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Coexpression cluster:C693: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!1.47e-114!56;UBERON:0005068!1.47e-114!56;UBERON:0006241!1.47e-114!56;UBERON:0007135!1.47e-114!56;UBERON:0000073!1.48e-102!53;UBERON:0002616!1.48e-102!53;UBERON:0001017!4.46e-93!81;UBERON:0000955!1.69e-86!68;UBERON:0006238!1.69e-86!68;UBERON:0001016!3.88e-83!89;UBERON:0003075!4.62e-80!82;UBERON:0007284!4.62e-80!82;UBERON:0002346!5.39e-76!86;UBERON:0002780!5.50e-73!41;UBERON:0001890!5.50e-73!41;UBERON:0003080!5.50e-73!41;UBERON:0006240!5.50e-73!41;UBERON:0007023!2.68e-65!114;UBERON:0003528!2.48e-64!34;UBERON:0002020!2.48e-64!34;UBERON:0001893!4.87e-64!34;UBERON:0010371!1.60e-61!104;UBERON:0002791!9.66e-57!32;UBERON:0001869!1.65e-56!32;UBERON:0010314!4.65e-52!132;UBERON:0003056!6.92e-51!61;UBERON:0004121!5.51e-42!171;UBERON:0000924!5.51e-42!171;UBERON:0006601!5.51e-42!171;UBERON:0003076!7.28e-42!15;UBERON:0003057!7.28e-42!15;UBERON:0000125!7.39e-38!9;UBERON:0002308!7.39e-38!9;UBERON:0002619!1.24e-37!22;UBERON:0000956!6.80e-33!25;UBERON:0000203!6.80e-33!25;UBERON:0001950!1.12e-30!20;UBERON:0011216!3.19e-30!223;UBERON:0004733!7.55e-30!12;UBERON:0002028!7.55e-30!12;UBERON:0007277!7.55e-30!12;UBERON:0002420!1.66e-29!9;UBERON:0007245!1.66e-29!9;UBERON:0010009!1.66e-29!9;UBERON:0010011!1.66e-29!9;UBERON:0000454!1.66e-29!9;UBERON:0009663!2.16e-29!7;UBERON:0000025!6.60e-28!192;UBERON:0004732!2.03e-27!13;UBERON:0002298!2.43e-27!6;UBERON:0004111!1.20e-20!240;UBERON:0002680!5.64e-18!9;UBERON:0001895!5.64e-18!9;UBERON:0010092!5.64e-18!9;UBERON:0000200!3.62e-17!6;UBERON:0000369!7.83e-17!4;UBERON:0002435!7.83e-17!4;UBERON:0000204!7.83e-17!4;UBERON:0010082!7.83e-17!4;UBERON:0000477!1.26e-15!373;UBERON:0000483!2.21e-15!306;UBERON:0000119!3.78e-15!309;UBERON:0001896!7.87e-15!3;UBERON:0005290!7.87e-15!3;UBERON:0010096!7.87e-15!3;UBERON:0002240!2.53e-14!3;UBERON:0005174!2.53e-14!3;UBERON:0001137!2.53e-14!3;UBERON:0000988!2.77e-14!3;UBERON:0000349!3.10e-14!5;UBERON:0000064!4.88e-14!218;UBERON:0005383!6.21e-13!3;UBERON:0005382!6.21e-13!3;UBERON:0000481!6.88e-11!342;UBERON:0002784!1.85e-10!4;UBERON:0001894!2.88e-10!7;UBERON:0006222!2.88e-10!7;UBERON:0002148!3.32e-10!2;UBERON:0006331!3.32e-10!2;UBERON:0009662!3.32e-10!2;UBERON:0001875!3.63e-10!2;UBERON:0