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Coexpression cluster:C376: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!8.80e-95!53;UBERON:0002616!8.80e-95!53;UBERON:0001049!1.65e-94!56;UBERON:0005068!1.65e-94!56;UBERON:0006241!1.65e-94!56;UBERON:0007135!1.65e-94!56;UBERON:0000955!3.88e-85!68;UBERON:0006238!3.88e-85!68;UBERON:0001893!4.76e-84!34;UBERON:0003528!9.26e-84!34;UBERON:0002020!9.26e-84!34;UBERON:0001869!4.40e-83!32;UBERON:0001017!2.13e-82!81;UBERON:0002780!1.48e-79!41;UBERON:0001890!1.48e-79!41;UBERON:0003080!1.48e-79!41;UBERON:0006240!1.48e-79!41;UBERON:0002619!3.32e-79!22;UBERON:0001016!3.45e-77!89;UBERON:0002791!2.41e-76!32;UBERON:0001950!3.05e-71!20;UBERON:0000956!1.85e-69!25;UBERON:0000203!1.85e-69!25;UBERON:0003075!6.91e-66!82;UBERON:0007284!6.91e-66!82;UBERON:0002346!1.78e-62!86;UBERON:0003056!2.52e-55!61;UBERON:0010371!2.45e-50!104;UBERON:0007023!1.06e-45!114;UBERON:0010314!2.33e-40!132;UBERON:0004121!1.21e-38!171;UBERON:0000924!1.21e-38!171;UBERON:0006601!1.21e-38!171;UBERON:0011216!2.68e-29!223;UBERON:0000200!4.01e-26!6;UBERON:0001871!2.12e-22!6;UBERON:0000025!4.22e-22!192;UBERON:0001872!6.77e-22!5;UBERON:0000349!8.04e-22!5;UBERON:0002298!4.12e-17!6;UBERON:0002420!2.08e-16!9;UBERON:0007245!2.08e-16!9;UBERON:0010009!2.08e-16!9;UBERON:0010011!2.08e-16!9;UBERON:0000454!2.08e-16!9;UBERON:0003076!2.51e-16!15;UBERON:0003057!2.51e-16!15;UBERON:0004111!4.72e-16!240;UBERON:0004733!4.99e-16!12;UBERON:0002028!4.99e-16!12;UBERON:0007277!4.99e-16!12;UBERON:0000125!5.56e-16!9;UBERON:0002308!5.56e-16!9;UBERON:0000477!6.02e-15!373;UBERON:0000064!6.76e-15!218;UBERON:0004732!1.01e-14!13;UBERON:0001870!4.67e-14!3;UBERON:0002021!4.68e-14!5;UBERON:0000988!3.49e-13!3;UBERON:0000483!1.08e-11!306;UBERON:0000119!1.68e-11!309;UBERON:0002680!2.04e-11!9;UBERON:0001895!2.04e-11!9;UBERON:0010092!2.04e-11!9;UBERON:0000481!2.01e-10!342;UBERON:0000369!4.78e-10!4;UBERON:0002435!4.78e-10!4;UBERON:0000204!4.78e-10!4;UBERON:0010082!4.78e-10!4;UBERON:0001876!6.93e-10!2;UBERON:0002702!9.40e-10!2;UBERON:0002771!1.22e-09!2;UBERON:0009663!1.23e-09!7;UBERON:0001954!1.51e-09!2;UBERON:0003022!1.51e-09!2;UBERON:0002421!1.51e-09!2;UBERON:0002600!1.51e-09!2;UBERON:0002148!3.24e-09!2;UBERON:0006331!3.24e-09!2;UBERON:0009662!3.24e-09!2;UBERON:0000062!2.62e-07!503;UBERON:0000923!8.08e-07!560;UBERON:0010316!8.08e-07!560;UBERON:0005291!8.08e-07!560;UBERON:0006598!8.08e-07!560;UBERON:0010317!8.08e-07!560;UBERON:0002532!8.08e-07!560
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6,0.0402644,0.657846,0.075633,0.580421,0.30962,0.274958,0.235446,0.0899939,0.00613255,0.808226,0.0857995,0.698764,0.557824,0.808735,0.680223,0.311854,0.186434,0.436473
|tfbs_overrepresentation_for_novel_motifs=0.765264,1.59687,0.741916,0.115973,0.339547,0.115097,0.930842,0.497522,0.747901,1.43201,0.327522,0.185675,2.24236,0.461744,0.145089,0.168654,0.312612,0.240825,0.386787,0.656547,0.0508801,0.51164,1.74297,0.0354608,0.242214,1.10054,0.0680967,1.1843,0.622658,0.601895,1.54095,0.341173,0.368873,0.561639,0.818635,0.866515,0.503302,0.746129,0.438438,3.55227,0.11321,0.985113,0.292915,0.334058,1.73228,1.27185,0.480607,1.07732,0.0895191,0.973887,1.1377,0.498457,1.085,0.402924,0.532737,0.466119,0.153794,0.82781,1.45544,0.825331,1.73422,0.939578,1.06217,0.792735,0.511492,0.266103,0.611096,0.954146,0.33304,0.800453,1.40858,0.150977,2.83074,0.530988,2.63419,2.46694,0.424496,0.764065,0.330507,0.234869,0.0374788,0.290785,0.171482,0.147002,1.22041,2.69448,0.101368,0.380635,0.227861,1.04966,0.695939,0.463366,0.354445,0.0778659,0.147147,0.0876739,0.10074,1.00892,0.231068,1.25395,0.0934024,0.349965,0.384158,0.846519,0.25774,0.66118,0.819287,0.456614,0.24191,1.73757,1.18654,0.381914,1.11419,1.14677,0.652077,0.0261337,2.42823,2.1058,0.730665,0.394953,0.523757,0.641925,0.113636,0.178598,0.753832,0.27955,0.154657,0.942299,0.561176,0.424823,0.463953,0.30248,0.573914,0.176484,0.707783,0.354931,0.086099,0.11017,0.668879,1.49486,1.10037,0.634967,0.155698,0.385822,0.259011,0.129436,1.27895,1.33792,0.273743,1.29735,0.350692,1.47636,0.464277,0.129488,0.938352,0.829202,0.216727,0.133083,0.889231,1.21172,1.53216,0.448609,0.329893,0.212291,0.270734,0.170987,0.874352,0.476964,0.760364
}}
}}

