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Coexpression cluster:C765: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!5.85e-65!56;UBERON:0005068!5.85e-65!56;UBERON:0006241!5.85e-65!56;UBERON:0007135!5.85e-65!56;UBERON:0000073!8.16e-63!53;UBERON:0002616!8.16e-63!53;UBERON:0001893!1.29e-54!34;UBERON:0003528!1.58e-54!34;UBERON:0002020!1.58e-54!34;UBERON:0001869!3.58e-51!32;UBERON:0002791!4.55e-51!32;UBERON:0002780!3.05e-50!41;UBERON:0001890!3.05e-50!41;UBERON:0003080!3.05e-50!41;UBERON:0006240!3.05e-50!41;UBERON:0001017!3.48e-50!81;UBERON:0000955!1.01e-49!68;UBERON:0006238!1.01e-49!68;UBERON:0001016!1.56e-47!89;UBERON:0003075!5.03e-44!82;UBERON:0007284!5.03e-44!82;UBERON:0002346!1.92e-43!86;UBERON:0000956!8.47e-42!25;UBERON:0000203!8.47e-42!25;UBERON:0002619!5.95e-37!22;UBERON:0007023!9.01e-36!114;UBERON:0003056!2.04e-34!61;UBERON:0010371!2.79e-33!104;UBERON:0001950!4.09e-33!20;UBERON:0010314!2.79e-28!132;UBERON:0004121!4.27e-24!171;UBERON:0000924!4.27e-24!171;UBERON:0006601!4.27e-24!171;UBERON:0011216!2.00e-21!223;UBERON:0003076!2.72e-15!15;UBERON:0003057!2.72e-15!15;UBERON:0002420!2.84e-14!9;UBERON:0007245!2.84e-14!9;UBERON:0010009!2.84e-14!9;UBERON:0010011!2.84e-14!9;UBERON:0000454!2.84e-14!9;UBERON:0000025!5.38e-14!192;UBERON:0000125!6.36e-14!9;UBERON:0002308!6.36e-14!9;UBERON:0000477!8.29e-14!373;UBERON:0004733!2.59e-13!12;UBERON:0002028!2.59e-13!12;UBERON:0007277!2.59e-13!12;UBERON:0000200!1.05e-12!6;UBERON:0002298!2.92e-12!6;UBERON:0004732!4.01e-12!13;UBERON:0001872!2.01e-11!5;UBERON:0000349!4.90e-11!5;UBERON:0004111!5.44e-11!240;UBERON:0009663!1.24e-10!7;UBERON:0001871!1.52e-10!6;UBERON:0000064!2.44e-10!218;UBERON:0000481!5.57e-10!342;UBERON:0000369!1.82e-09!4;UBERON:0002435!1.82e-09!4;UBERON:0000204!1.82e-09!4;UBERON:0010082!1.82e-09!4;UBERON:0000483!1.56e-08!306;UBERON:0000119!2.60e-08!309;UBERON:0002680!2.81e-08!9;UBERON:0001895!2.81e-08!9;UBERON:0010092!2.81e-08!9;UBERON:0000922!4.22e-08!592;UBERON:0005383!1.21e-07!3;UBERON:0005382!1.21e-07!3;UBERON:0000062!1.62e-07!503;UBERON:0001870!2.87e-07!3;UBERON:0002021!2.95e-07!5;UBERON:0001896!2.99e-07!3;UBERON:0005290!2.99e-07!3;UBERON:0010096!2.99e-07!3;UBERON:0005423!3.15e-07!581
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|tfbs_overrepresentation_for_novel_motifs=0.253158,0.306045,0.246925,0.975357,1.14634,0.371921,0.44126,0.121034,0.11927,0.185549,0.344881,1.2098,0.0905352,0.430675,0.211157,0.230406,0.650562,0.168654,0.0986515,0.14663,0.246975,0.691891,0.36495,0.20812,0.779948,0.50266,0.267398,0.363006,0.214796,0.068246,0.325512,0.685875,0.14393,0.0919867,0.184525,0.0681075,0.182011,0.372963,0.163827,0.107051,1.0326,0.311187,1.97728,4.19172,0.00493315,0.273032,0.442265,0.335245,1.04773,0.214901,0.515974,0.453148,0.0475371,0.760015,0.908824,0.433372,4.27866,0.40339,0.240754,0.402472,0.725346,0.444449,0.119615,0.624068,0.461047,0.591283,0.99547,1.35949,1.61987,1.19869,0.299692,0.125091,0.0464399,0.906867,0.0876634,0.0798316,0.071925,0.607953,0.672773,0.280653,1.6609,0.623044,2.03019,0.123028,0.856604,0.00700967,0.0364455,0.233,0.540459,1.45821,1.08742,0.830286,0.702047,4.34615,0.212875,0.159241,0.0976799,0.743159,0.544807,0.0567143,0.164861,0.696605,0.737766,0.654073,0.580349,0.340854,0.638916,0.427507,0.285742,0.199366,0.256397,0.735091,0.679564,0.353283,1.04009,0.180771,0.0096263,0.324453,0.58906,3.55142,0.898765,0.538171,0.369441,0.471181,1.14929,0.608677,0.435413,0.706859,0.940494,0.482616,0.830959,0.328039,0.954592,0.468088,1.10012,0.0617084,0.32024,0.363513,2.40453,1.9115,1.51034,1.02151,0.437004,0.739749,0.582016,1.02425,0.566218,1.75262,0.308276,0.449933,0.0413159,0.0216333,0.831331,0.113748,0.444001,1.22899,0.525224,0.200973,0.286011,0.261307,1.02032,0.813307,0.672017,0.729849,0.597299,0.459987,0.137885,0.440034,0.000550667
}}
}}

