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Coexpression cluster:C586: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!4.19e-72!53;UBERON:0002616!4.19e-72!53;UBERON:0001049!4.24e-68!56;UBERON:0005068!4.24e-68!56;UBERON:0006241!4.24e-68!56;UBERON:0007135!4.24e-68!56;UBERON:0000955!7.62e-65!68;UBERON:0006238!7.62e-65!68;UBERON:0001869!2.35e-59!32;UBERON:0001893!8.74e-56!34;UBERON:0003528!9.70e-56!34;UBERON:0002020!9.70e-56!34;UBERON:0001017!4.85e-54!81;UBERON:0002791!2.04e-52!32;UBERON:0002780!9.30e-52!41;UBERON:0001890!9.30e-52!41;UBERON:0003080!9.30e-52!41;UBERON:0006240!9.30e-52!41;UBERON:0002619!2.09e-50!22;UBERON:0001016!2.40e-48!89;UBERON:0001950!4.47e-47!20;UBERON:0003075!1.68e-45!82;UBERON:0007284!1.68e-45!82;UBERON:0000956!2.54e-44!25;UBERON:0000203!2.54e-44!25;UBERON:0002346!3.20e-43!86;UBERON:0010371!4.17e-35!104;UBERON:0007023!6.22e-35!114;UBERON:0003056!5.59e-34!61;UBERON:0000200!9.77e-30!6;UBERON:0010314!1.91e-29!132;UBERON:0004121!1.52e-23!171;UBERON:0000924!1.52e-23!171;UBERON:0006601!1.52e-23!171;UBERON:0004733!4.67e-21!12;UBERON:0002028!4.67e-21!12;UBERON:0007277!4.67e-21!12;UBERON:0004732!2.10e-19!13;UBERON:0002298!7.00e-19!6;UBERON:0011216!1.09e-18!223;UBERON:0000025!3.59e-17!192;UBERON:0001871!7.79e-17!6;UBERON:0003076!9.33e-17!15;UBERON:0003057!9.33e-17!15;UBERON:0000369!1.92e-16!4;UBERON:0002435!1.92e-16!4;UBERON:0000204!1.92e-16!4;UBERON:0010082!1.92e-16!4;UBERON:0002771!2.08e-15!2;UBERON:0000349!1.07e-13!5;UBERON:0001872!2.03e-13!5;UBERON:0000064!3.69e-13!218;UBERON:0002680!3.89e-13!9;UBERON:0001895!3.89e-13!9;UBERON:0010092!3.89e-13!9;UBERON:0002420!6.42e-13!9;UBERON:0007245!6.42e-13!9;UBERON:0010009!6.42e-13!9;UBERON:0010011!6.42e-13!9;UBERON:0000454!6.42e-13!9;UBERON:0004111!6.90e-13!240;UBERON:0000125!9.32e-13!9;UBERON:0002308!9.32e-13!9;UBERON:0001870!1.22e-10!3;UBERON:0005383!2.38e-10!3;UBERON:0005382!2.38e-10!3;UBERON:0001896!2.49e-10!3;UBERON:0005290!2.49e-10!3;UBERON:0010096!2.49e-10!3;UBERON:0000988!2.88e-10!3;UBERON:0009663!1.25e-09!7;UBERON:0000477!2.01e-09!373;UBERON:0000483!3.61e-09!306;UBERON:0000119!4.89e-09!309;UBERON:0003112!1.02e-08!1;UBERON:0011158!1.02e-08!1;UBERON:0003128!1.02e-08!1;UBERON:0001703!1.02e-08!1;UBERON:0002241!1.02e-08!1;UBERON:0004761!1.02e-08!1;UBERON:0009617!1.02e-08!1;UBERON:0000481!1.15e-08!342;UBERON:0002022!1.18e-08!1;UBERON:0007190!1.59e-08!1;UBERON:0001874!1.84e-08!1;UBERON:0001882!2.13e-08!1;UBERON:0005403!2.13e-08!1;UBERON:0002902!3.06e-08!1;UBERON:0009899!3.06e-08!1;UBERON:0002581!3.53e-08!1
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|tfbs_overrepresentation_for_novel_motifs=0.514064,0.217977,0.167518,0.277483,0.429786,0.757608,0.899058,0.241,0.510737,0.1732,0.252096,0.3759,0.0469688,0.329255,0.427489,0.153757,0.534852,0.33964,0.431744,0.351904,0.968262,0.213423,0.26993,0.833341,0.581509,0.395548,0.348576,0.268197,0.434999,0.131814,0.662646,0.568576,0.0851517,0.180835,0.116543,0.323509,0.114552,0.27709,0.675484,0.0583135,0.370199,0.222502,0.118046,0.136946,0.0661778,0.189598,0.901103,0.243586,0.0362731,0.141004,0.407934,0.349819,0.224172,0.639823,0.784252,0.331716,0.442382,0.821863,0.310516,0.303639,0.606437,0.90555,0.0672442,0.509653,0.357077,0.478604,0.869007,1.22829,0.559029,1.06908,0.212516,0.249409,0.219458,0.782342,0.171892,0.357608,0.930185,0.494371,0.556046,0.196113,0.443974,0.50868,0.938671,0.245133,0.733386,0.08967,0.872841,0.0308053,0.430803,1.32629,0.95934,0.70782,0.584068,0.622541,0.431036,0.658841,0.750268,0.623577,0.434875,0.0255063,0.10113,0.578851,0.618385,1.33072,0.468285,0.248535,0.523764,0.326366,0.20048,0.403142,1.00057,0.61581,0.163638,0.719501,0.912801,0.113572,0.570177,0.234099,0.476505,0.304012,0.77444,0.428661,0.75254,0.366411,1.02031,0.495057,0.33358,0.588683,0.815183,0.0973529,0.708473,0.237246,0.828971,0.363559,0.971853,0.283882,0.230408,0.740422,0.930667,1.77777,1.3781,0.894557,0.335034,0.620293,0.469857,0.297516,0.454976,1.61933,0.627312,0.294496,0.197244,0.108176,0.708834,0.225902,1.6213,1.09904,0.41656,0.129698,1.10122,0.179634,0.893382,0.691354,1.36699,0.181952,0.48429,0.356103,0.580438,0.337803,0.162843
}}
}}

