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Coexpression cluster:C2389: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!8.78e-89!56;UBERON:0005068!8.78e-89!56;UBERON:0006241!8.78e-89!56;UBERON:0007135!8.78e-89!56;UBERON:0000073!8.79e-81!53;UBERON:0002616!8.79e-81!53;UBERON:0001017!4.02e-73!81;UBERON:0001893!5.41e-72!34;UBERON:0003528!6.00e-72!34;UBERON:0002020!6.00e-72!34;UBERON:0002780!7.70e-72!41;UBERON:0001890!7.70e-72!41;UBERON:0003080!7.70e-72!41;UBERON:0006240!7.70e-72!41;UBERON:0001016!1.04e-67!89;UBERON:0001869!3.50e-67!32;UBERON:0000955!7.60e-67!68;UBERON:0006238!7.60e-67!68;UBERON:0002791!1.37e-66!32;UBERON:0003075!2.37e-60!82;UBERON:0007284!2.37e-60!82;UBERON:0002346!4.82e-57!86;UBERON:0010371!1.92e-50!104;UBERON:0002619!2.14e-50!22;UBERON:0007023!1.27e-49!114;UBERON:0003056!1.09e-48!61;UBERON:0000956!3.00e-48!25;UBERON:0000203!3.00e-48!25;UBERON:0001950!4.88e-45!20;UBERON:0010314!8.74e-39!132;UBERON:0004121!1.32e-36!171;UBERON:0000924!1.32e-36!171;UBERON:0006601!1.32e-36!171;UBERON:0011216!3.54e-26!223;UBERON:0000125!4.19e-25!9;UBERON:0002308!4.19e-25!9;UBERON:0002420!4.84e-25!9;UBERON:0007245!4.84e-25!9;UBERON:0010009!4.84e-25!9;UBERON:0010011!4.84e-25!9;UBERON:0000454!4.84e-25!9;UBERON:0000025!9.87e-21!192;UBERON:0009663!7.08e-20!7;UBERON:0000200!3.24e-19!6;UBERON:0003076!1.27e-17!15;UBERON:0003057!1.27e-17!15;UBERON:0002021!3.42e-16!5;UBERON:0004111!3.45e-16!240;UBERON:0000349!4.48e-15!5;UBERON:0000483!4.54e-15!306;UBERON:0000119!8.41e-15!309;UBERON:0000064!6.47e-13!218;UBERON:0000369!1.26e-12!4;UBERON:0002435!1.26e-12!4;UBERON:0000204!1.26e-12!4;UBERON:0010082!1.26e-12!4;UBERON:0002298!4.94e-12!6;UBERON:0000477!2.32e-11!373;UBERON:0004733!5.94e-11!12;UBERON:0002028!5.94e-11!12;UBERON:0007277!5.94e-11!12;UBERON:0001871!6.01e-11!6;UBERON:0001872!9.70e-11!5;UBERON:0001870!1.92e-10!3;UBERON:0004732!4.96e-10!13;UBERON:0000481!9.17e-10!342;UBERON:0005383!9.70e-10!3;UBERON:0005382!9.70e-10!3;UBERON:0002240!1.09e-09!3;UBERON:0005174!1.09e-09!3;UBERON:0001137!1.09e-09!3;UBERON:0000988!2.22e-09!3;UBERON:0002680!7.41e-08!9;UBERON:0001895!7.41e-08!9;UBERON:0010092!7.41e-08!9;UBERON:0002702!1.49e-07!2;UBERON:0002771!1.79e-07!2;UBERON:0001873!4.01e-07!2;UBERON:0010122!4.01e-07!2;UBERON:0001897!5.26e-07!2;UBERON:0001954!5.26e-07!2;UBERON:0003022!5.26e-07!2;UBERON:0002421!5.26e-07!2;UBERON:0010225!5.26e-07!2;UBERON:0002600!5.26e-07!2;UBERON:0002148!6.49e-07!2;UBERON:0006331!6.49e-07!2;UBERON:0009662!6.49e-07!2;UBERON:0001876!7.53e-07!2
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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.462021,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,1.53003,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,1.49582,1.23038,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.314427,0.61613,0.822818,0.694903,0.99221,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,2.26787,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.336329,0.321165,0.823598,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,5.26138,1.44378,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,1.32435,1.15724,0.934671,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,1.52945,0.516141,1.44917,1.14697,1.40954,0.717043,1.46636,0.489254,0.785429,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,2.02143,1.24863,0.68598,1.37788,0.852645,1.52813,18.5143,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.521611,1.24902,1.76758,0.824835,1.65997,0.917558,2.22181,2.59378,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.156682
}}
}}

