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Coexpression cluster:C3136: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!2.40e-66!57;UBERON:0005068!2.40e-66!57;UBERON:0006241!2.40e-66!57;UBERON:0007135!2.40e-66!57;UBERON:0002616!1.89e-60!59;UBERON:0001017!8.05e-58!82;UBERON:0005743!1.31e-56!86;UBERON:0002780!2.76e-56!41;UBERON:0001890!2.76e-56!41;UBERON:0006240!2.76e-56!41;UBERON:0003075!9.14e-55!86;UBERON:0007284!9.14e-55!86;UBERON:0003080!1.04e-54!42;UBERON:0000955!2.12e-54!69;UBERON:0006238!2.12e-54!69;UBERON:0002346!7.81e-54!90;UBERON:0000073!7.67e-52!94;UBERON:0001016!7.67e-52!94;UBERON:0002020!1.43e-50!34;UBERON:0003528!1.43e-50!34;UBERON:0001893!1.81e-50!34;UBERON:0002791!2.59e-48!33;UBERON:0001869!4.00e-47!32;UBERON:0007023!2.77e-45!115;UBERON:0003056!6.75e-41!61;UBERON:0000153!2.53e-40!129;UBERON:0007811!2.53e-40!129;UBERON:0002619!7.81e-40!22;UBERON:0000033!8.56e-40!123;UBERON:0000924!4.04e-36!173;UBERON:0006601!4.04e-36!173;UBERON:0004121!5.25e-36!169;UBERON:0001950!5.90e-36!20;UBERON:0000956!1.93e-34!25;UBERON:0000203!1.93e-34!25;UBERON:0000025!8.07e-18!194;UBERON:0002420!8.72e-18!9;UBERON:0007245!8.72e-18!9;UBERON:0010009!8.72e-18!9;UBERON:0010011!8.72e-18!9;UBERON:0000454!8.72e-18!9;UBERON:0002308!1.36e-17!9;UBERON:0000125!1.36e-17!9;UBERON:0000200!1.95e-14!6;UBERON:0001871!9.35e-14!7;UBERON:0004111!9.88e-14!241;UBERON:0009663!9.88e-14!7;UBERON:0002298!3.43e-13!8;UBERON:0000477!3.88e-13!286;UBERON:0003076!9.72e-13!15;UBERON:0003057!9.72e-13!15;UBERON:0000064!4.26e-12!219;UBERON:0000475!9.79e-12!365;UBERON:0000349!1.09e-11!5;UBERON:0000483!2.04e-11!309;UBERON:0002021!3.62e-11!5;UBERON:0000119!3.73e-11!312;UBERON:0004733!1.64e-10!12;UBERON:0002028!1.64e-10!12;UBERON:0007277!1.64e-10!12;UBERON:0000481!5.29e-10!347;UBERON:0004732!1.40e-09!13;UBERON:0000062!2.69e-09!511;UBERON:0000922!4.31e-09!612;UBERON:0000369!5.71e-09!4;UBERON:0002435!5.71e-09!4;UBERON:0000204!5.71e-09!4;UBERON:0010082!5.71e-09!4;UBERON:0001872!4.08e-08!5;UBERON:0002771!5.30e-08!3;UBERON:0000923!7.44e-08!604;UBERON:0005291!7.44e-08!604;UBERON:0006598!7.44e-08!604;UBERON:0002532!7.44e-08!604;UBERON:0002050!8.32e-08!605;UBERON:0005423!8.32e-08!605;UBERON:0000988!9.45e-08!3;UBERON:0001896!1.40e-07!3;UBERON:0005290!1.40e-07!3;UBERON:0010096!1.40e-07!3;UBERON:0001894!2.01e-07!7;UBERON:0006222!2.01e-07!7;UBERON:0006331!3.74e-07!3;UBERON:0005383!7.27e-07!3;UBERON:0005382!7.27e-07!3;UBERON:0000468!7.69e-07!659
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}}
}}

Revision as of 18:55, 8 August 2012


Full id: C3136_medial_pons_parietal_amygdala_paracentral_brain_frontal



Phase1 CAGE Peaks

Hg19::chr11:26353753..26353767,+p7@ANO3
Hg19::chr1:236917218..236917230,+p8@ACTN2
Hg19::chr5:126984919..126984976,+p3@CTXN3