006514!3.63e-10!2;UBERON:0001897!4.54e-10!2;UBERON:0010225!4.54e-10!2;UBERON:0001954!6.77e-10!2;UBERON:0003022!6.77e-10!2;UBERON:0002421!6.77e-10!2;UBERON:0002600!6.77e-10!2;UBERON:0001871!9.50e-10!6;UBERON:0001873!3.98e-09!2;UBERON:0010122!3.98e-09!2;UBERON:0002771!4.51e-09!2;UBERON:0002360!5.57e-09!2;UBERON:0000094!5.57e-09!2;UBERON:0010743!5.57e-09!2;UBERON:0000062!1.74e-08!503;UBERON:0001872!4.54e-08!5;UBERON:0002021!4.66e-08!5;UBERON:0002037!1.39e-07!6;UBERON:0006215!1.39e-07!6;UBERON:0000923!2.42e-07!560;UBERON:0010316!2.42e-07!560;UBERON:0005291!2.42e-07!560;UBERON:0006598!2.42e-07!560;UBERON:0010317!2.42e-07!560;UBERON:0002532!2.42e-07!560;UBERON:0002050!3.17e-07!564;UBERON:0005423!9.70e-07!581
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|tfbs_overrepresentation_for_novel_motifs=0.649083,0.128687,0.635061,0.345441,0.556358,0.910346,0.411652,0.340819,1.13732,0.782861,0.851693,0.451026,1.41978,0.401301,1.05539,0.207465,0.617549,0.148925,0.285173,0.533397,1.18892,0.356848,0.337221,1.64894,0.722285,0.471832,0.499542,0.335332,0.562141,0.454328,0.809412,0.65246,0.790946,0.268295,0.163884,0.117596,0.161511,0.912597,0.14439,0.306232,0.162847,0.777985,0.658594,0.187953,1.55214,0.693545,0.412635,0.308385,0.188988,0.192687,0.484909,0.423285,0.347648,0.725869,0.873575,1.83807,1.70369,0.374657,0.789982,0.373762,0.691524,0.414771,0.103208,0.591384,0.43102,0.559038,0.959746,1.32257,0.642589,1.16217,0.273995,1.17358,0.341688,0.871629,0.546891,0.510252,0.216432,0.575479,0.639503,0.710503,0.611084,0.590372,0.4307,0.703506,0.821696,0.00480132,0.0287315,1.17597,0.508983,1.42111,1.05129,0.795567,0.66846,0.130784,0.190761,0.853171,0.282722,0.709167,0.51326,0.701432,0.145361,0.663075,0.703825,0.621018,0.54826,0.313822,0.606045,1.02975,0.260543,0.177931,0.656353,0.701175,0.21882,0.325885,1.00416,0.483536,0.889895,0.297931,0.556847,0.414358,0.863578,0.506732,0.341589,0.44095,1.11293,0.576194,0.405934,0.673222,0.905059,0.856092,0.796235,0.301402,0.919079,0.437919,1.06395,0.740677,0.293853,0.892152,1.02226,1.87395,1.47317,0.985665,0.407489,0.70579,0.549903,0.367151,0.534339,1.71519,0.282284,0.128495,0.133101,0.0750447,0.796604,0.0978005,0.414334,1.19239,0.494,0.179455,0.260802,0.237047,0.984474,1.8329,0.638755,0.239672,0.564971,0.429983,1.25158,0.410452,0.51183
}}
}}