Revision as of 14:10, 26 November 2012


Full id: C376_brain_temporal_insula_frontal_occipital_postcentral_paracentral



Phase1 CAGE Peaks

Hg19::chr11:20690677..20690691,+p4@NELL1
Hg19::chr11:70672700..70672711,-p21@SHANK2
Hg19::chr15:52043722..52043735,-p7@LYSMD2
Hg19::chr15:75249573..75249587,-p12@RPP25
Hg19::chr15:77988485..77988494,-p27@LINGO1
Hg19::chr16:2230120..2230121,-p@chr16:2230120..2230121
-
Hg19::chr16:57406456..57406465,+p3@CX3CL1
Hg19::chr19:12945382..12945400,-p2@RTBDN
Hg19::chr19:12945478..12945499,-p6@RTBDN
Hg19::chr19:18311186..18311201,+p@chr19:18311186..18311201
+
Hg19::chr19:40724239..40724242,-p3@TTC9B
Hg19::chr19:42482880..42482902,+p@chr19:42482880..42482902
+
Hg19::chr19:46296190..46296207,-p4@DMWD
Hg19::chr19:822429..822477,-p4@MIR3187
Hg19::chr1:155291286..155291312,+p10@RUSC1
Hg19::chr20:36560066..36560087,-p@chr20:36560066..36560087
-
Hg19::chr2:73511460..73511470,-p8@FBXO41
Hg19::chr2:74757308..74757330,+p6@HTRA2
Hg19::chr3:68053515..68053522,+p5@FAM19A1
Hg19::chr4:150999349..150999359,+p13@DCLK2
Hg19::chr4:6564686..6564690,-p@chr4:6564686..6564690
-
Hg19::chr5:112043148..112043155,+p14@APC
Hg19::chr5:63257007..63257019,-p7@HTR1A
Hg19::chr6:33395473..33395504,+p1@AK124666
Hg19::chr7:45613934..45613945,+p4@ADCY1
Hg19::chr8:10158713..10158718,+p22@MSRA
Hg19::chr8:4852171..4852180,-p14@CSMD1
Hg19::chr9:139872612..139872634,+p@chr9:139872612..139872634
+
Hg19::chr9:34957921..34957934,+p7@KIAA1045