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:0051370ZASP binding0.00256093253267397
GO:0051374FATZ 1 binding0.00256093253267397
GO:0051373FATZ binding0.00341452645300212
GO:0031143pseudopodium0.00512163890781363
GO:0043197dendritic spine0.00614578576334893
GO:0030175filopodium0.00658447968675831
GO:0051289protein homotetramerization0.00658447968675831
GO:0048041focal adhesion formation0.00832156070721741
GO:0051262protein tetramerization0.00967235568457086
GO:0030035microspike biogenesis0.0116364904660761
GO:0005884actin filament0.0116364904660761
GO:0005925focal adhesion0.0119438065733289
GO:0005924cell-substrate adherens junction0.0119438065733289
GO:0030425dendrite0.0119438065733289
GO:0030055cell-matrix junction0.0119438065733289
GO:0005178integrin binding0.0119438065733289
GO:0051260protein homooligomerization0.0119438065733289
GO:0008307structural constituent of muscle0.0119438065733289
GO:0044463cell projection part0.0126612986249979
GO:0030031cell projection biogenesis0.0127954278973855
GO:0005912adherens junction0.0131602361543361
GO:0051259protein oligomerization0.0144213874903024
GO:0043005neuron projection0.0180166334790902
GO:0016323basolateral plasma membrane0.0181175114842883
GO:0007160cell-matrix adhesion0.0195096332609514
GO:0032403protein complex binding0.0195096332609514
GO:0031589cell-substrate adhesion0.0195096332609514
GO:0032990cell part morphogenesis0.0347246198242458
GO:0030030cell projection organization and biogenesis0.0347246198242458
GO:0048858cell projection morphogenesis0.0347246198242458
GO:0015629actin cytoskeleton0.0486932053992805
GO:0042995cell projection0.0498681839186583



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 tube2.40e-6657
neural rod2.40e-6657
future spinal cord2.40e-6657
neural keel2.40e-6657
regional part of brain1.89e-6059
central nervous system8.05e-5882
regional part of forebrain2.76e-5641
forebrain2.76e-5641
future forebrain2.76e-5641
neural plate9.14e-5586
presumptive neural plate9.14e-5586
anterior neural tube1.04e-5442
brain2.12e-5469
future brain2.12e-5469
neurectoderm7.81e-5490
regional part of nervous system7.67e-5294
nervous system7.67e-5294
gray matter1.43e-5034
brain grey matter1.43e-5034
telencephalon1.81e-5034
regional part of telencephalon2.59e-4833
cerebral hemisphere4.00e-4732
adult organism2.77e-45115
pre-chordal neural plate6.75e-4161
anterior region of body2.53e-40129
craniocervical region2.53e-40129
regional part of cerebral cortex7.81e-4022
head8.56e-40123
ectoderm4.04e-36173
presumptive ectoderm4.04e-36173
ectoderm-derived structure5.25e-36169
neocortex5.90e-3620
cerebral cortex1.93e-3425
pallium1.93e-3425
tube8.07e-18194
basal ganglion8.72e-189
nuclear complex of neuraxis8.72e-189
aggregate regional part of brain8.72e-189
collection of basal ganglia8.72e-189
cerebral subcortex8.72e-189
nucleus of brain1.36e-179
neural nucleus1.36e-179
gyrus1.95e-146
temporal lobe9.35e-147
anatomical conduit9.88e-14241
telencephalic nucleus9.88e-147
brainstem3.43e-138
anatomical cluster3.88e-13286
posterior neural tube9.72e-1315
chordal neural plate9.72e-1315
organ part4.26e-12219
organism subdivision9.79e-12365
limbic system1.09e-115
epithelium2.04e-11309
occipital lobe3.62e-115
cell layer3.73e-11312
segmental subdivision of hindbrain1.64e-1012
hindbrain1.64e-1012
presumptive hindbrain1.64e-1012
multi-tissue structure5.29e-10347
segmental subdivision of nervous system1.40e-0913
organ2.69e-09511
embryo4.31e-09612
corpus striatum5.71e-094
striatum5.71e-094
ventral part of telencephalon5.71e-094
future corpus striatum5.71e-094
parietal lobe4.08e-085
middle temporal gyrus5.30e-083
germ layer7.44e-08604
embryonic tissue7.44e-08604
presumptive structure7.44e-08604
epiblast (generic)7.44e-08604
embryonic structure8.32e-08605
developing anatomical structure8.32e-08605
pons9.45e-083
medulla oblongata1.40e-073
myelencephalon1.40e-073
future myelencephalon1.40e-073
diencephalon2.01e-077
future diencephalon2.01e-077
brainstem nucleus3.74e-073
caudate-putamen7.27e-073
dorsal striatum7.27e-073
multi-cellular organism7.69e-07659


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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