Revision as of 14:24, 26 November 2012


Full id: C693_cerebellum_medulla_spinal_locus_Hepatocyte_pons_thalamus



Phase1 CAGE Peaks

Hg19::chr11:7369947..7369952,+p@chr11:7369947..7369952
+
Hg19::chr12:109273861..109273889,+p1@DAO
Hg19::chr19:29493456..29493477,+p1@LOC100505835
Hg19::chr19:29493486..29493497,+p2@LOC100505835
Hg19::chr1:90885631..90885647,-p@chr1:90885631..90885647
-
Hg19::chr1:90885681..90885693,-p@chr1:90885681..90885693
-
Hg19::chr3:125997081..125997085,+p@chr3:125997081..125997085
+
Hg19::chr3:147111505..147111529,+p6@ZIC1
Hg19::chr6:138959791..138959803,-p@chr6:138959791..138959803
-
Hg19::chr9:73736331..73736347,-p3@TRPM3
Hg19::chrX:106692537..106692551,+p@chrX:106692537..106692551
+
Hg19::chrX:106692569..106692585,+p@chrX:106692569..106692585
+


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

GO IDGO nameFDR corrected p-value
GO:0003884D-amino-acid oxidase activity0.0358467233571613
GO:0008589regulation of smoothened signaling pathway0.0358467233571613
GO:0007224smoothened signaling pathway0.0453250397872941
GO:0016641oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor0.0453250397872941
GO:0042472inner ear morphogenesis0.0453250397872941
GO:0016638oxidoreductase activity, acting on the CH-NH2 group of donors0.0453250397872941
GO:0042471ear morphogenesis0.0453250397872941
GO:0048839inner ear development0.0477464012889728
GO:0043583ear development0.0477464012889728



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 tube1.47e-11456
neural rod1.47e-11456
future spinal cord1.47e-11456
neural keel1.47e-11456
regional part of nervous system1.48e-10253
regional part of brain1.48e-10253
central nervous system4.46e-9381
brain1.69e-8668
future brain1.69e-8668
nervous system3.88e-8389
neural plate4.62e-8082
presumptive neural plate4.62e-8082
neurectoderm5.39e-7686
regional part of forebrain5.50e-7341
forebrain5.50e-7341
anterior neural tube5.50e-7341
future forebrain5.50e-7341
adult organism2.68e-65114
brain grey matter2.48e-6434
gray matter2.48e-6434
telencephalon4.87e-6434
ecto-epithelium1.60e-61104
regional part of telencephalon9.66e-5732
cerebral hemisphere1.65e-5632
structure with developmental contribution from neural crest4.65e-52132
pre-chordal neural plate6.92e-5161
ectoderm-derived structure5.51e-42171
ectoderm5.51e-42171
presumptive ectoderm5.51e-42171
posterior neural tube7.28e-4215
chordal neural plate7.28e-4215
neural nucleus7.39e-389
nucleus of brain7.39e-389
regional part of cerebral cortex1.24e-3722
cerebral cortex6.80e-3325
pallium6.80e-3325
neocortex1.12e-3020
organ system subdivision3.19e-30223
segmental subdivision of hindbrain7.55e-3012
hindbrain7.55e-3012
presumptive hindbrain7.55e-3012
basal ganglion1.66e-299
nuclear complex of neuraxis1.66e-299
aggregate regional part of brain1.66e-299
collection of basal ganglia1.66e-299
cerebral subcortex1.66e-299
telencephalic nucleus2.16e-297
tube6.60e-28192
segmental subdivision of nervous system2.03e-2713
brainstem2.43e-276
anatomical conduit1.20e-20240
regional part of metencephalon5.64e-189
metencephalon5.64e-189
future metencephalon5.64e-189
gyrus3.62e-176
corpus striatum7.83e-174
striatum7.83e-174
ventral part of telencephalon7.83e-174
future corpus striatum7.83e-174
anatomical cluster1.26e-15373
epithelium2.21e-15306
cell layer3.78e-15309
medulla oblongata7.87e-153
myelencephalon7.87e-153
future myelencephalon7.87e-153
spinal cord2.53e-143
dorsal region element2.53e-143
dorsum2.53e-143
pons2.77e-143
limbic system3.10e-145
organ part4.88e-14218
caudate-putamen6.21e-133
dorsal striatum6.21e-133
multi-tissue structure6.88e-11342
regional part of diencephalon1.85e-104
diencephalon2.88e-107
future diencephalon2.88e-107
locus ceruleus3.32e-102
brainstem nucleus3.32e-102
hindbrain nucleus3.32e-102
globus pallidus3.63e-102
pallidum3.63e-102
dorsal plus ventral thalamus4.54e-102
thalamic complex4.54e-102
Ammon's horn6.77e-102
lobe parts of cerebral cortex6.77e-102
hippocampal formation6.77e-102
limbic lobe6.77e-102
temporal lobe9.50e-106
caudate nucleus3.98e-092
future caudate nucleus3.98e-092
middle temporal gyrus4.51e-092
meninx5.57e-092
membrane organ5.57e-092
meningeal cluster5.57e-092
organ1.74e-08503
parietal lobe4.54e-085
occipital lobe4.66e-085
cerebellum1.39e-076
rhombic lip1.39e-076


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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