Revision as of 14:27, 26 November 2012


Full id: C765_cerebellum_parietal_occipital_hippocampus_caudate_medial_middle



Phase1 CAGE Peaks

Hg19::chr1:14978449..14978454,+p@chr1:14978449..14978454
+
Hg19::chr1:14978553..14978564,+p@chr1:14978553..14978564
+
Hg19::chr1:14978669..14978680,+p@chr1:14978669..14978680
+
Hg19::chr1:14978683..14978695,+p@chr1:14978683..14978695
+
Hg19::chr1:14978712..14978721,+p@chr1:14978712..14978721
+
Hg19::chr1:14978742..14978753,+p@chr1:14978742..14978753
+
Hg19::chr1:14978759..14978773,+p@chr1:14978759..14978773
+
Hg19::chr1:14978808..14978827,+p@chr1:14978808..14978827
+
Hg19::chr1:14978851..14978885,+p@chr1:14978851..14978885
+
Hg19::chr22:49016088..49016100,+p@chr22:49016088..49016100
+
Hg19::chr8:10306478..10306490,+p@chr8:10306478..10306490
+


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
neural tube5.85e-6556
neural rod5.85e-6556
future spinal cord5.85e-6556
neural keel5.85e-6556
regional part of nervous system8.16e-6353
regional part of brain8.16e-6353
telencephalon1.29e-5434
brain grey matter1.58e-5434
gray matter1.58e-5434
cerebral hemisphere3.58e-5132
regional part of telencephalon4.55e-5132
regional part of forebrain3.05e-5041
forebrain3.05e-5041
anterior neural tube3.05e-5041
future forebrain3.05e-5041
central nervous system3.48e-5081
brain1.01e-4968
future brain1.01e-4968
nervous system1.56e-4789
neural plate5.03e-4482
presumptive neural plate5.03e-4482
neurectoderm1.92e-4386
cerebral cortex8.47e-4225
pallium8.47e-4225
regional part of cerebral cortex5.95e-3722
adult organism9.01e-36114
pre-chordal neural plate2.04e-3461
ecto-epithelium2.79e-33104
neocortex4.09e-3320
structure with developmental contribution from neural crest2.79e-28132
ectoderm-derived structure4.27e-24171
ectoderm4.27e-24171
presumptive ectoderm4.27e-24171
organ system subdivision2.00e-21223
posterior neural tube2.72e-1515
chordal neural plate2.72e-1515
basal ganglion2.84e-149
nuclear complex of neuraxis2.84e-149
aggregate regional part of brain2.84e-149
collection of basal ganglia2.84e-149
cerebral subcortex2.84e-149
tube5.38e-14192
neural nucleus6.36e-149
nucleus of brain6.36e-149
anatomical cluster8.29e-14373
segmental subdivision of hindbrain2.59e-1312
hindbrain2.59e-1312
presumptive hindbrain2.59e-1312
gyrus1.05e-126
brainstem2.92e-126
segmental subdivision of nervous system4.01e-1213
parietal lobe2.01e-115
limbic system4.90e-115
anatomical conduit5.44e-11240
telencephalic nucleus1.24e-107
temporal lobe1.52e-106
organ part2.44e-10218
multi-tissue structure5.57e-10342
corpus striatum1.82e-094
striatum1.82e-094
ventral part of telencephalon1.82e-094
future corpus striatum1.82e-094
epithelium1.56e-08306
cell layer2.60e-08309
regional part of metencephalon2.81e-089
metencephalon2.81e-089
future metencephalon2.81e-089
embryo4.22e-08592
caudate-putamen1.21e-073
dorsal striatum1.21e-073
organ1.62e-07503
frontal cortex2.87e-073
occipital lobe2.95e-075
medulla oblongata2.99e-073
myelencephalon2.99e-073
future myelencephalon2.99e-073
developing anatomical structure3.15e-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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