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:0051983regulation of chromosome segregation0.0315259625574002
GO:0051041positive regulation of calcium-independent cell-cell adhesion0.0315259625574002
GO:0051988regulation of attachment of spindle microtubules to kinetochore0.0315259625574002
GO:0050902leukocyte adhesive activation0.0315259625574002
GO:0051040regulation of calcium-independent cell-cell adhesion0.0315259625574002
GO:0008608attachment of spindle microtubules to kinetochore0.0315259625574002



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 system8.80e-9553
regional part of brain8.80e-9553
neural tube1.65e-9456
neural rod1.65e-9456
future spinal cord1.65e-9456
neural keel1.65e-9456
brain3.88e-8568
future brain3.88e-8568
telencephalon4.76e-8434
brain grey matter9.26e-8434
gray matter9.26e-8434
cerebral hemisphere4.40e-8332
central nervous system2.13e-8281
regional part of forebrain1.48e-7941
forebrain1.48e-7941
anterior neural tube1.48e-7941
future forebrain1.48e-7941
regional part of cerebral cortex3.32e-7922
nervous system3.45e-7789
regional part of telencephalon2.41e-7632
neocortex3.05e-7120
cerebral cortex1.85e-6925
pallium1.85e-6925
neural plate6.91e-6682
presumptive neural plate6.91e-6682
neurectoderm1.78e-6286
pre-chordal neural plate2.52e-5561
ecto-epithelium2.45e-50104
adult organism1.06e-45114
structure with developmental contribution from neural crest2.33e-40132
ectoderm-derived structure1.21e-38171
ectoderm1.21e-38171
presumptive ectoderm1.21e-38171
organ system subdivision2.68e-29223
gyrus4.01e-266
temporal lobe2.12e-226
tube4.22e-22192
parietal lobe6.77e-225
limbic system8.04e-225
brainstem4.12e-176
basal ganglion2.08e-169
nuclear complex of neuraxis2.08e-169
aggregate regional part of brain2.08e-169
collection of basal ganglia2.08e-169
cerebral subcortex2.08e-169
posterior neural tube2.51e-1615
chordal neural plate2.51e-1615
anatomical conduit4.72e-16240
segmental subdivision of hindbrain4.99e-1612
hindbrain4.99e-1612
presumptive hindbrain4.99e-1612
neural nucleus5.56e-169
nucleus of brain5.56e-169
anatomical cluster6.02e-15373
organ part6.76e-15218
segmental subdivision of nervous system1.01e-1413
frontal cortex4.67e-143
occipital lobe4.68e-145
pons3.49e-133
epithelium1.08e-11306
cell layer1.68e-11309
regional part of metencephalon2.04e-119
metencephalon2.04e-119
future metencephalon2.04e-119
multi-tissue structure2.01e-10342
corpus striatum4.78e-104
striatum4.78e-104
ventral part of telencephalon4.78e-104
future corpus striatum4.78e-104
amygdala6.93e-102
middle frontal gyrus9.40e-102
middle temporal gyrus1.22e-092
telencephalic nucleus1.23e-097
Ammon's horn1.51e-092
lobe parts of cerebral cortex1.51e-092
hippocampal formation1.51e-092
limbic lobe1.51e-092
locus ceruleus3.24e-092
brainstem nucleus3.24e-092
hindbrain nucleus3.24e-092
organ2.62e-07503
germ layer8.08e-07560
germ layer / neural crest8.08e-07560
embryonic tissue8.08e-07560
presumptive structure8.08e-07560
germ layer / neural crest derived structure8.08e-07560
epiblast (generic)8.08e-07560


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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