anatomical cluster1.77e-12373
gyrus2.23e-126
epithelium6.07e-12306
cell layer1.02e-11309
telencephalic nucleus5.23e-117
multi-tissue structure7.40e-11342
caudate-putamen2.35e-103
dorsal striatum2.35e-103
medulla oblongata1.80e-093
myelencephalon1.80e-093
future myelencephalon1.80e-093
pons2.03e-093
pituitary gland6.07e-082
regional part of metencephalon7.93e-089
metencephalon7.93e-089
future metencephalon7.93e-089
amygdala1.20e-072
diencephalon1.69e-077
future diencephalon1.69e-077
caudate nucleus1.93e-072
future caudate nucleus1.93e-072
open tracheal system trachea2.72e-072
Ammon's horn3.70e-072
lobe parts of cerebral cortex3.70e-072
hippocampal formation3.70e-072
limbic lobe3.70e-072
organ3.84e-07503
locus ceruleus7.67e-072
brainstem nucleus7.67e-072
hindbrain nucleus7.67e-072
middle temporal gyrus9.73e-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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