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Coexpression cluster:C1539: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!9.42e-59!114;UBERON:0001017!5.85e-56!81;UBERON:0001016!3.01e-54!89;UBERON:0001049!1.61e-53!56;UBERON:0005068!1.61e-53!56;UBERON:0006241!1.61e-53!56;UBERON:0007135!1.61e-53!56;UBERON:0000073!5.96e-53!53;UBERON:0002616!5.96e-53!53;UBERON:0002346!1.18e-45!86;UBERON:0000955!1.76e-45!68;UBERON:0006238!1.76e-45!68;UBERON:0003075!1.32e-43!82;UBERON:0007284!1.32e-43!82;UBERON:0002780!2.02e-40!41;UBERON:0001890!2.02e-40!41;UBERON:0003080!2.02e-40!41;UBERON:0006240!2.02e-40!41;UBERON:0001893!6.55e-39!34;UBERON:0003528!1.05e-38!34;UBERON:0002020!1.05e-38!34;UBERON:0001869!7.78e-38!32;UBERON:0002791!4.89e-37!32;UBERON:0004121!1.43e-32!171;UBERON:0000924!1.43e-32!171;UBERON:0006601!1.43e-32!171;UBERON:0003056!1.65e-32!61;UBERON:0010371!6.31e-32!104;UBERON:0000956!7.74e-31!25;UBERON:0000203!7.74e-31!25;UBERON:0002619!8.81e-28!22;UBERON:0010314!1.42e-27!132;UBERON:0011216!2.56e-27!223;UBERON:0001950!2.11e-25!20;UBERON:0003076!8.81e-14!15;UBERON:0003057!8.81e-14!15;UBERON:0000477!9.53e-14!373;UBERON:0004733!2.37e-13!12;UBERON:0002028!2.37e-13!12;UBERON:0007277!2.37e-13!12;UBERON:0004732!4.99e-12!13;UBERON:0000468!8.29e-12!656;UBERON:0000064!1.04e-10!218;UBERON:0002680!2.25e-10!9;UBERON:0001895!2.25e-10!9;UBERON:0010092!2.25e-10!9;UBERON:0000481!2.60e-10!342;UBERON:0002420!4.32e-10!9;UBERON:0007245!4.32e-10!9;UBERON:0010009!4.32e-10!9;UBERON:0010011!4.32e-10!9;UBERON:0000454!4.32e-10!9;UBERON:0000025!1.09e-09!192;UBERON:0000125!2.61e-09!9;UBERON:0002308!2.61e-09!9;UBERON:0000922!2.80e-09!592;UBERON:0001871!3.22e-09!6;UBERON:0000200!1.12e-08!6;UBERON:0000062!8.84e-08!503;UBERON:0004111!9.81e-08!240;UBERON:0002037!1.08e-07!6;UBERON:0006215!1.08e-07!6;UBERON:0009663!1.09e-07!7;UBERON:0000349!1.26e-07!5;UBERON:0002021!1.67e-07!5;UBERON:0000467!2.35e-07!624;UBERON:0002050!2.40e-07!564;UBERON:0002298!2.75e-07!6;UBERON:0000923!2.78e-07!560;UBERON:0010316!2.78e-07!560;UBERON:0005291!2.78e-07!560;UBERON:0006598!2.78e-07!560;UBERON:0010317!2.78e-07!560;UBERON:0002532!2.78e-07!560;UBERON:0000480!2.79e-07!625;UBERON:0001872!3.14e-07!5;UBERON:0005423!4.47e-07!581
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|tfbs_overrepresentation_for_novel_motifs=1.12961,0.946942,1.11302,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.555913,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.664996,0.127969,0.436569,0.6169,0.576478,1.00694,0.483957,0.730467,0.202389,0.574247,0.396295,2.34526,0.530785,0.92701,0.816912,1.19786,0.35719,0.134746,1.66498,3.57219,0.329602,0.69481,0.355745,2.20706,0.323162,0.390088,1.41477,0.468392,1.59472,0.542147,0.304272,0.396429,0.745008,0.675919,0.891214,1.00488,1.15929,0.653901,0.400834,1.50361,0.547548,0.619193,0.968558,1.59978,0.267534,0.861462,4.00181,0.826413,1.24834,1.61834,0.916468,1.45553,1.25018,0.275507,2.04216,1.15727,2.57543,0.206105,0.562953,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.749276,1.10535,1.55864,0.794988,0.181871,1.81827,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.982236,0.44815,0.978783,0.430775,3.47269,1.29401,0.352243,3.49606,1.31236,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,2.3703,1.07876,1.32127,1.20639,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,1.48535,0.799467,2.01411,0.510514,0.306342,0.424432,2.79981,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,1.15112,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,1.48859
}}
}}