Revision as of 15:28, 26 November 2012


Full id: C2389_caudate_parietal_small_smallcell_occipital_merkel_medial



Phase1 CAGE Peaks

Hg19::chr16:7353211..7353229,+p@chr16:7353211..7353229
+
Hg19::chr16:7354219..7354246,+p@chr16:7354219..7354246
+
Hg19::chr16:7354337..7354363,+p@chr16:7354337..7354363
+
Hg19::chr16:7355031..7355049,+p@chr16:7355031..7355049
+


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 cell1.27e-072
Uber Anatomy
Ontology termp-valuen
neural tube8.78e-8956
neural rod8.78e-8956
future spinal cord8.78e-8956
neural keel8.78e-8956
regional part of nervous system8.79e-8153
regional part of brain8.79e-8153
central nervous system4.02e-7381
telencephalon5.41e-7234
brain grey matter6.00e-7234
gray matter6.00e-7234
regional part of forebrain7.70e-7241
forebrain7.70e-7241
anterior neural tube7.70e-7241
future forebrain7.70e-7241
nervous system1.04e-6789
cerebral hemisphere3.50e-6732
brain7.60e-6768
future brain7.60e-6768
regional part of telencephalon1.37e-6632
neural plate2.37e-6082
presumptive neural plate2.37e-6082
neurectoderm4.82e-5786
ecto-epithelium1.92e-50104
regional part of cerebral cortex2.14e-5022
adult organism1.27e-49114
pre-chordal neural plate1.09e-4861
cerebral cortex3.00e-4825
pallium3.00e-4825
neocortex4.88e-4520
structure with developmental contribution from neural crest8.74e-39132
ectoderm-derived structure1.32e-36171
ectoderm1.32e-36171
presumptive ectoderm1.32e-36171
organ system subdivision3.54e-26223
neural nucleus4.19e-259
nucleus of brain4.19e-259
basal ganglion4.84e-259
nuclear complex of neuraxis4.84e-259
aggregate regional part of brain4.84e-259
collection of basal ganglia4.84e-259
cerebral subcortex4.84e-259
tube9.87e-21192
telencephalic nucleus7.08e-207
gyrus3.24e-196
posterior neural tube1.27e-1715
chordal neural plate1.27e-1715
occipital lobe3.42e-165
anatomical conduit3.45e-16240
limbic system4.48e-155
epithelium4.54e-15306
cell layer8.41e-15309
organ part6.47e-13218
corpus striatum1.26e-124
striatum1.26e-124
ventral part of telencephalon1.26e-124
future corpus striatum1.26e-124
brainstem4.94e-126
anatomical cluster2.32e-11373
segmental subdivision of hindbrain5.94e-1112
hindbrain5.94e-1112
presumptive hindbrain5.94e-1112
temporal lobe6.01e-116
parietal lobe9.70e-115
frontal cortex1.92e-103
segmental subdivision of nervous system4.96e-1013
multi-tissue structure9.17e-10342
caudate-putamen9.70e-103
dorsal striatum9.70e-103
spinal cord1.09e-093
dorsal region element1.09e-093
dorsum1.09e-093
pons2.22e-093
regional part of metencephalon7.41e-089
metencephalon7.41e-089
future metencephalon7.41e-089
middle frontal gyrus1.49e-072
middle temporal gyrus1.79e-072
caudate nucleus4.01e-072
future caudate nucleus4.01e-072
dorsal plus ventral thalamus5.26e-072
Ammon's horn5.26e-072
lobe parts of cerebral cortex5.26e-072
hippocampal formation5.26e-072
thalamic complex5.26e-072
limbic lobe5.26e-072
locus ceruleus6.49e-072
brainstem nucleus6.49e-072
hindbrain nucleus6.49e-072
amygdala7.53e-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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