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|full_id=C4570_placenta_hippocampus_pons_amygdala_occipital_medulla_cerebellum
|full_id=C4570_placenta_hippocampus_pons_amygdala_occipital_medulla_cerebellum
|id=C4570
|id=C4570
|ontology_enrichment_celltype=CL:0002274!8.63e-09!5;CL:0000457!8.63e-09!5;CL:0002191!8.63e-09!5;CL:0000097!8.63e-09!5;CL:0000831!8.63e-09!5;CL:0002028!8.63e-09!5
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.46e-61!57;UBERON:0005068!1.46e-61!57;UBERON:0006241!1.46e-61!57;UBERON:0007135!1.46e-61!57;UBERON:0000955!1.67e-54!69;UBERON:0006238!1.67e-54!69;UBERON:0002616!2.55e-53!59;UBERON:0001017!2.08e-52!82;UBERON:0005743!3.38e-51!86;UBERON:0007023!1.96e-50!115;UBERON:0002020!8.19e-50!34;UBERON:0003528!8.19e-50!34;UBERON:0001893!1.16e-49!34;UBERON:0002780!1.14e-48!41;UBERON:0001890!1.14e-48!41;UBERON:0006240!1.14e-48!41;UBERON:0000073!1.39e-48!94;UBERON:0001016!1.39e-48!94;UBERON:0002791!8.81e-48!33;UBERON:0003080!2.86e-47!42;UBERON:0001869!1.40e-46!32;UBERON:0003075!1.76e-43!86;UBERON:0007284!1.76e-43!86;UBERON:0002346!7.00e-41!90;UBERON:0002619!3.17e-40!22;UBERON:0001950!3.34e-36!20;UBERON:0000956!1.01e-34!25;UBERON:0000203!1.01e-34!25;UBERON:0003056!4.64e-31!61;UBERON:0000033!4.79e-27!123;UBERON:0000153!4.11e-25!129;UBERON:0007811!4.11e-25!129;UBERON:0004121!3.40e-22!169;UBERON:0000924!2.56e-21!173;UBERON:0006601!2.56e-21!173;UBERON:0002420!7.54e-17!9;UBERON:0007245!7.54e-17!9;UBERON:0010009!7.54e-17!9;UBERON:0010011!7.54e-17!9;UBERON:0000454!7.54e-17!9;UBERON:0002308!1.94e-16!9;UBERON:0000125!1.94e-16!9;UBERON:0003076!7.55e-15!15;UBERON:0003057!7.55e-15!15;UBERON:0000025!1.78e-13!194;UBERON:0004733!5.98e-13!12;UBERON:0002028!5.98e-13!12;UBERON:0007277!5.98e-13!12;UBERON:0009663!7.16e-13!7;UBERON:0000200!1.08e-12!6;UBERON:0001871!1.29e-12!7;UBERON:0002298!4.59e-12!8;UBERON:0004732!8.73e-12!13;UBERON:0000349!1.46e-11!5;UBERON:0001872!1.29e-10!5;UBERON:0002021!1.57e-10!5;UBERON:0004111!5.63e-10!241;UBERON:0000062!1.09e-08!511;UBERON:0000064!2.12e-08!219;UBERON:0000369!3.05e-08!4;UBERON:0002435!3.05e-08!4;UBERON:0000204!3.05e-08!4;UBERON:0010082!3.05e-08!4;UBERON:0002680!4.11e-08!9;UBERON:0001895!4.11e-08!9;UBERON:0010092!4.11e-08!9;UBERON:0000483!6.21e-08!309;UBERON:0000119!1.02e-07!312;UBERON:0000477!2.56e-07!286;UBERON:0000988!2.89e-07!3;UBERON:0002771!3.91e-07!3;UBERON:0000475!4.62e-07!365;UBERON:0001896!5.27e-07!3;UBERON:0005290!5.27e-07!3;UBERON:0010096!5.27e-07!3
}}
}}

Revision as of 14:50, 21 May 2012


Full id: C4570_placenta_hippocampus_pons_amygdala_occipital_medulla_cerebellum



Phase1 CAGE Peaks

Hg19::chr6:143929225..143929246,+p9@PHACTR2
Hg19::chr6:143929307..143929322,+p4@PHACTR2
Hg19::chr6:143929329..143929340,+p13@PHACTR2


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>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
neural tube1.46e-6157
neural rod1.46e-6157
future spinal cord1.46e-6157
neural keel1.46e-6157
brain1.67e-5469
future brain1.67e-5469
regional part of brain2.55e-5359
central nervous system2.08e-5282
adult organism1.96e-50115
gray matter8.19e-5034
brain grey matter8.19e-5034
telencephalon1.16e-4934
regional part of forebrain1.14e-4841
forebrain1.14e-4841
future forebrain1.14e-4841
regional part of nervous system1.39e-4894
nervous system1.39e-4894
regional part of telencephalon8.81e-4833
anterior neural tube2.86e-4742
cerebral hemisphere1.40e-4632
neural plate1.76e-4386
presumptive neural plate1.76e-4386
neurectoderm7.00e-4190
regional part of cerebral cortex3.17e-4022
neocortex3.34e-3620
cerebral cortex1.01e-3425
pallium1.01e-3425
pre-chordal neural plate4.64e-3161
head4.79e-27123
anterior region of body4.11e-25129
craniocervical region4.11e-25129
ectoderm-derived structure3.40e-22169
ectoderm2.56e-21173
presumptive ectoderm2.56e-21173
basal ganglion7.54e-179
nuclear complex of neuraxis7.54e-179
aggregate regional part of brain7.54e-179
collection of basal ganglia7.54e-179
cerebral subcortex7.54e-179
nucleus of brain1.94e-169
neural nucleus1.94e-169
posterior neural tube7.55e-1515
chordal neural plate7.55e-1515
tube1.78e-13194
segmental subdivision of hindbrain5.98e-1312
hindbrain5.98e-1312
presumptive hindbrain5.98e-1312
telencephalic nucleus7.16e-137
gyrus1.08e-126
temporal lobe1.29e-127
brainstem4.59e-128
segmental subdivision of nervous system8.73e-1213
limbic system1.46e-115
parietal lobe1.29e-105
occipital lobe1.57e-105
anatomical conduit5.63e-10241
organ1.09e-08511
organ part2.12e-08219
corpus striatum3.05e-084
striatum3.05e-084
ventral part of telencephalon3.05e-084
future corpus striatum3.05e-084
regional part of metencephalon4.11e-089
metencephalon4.11e-089
future metencephalon4.11e-089
epithelium6.21e-08309
cell layer1.02e-07312
anatomical cluster2.56e-07286
pons2.89e-073
middle temporal gyrus3.91e-073
organism subdivision4.62e-07365
medulla oblongata5.27e-073
myelencephalon5.27e-073
future myelencephalon5.27e-073


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.