Revision as of 14:57, 26 November 2012


Full id: C1539_carcinoid_cerebellum_temporal_neuroectodermal_occipital_insula_postcentral



Phase1 CAGE Peaks

Hg19::chr7:70596291..70596318,+p@chr7:70596291..70596318
+
Hg19::chr7:70596521..70596558,+p@chr7:70596521..70596558
+
Hg19::chr7:70596628..70596711,+p1@WBSCR17
Hg19::chr7:70596874..70596898,+p3@WBSCR17
Hg19::chr7:70596902..70596919,+p4@WBSCR17
Hg19::chr7:70597109..70597144,+p2@WBSCR17


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 cell8.71e-098
neural cell4.34e-0825
neuron2.06e-076
neuroblast2.06e-076
electrically signaling cell2.06e-076
Uber Anatomy
Ontology termp-valuen
adult organism9.42e-59114
central nervous system5.85e-5681
nervous system3.01e-5489
neural tube1.61e-5356
neural rod1.61e-5356
future spinal cord1.61e-5356
neural keel1.61e-5356
regional part of nervous system5.96e-5353
regional part of brain5.96e-5353
neurectoderm1.18e-4586
brain1.76e-4568
future brain1.76e-4568
neural plate1.32e-4382
presumptive neural plate1.32e-4382
regional part of forebrain2.02e-4041
forebrain2.02e-4041
anterior neural tube2.02e-4041
future forebrain2.02e-4041
telencephalon6.55e-3934
brain grey matter1.05e-3834
gray matter1.05e-3834
cerebral hemisphere7.78e-3832
regional part of telencephalon4.89e-3732
ectoderm-derived structure1.43e-32171
ectoderm1.43e-32171
presumptive ectoderm1.43e-32171
pre-chordal neural plate1.65e-3261
ecto-epithelium6.31e-32104
cerebral cortex7.74e-3125
pallium7.74e-3125
regional part of cerebral cortex8.81e-2822
structure with developmental contribution from neural crest1.42e-27132
organ system subdivision2.56e-27223
neocortex2.11e-2520
posterior neural tube8.81e-1415
chordal neural plate8.81e-1415
anatomical cluster9.53e-14373
segmental subdivision of hindbrain2.37e-1312
hindbrain2.37e-1312
presumptive hindbrain2.37e-1312
segmental subdivision of nervous system4.99e-1213
multi-cellular organism8.29e-12656
organ part1.04e-10218
regional part of metencephalon2.25e-109
metencephalon2.25e-109
future metencephalon2.25e-109
multi-tissue structure2.60e-10342
basal ganglion4.32e-109
nuclear complex of neuraxis4.32e-109
aggregate regional part of brain4.32e-109
collection of basal ganglia4.32e-109
cerebral subcortex4.32e-109
tube1.09e-09192
neural nucleus2.61e-099
nucleus of brain2.61e-099
embryo2.80e-09592
temporal lobe3.22e-096
gyrus1.12e-086
organ8.84e-08503
anatomical conduit9.81e-08240
cerebellum1.08e-076
rhombic lip1.08e-076
telencephalic nucleus1.09e-077
limbic system1.26e-075
occipital lobe1.67e-075
anatomical system2.35e-07624
embryonic structure2.40e-07564
brainstem2.75e-076
germ layer2.78e-07560
germ layer / neural crest2.78e-07560
embryonic tissue2.78e-07560
presumptive structure2.78e-07560
germ layer / neural crest derived structure2.78e-07560
epiblast (generic)2.78e-07560
anatomical group2.79e-07625
parietal lobe3.14e-075
developing anatomical structure4.47e-07581


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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