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Coexpression cluster:C2274: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!6.10e-65!81;UBERON:0001049!9.80e-62!56;UBERON:0005068!9.80e-62!56;UBERON:0006241!9.80e-62!56;UBERON:0007135!9.80e-62!56;UBERON:0001016!1.12e-58!89;UBERON:0000073!1.21e-57!53;UBERON:0002616!1.21e-57!53;UBERON:0002780!5.67e-53!41;UBERON:0001890!5.67e-53!41;UBERON:0003080!5.67e-53!41;UBERON:0006240!5.67e-53!41;UBERON:0000955!1.33e-51!68;UBERON:0006238!1.33e-51!68;UBERON:0003528!6.58e-49!34;UBERON:0002020!6.58e-49!34;UBERON:0001893!8.97e-49!34;UBERON:0001869!1.74e-46!32;UBERON:0002791!5.71e-46!32;UBERON:0002346!1.06e-40!86;UBERON:0003075!2.49e-40!82;UBERON:0007284!2.49e-40!82;UBERON:0007023!1.72e-37!114;UBERON:0000956!1.03e-36!25;UBERON:0000203!1.03e-36!25;UBERON:0002619!1.12e-36!22;UBERON:0001950!1.58e-33!20;UBERON:0003056!4.32e-33!61;UBERON:0010371!1.29e-32!104;UBERON:0004121!4.87e-31!171;UBERON:0000924!4.87e-31!171;UBERON:0006601!4.87e-31!171;UBERON:0010314!8.25e-25!132;UBERON:0011216!4.84e-21!223;UBERON:0002420!8.45e-14!9;UBERON:0007245!8.45e-14!9;UBERON:0010009!8.45e-14!9;UBERON:0010011!8.45e-14!9;UBERON:0000454!8.45e-14!9;UBERON:0000125!2.07e-13!9;UBERON:0002308!2.07e-13!9;UBERON:0000025!6.51e-13!192;UBERON:0000477!2.38e-12!373;UBERON:0001871!3.26e-12!6;UBERON:0000200!8.09e-11!6;UBERON:0009663!1.35e-10!7;UBERON:0003076!1.56e-10!15;UBERON:0003057!1.56e-10!15;UBERON:0000349!1.98e-09!5;UBERON:0001872!2.33e-09!5;UBERON:0002298!2.85e-09!6;UBERON:0002021!4.13e-09!5;UBERON:0004111!4.34e-08!240;UBERON:0000481!1.31e-07!342;UBERON:0000483!1.53e-07!306;UBERON:0000119!2.64e-07!309;UBERON:0004733!3.67e-07!12;UBERON:0002028!3.67e-07!12;UBERON:0007277!3.67e-07!12;UBERON:0000369!5.54e-07!4;UBERON:0002435!5.54e-07!4;UBERON:0000204!5.54e-07!4;UBERON:0010082!5.54e-07!4
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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.902371,1.68405,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.285913,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.314427,0.61613,1.92371,0.694903,0.99221,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,1.03936,0.248021,1.32819,0.336329,0.859396,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,0.109222,1.18341,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,2.11025,0.465545,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.774456,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,1.58937,1.95303,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
}}
}}

Revision as of 15:23, 26 November 2012


Full id: C2274_amygdala_argyrophil_liposarcoma_parietal_medial_brain_insula



Phase1 CAGE Peaks

Hg19::chr13:96742352..96742378,+p@chr13:96742352..96742378
+
Hg19::chr13:96742396..96742407,+p@chr13:96742396..96742407
+
Hg19::chr13:97154628..97154630,+p@chr13:97154628..97154630
+
Hg19::chr13:97320979..97320984,+p@chr13:97320979..97320984
+


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
neuronal stem cell4.25e-088
neuron4.49e-086
neuroblast4.49e-086
electrically signaling cell4.49e-086
Uber Anatomy
Ontology termp-valuen
central nervous system6.10e-6581
neural tube9.80e-6256
neural rod9.80e-6256
future spinal cord9.80e-6256
neural keel9.80e-6256
nervous system1.12e-5889
regional part of nervous system1.21e-5753
regional part of brain1.21e-5753
regional part of forebrain5.67e-5341
forebrain5.67e-5341
anterior neural tube5.67e-5341
future forebrain5.67e-5341
brain1.33e-5168
future brain1.33e-5168
brain grey matter6.58e-4934
gray matter6.58e-4934
telencephalon8.97e-4934
cerebral hemisphere1.74e-4632
regional part of telencephalon5.71e-4632
neurectoderm1.06e-4086
neural plate2.49e-4082
presumptive neural plate2.49e-4082
adult organism1.72e-37114
cerebral cortex1.03e-3625
pallium1.03e-3625
regional part of cerebral cortex1.12e-3622
neocortex1.58e-3320
pre-chordal neural plate4.32e-3361
ecto-epithelium1.29e-32104
ectoderm-derived structure4.87e-31171
ectoderm4.87e-31171
presumptive ectoderm4.87e-31171
structure with developmental contribution from neural crest8.25e-25132
organ system subdivision4.84e-21223
basal ganglion8.45e-149
nuclear complex of neuraxis8.45e-149
aggregate regional part of brain8.45e-149
collection of basal ganglia8.45e-149
cerebral subcortex8.45e-149
neural nucleus2.07e-139
nucleus of brain2.07e-139
tube6.51e-13192
anatomical cluster2.38e-12373
temporal lobe3.26e-126
gyrus8.09e-116
telencephalic nucleus1.35e-107
posterior neural tube1.56e-1015
chordal neural plate1.56e-1015
limbic system1.98e-095
parietal lobe2.33e-095
brainstem2.85e-096
occipital lobe4.13e-095
anatomical conduit4.34e-08240
multi-tissue structure1.31e-07342
epithelium1.53e-07306
cell layer2.64e-07309
segmental subdivision of hindbrain3.67e-0712
hindbrain3.67e-0712
presumptive hindbrain3.67e-0712
corpus striatum5.54e-074
striatum5.54e-074
ventral part of telencephalon5.54e-074
future corpus striatum5.54e-074


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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