Revision as of 14:19, 26 November 2012


Full id: C586_cerebellum_brain_occipital_middle_parietal_medial_amygdala



Phase1 CAGE Peaks

Hg19::chr11:132807611..132807618,-p@chr11:132807611..132807618
-
Hg19::chr11:132814188..132814199,-p@chr11:132814188..132814199
-
Hg19::chr13:102746160..102746164,-p@chr13:102746160..102746164
-
Hg19::chr16:6493692..6493697,+p@chr16:6493692..6493697
+
Hg19::chr17:884354..884374,-p@chr17:884354..884374
-
Hg19::chr19:13317729..13317738,-p@chr19:13317729..13317738
-
Hg19::chr1:18433873..18433888,+p8@IGSF21
Hg19::chr20:33815160..33815166,-p@chr20:33815160..33815166
-
Hg19::chr22:51158914..51158921,+p13@SHANK3
Hg19::chr5:160820302..160820306,-p@chr5:160820302..160820306
-
Hg19::chr5:176256892..176256896,+p@chr5:176256892..176256896
+
Hg19::chr7:153634554..153634556,+p@chr7:153634554..153634556
+
Hg19::chr7:36561860..36561869,-p@chr7:36561860..36561869
-
Hg19::chr8:9776684..9776691,-p@chr8:9776684..9776691
-
Hg19::chr9:114312975..114312986,+p@chr9:114312975..114312986
+


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:0001838embryonic epithelial tube formation0.0187743671962285
GO:0016331morphogenesis of embryonic epithelium0.0187743671962285
GO:0002009morphogenesis of an epithelium0.0304695680059167
GO:0035239tube morphogenesis0.0304695680059167
GO:0048598embryonic morphogenesis0.0304695680059167
GO:0035295tube development0.0304695680059167
GO:0045211postsynaptic membrane0.0304695680059167
GO:0000165MAPKKK cascade0.0304695680059167
GO:0044456synapse part0.0304695680059167
GO:0009790embryonic development0.0399830940917626



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
regional part of nervous system4.19e-7253
regional part of brain4.19e-7253
neural tube4.24e-6856
neural rod4.24e-6856
future spinal cord4.24e-6856
neural keel4.24e-6856
brain7.62e-6568
future brain7.62e-6568
cerebral hemisphere2.35e-5932
telencephalon8.74e-5634
brain grey matter9.70e-5634
gray matter9.70e-5634
central nervous system4.85e-5481
regional part of telencephalon2.04e-5232
regional part of forebrain9.30e-5241
forebrain9.30e-5241
anterior neural tube9.30e-5241
future forebrain9.30e-5241
regional part of cerebral cortex2.09e-5022
nervous system2.40e-4889
neocortex4.47e-4720
neural plate1.68e-4582
presumptive neural plate1.68e-4582
cerebral cortex2.54e-4425
pallium2.54e-4425
neurectoderm3.20e-4386
ecto-epithelium4.17e-35104
adult organism6.22e-35114
pre-chordal neural plate5.59e-3461
gyrus9.77e-306
structure with developmental contribution from neural crest1.91e-29132
ectoderm-derived structure1.52e-23171
ectoderm1.52e-23171
presumptive ectoderm1.52e-23171
segmental subdivision of hindbrain4.67e-2112
hindbrain4.67e-2112
presumptive hindbrain4.67e-2112
segmental subdivision of nervous system2.10e-1913
brainstem7.00e-196
organ system subdivision1.09e-18223
tube3.59e-17192
temporal lobe7.79e-176
posterior neural tube9.33e-1715
chordal neural plate9.33e-1715
corpus striatum1.92e-164
striatum1.92e-164
ventral part of telencephalon1.92e-164
future corpus striatum1.92e-164
middle temporal gyrus2.08e-152
limbic system1.07e-135
parietal lobe2.03e-135
organ part3.69e-13218
regional part of metencephalon3.89e-139
metencephalon3.89e-139
future metencephalon3.89e-139
basal ganglion6.42e-139
nuclear complex of neuraxis6.42e-139
aggregate regional part of brain6.42e-139
collection of basal ganglia6.42e-139
cerebral subcortex6.42e-139
anatomical conduit6.90e-13240
neural nucleus9.32e-139
nucleus of brain9.32e-139
frontal cortex1.22e-103
caudate-putamen2.38e-103
dorsal striatum2.38e-103
medulla oblongata2.49e-103
myelencephalon2.49e-103
future myelencephalon2.49e-103
pons2.88e-103
telencephalic nucleus1.25e-097
anatomical cluster2.01e-09373
epithelium3.61e-09306
cell layer4.89e-09309
olfactory region1.02e-081
primary subdivision of skull1.02e-081
cranium1.02e-081
neurocranium1.02e-081
chondrocranium1.02e-081
cartilaginous neurocranium1.02e-081
head paraxial mesoderm1.02e-081
multi-tissue structure1.15e-08342
insula1.18e-081
paracentral gyrus1.59e-081
putamen1.84e-081
nucleus accumbens2.13e-081
ventral striatum2.13e-081
occipital pole3.06e-081
pole of cerebral hemisphere3.06e-081
postcentral gyrus3.53e-081


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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