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Coexpression cluster:C3468: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!2.20e-59!57;UBERON:0005068!2.20e-59!57;UBERON:0006241!2.20e-59!57;UBERON:0007135!2.20e-59!57;UBERON:0005743!1.23e-57!86;UBERON:0001017!4.26e-56!82;UBERON:0000073!3.86e-53!94;UBERON:0001016!3.86e-53!94;UBERON:0000955!2.81e-51!69;UBERON:0006238!2.81e-51!69;UBERON:0002616!4.04e-51!59;UBERON:0001893!6.69e-49!34;UBERON:0001869!9.16e-49!32;UBERON:0002020!1.29e-48!34;UBERON:0003528!1.29e-48!34;UBERON:0002791!7.67e-47!33;UBERON:0002780!1.67e-45!41;UBERON:0001890!1.67e-45!41;UBERON:0006240!1.67e-45!41;UBERON:0003080!3.26e-44!42;UBERON:0003075!1.73e-43!86;UBERON:0007284!1.73e-43!86;UBERON:0002346!5.77e-41!90;UBERON:0000956!7.69e-35!25;UBERON:0000203!7.69e-35!25;UBERON:0003056!6.25e-34!61;UBERON:0002619!1.01e-29!22;UBERON:0000033!1.44e-27!123;UBERON:0001950!3.63e-26!20;UBERON:0000153!1.11e-25!129;UBERON:0007811!1.11e-25!129;UBERON:0007023!2.80e-24!115;UBERON:0004121!2.93e-23!169;UBERON:0000924!2.15e-22!173;UBERON:0006601!2.15e-22!173;UBERON:0003076!1.13e-15!15;UBERON:0003057!1.13e-15!15;UBERON:0002308!4.91e-15!9;UBERON:0000125!4.91e-15!9;UBERON:0004733!1.93e-13!12;UBERON:0002028!1.93e-13!12;UBERON:0007277!1.93e-13!12;UBERON:0000025!8.59e-13!194;UBERON:0000200!1.63e-12!6;UBERON:0004732!2.95e-12!13;UBERON:0002420!1.40e-11!9;UBERON:0007245!1.40e-11!9;UBERON:0010009!1.40e-11!9;UBERON:0010011!1.40e-11!9;UBERON:0000454!1.40e-11!9;UBERON:0009663!1.57e-11!7;UBERON:0000369!5.73e-10!4;UBERON:0002435!5.73e-10!4;UBERON:0000204!5.73e-10!4;UBERON:0010082!5.73e-10!4;UBERON:0000064!9.08e-10!219;UBERON:0002298!2.50e-09!8;UBERON:0004111!3.24e-09!241;UBERON:0001871!4.47e-09!7;UBERON:0000473!1.22e-08!8;UBERON:0002680!1.28e-08!9;UBERON:0001895!1.28e-08!9;UBERON:0010092!1.28e-08!9;UBERON:0005383!7.48e-08!3;UBERON:0005382!7.48e-08!3;UBERON:0001872!1.17e-07!5;UBERON:0000988!1.79e-07!3;UBERON:0000349!3.05e-07!5;UBERON:0002021!4.79e-07!5;UBERON:0000483!5.48e-07!309;UBERON:0001896!6.80e-07!3;UBERON:0005290!6.80e-07!3;UBERON:0010096!6.80e-07!3;UBERON:0000119!8.35e-07!312;UBERON:0002771!9.50e-07!3
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}}
}}

Revision as of 19:11, 8 August 2012


Full id: C3468_non_iPS_pons_H9_teratocarcinoma_caudate_brain



Phase1 CAGE Peaks

Hg19::chr14:96342981..96343004,+p2@LOC100507043
Hg19::chr14:96343050..96343059,+p4@LOC100507043
Hg19::chr14:96343100..96343115,+p1@LOC100507043


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>


Cell Type
Ontology termp-valuen
embryonic stem cell6.47e-135
oligodendrocyte9.56e-087
macroglial cell9.56e-087
astrocyte9.56e-087
oligodendrocyte precursor cell9.56e-087
astrocyte of the cerebral cortex8.74e-073
Uber Anatomy
Ontology termp-valuen
neural tube2.20e-5957
neural rod2.20e-5957
future spinal cord2.20e-5957
neural keel2.20e-5957
central nervous system4.26e-5682
regional part of nervous system3.86e-5394
nervous system3.86e-5394
brain2.81e-5169
future brain2.81e-5169
regional part of brain4.04e-5159
telencephalon6.69e-4934
cerebral hemisphere9.16e-4932
gray matter1.29e-4834
brain grey matter1.29e-4834
regional part of telencephalon7.67e-4733
regional part of forebrain1.67e-4541
forebrain1.67e-4541
future forebrain1.67e-4541
anterior neural tube3.26e-4442
neural plate1.73e-4386
presumptive neural plate1.73e-4386
neurectoderm5.77e-4190
cerebral cortex7.69e-3525
pallium7.69e-3525
pre-chordal neural plate6.25e-3461
regional part of cerebral cortex1.01e-2922
head1.44e-27123
neocortex3.63e-2620
anterior region of body1.11e-25129
craniocervical region1.11e-25129
adult organism2.80e-24115
ectoderm-derived structure2.93e-23169
ectoderm2.15e-22173
presumptive ectoderm2.15e-22173
posterior neural tube1.13e-1515
chordal neural plate1.13e-1515
nucleus of brain4.91e-159
neural nucleus4.91e-159
segmental subdivision of hindbrain1.93e-1312
hindbrain1.93e-1312
presumptive hindbrain1.93e-1312
tube8.59e-13194
gyrus1.63e-126
segmental subdivision of nervous system2.95e-1213
basal ganglion1.40e-119
nuclear complex of neuraxis1.40e-119
aggregate regional part of brain1.40e-119
collection of basal ganglia1.40e-119
cerebral subcortex1.40e-119
telencephalic nucleus1.57e-117
corpus striatum5.73e-104
striatum5.73e-104
ventral part of telencephalon5.73e-104
future corpus striatum5.73e-104
organ part9.08e-10219
brainstem2.50e-098
anatomical conduit3.24e-09241
temporal lobe4.47e-097
testis1.22e-088
regional part of metencephalon1.28e-089
metencephalon1.28e-089
future metencephalon1.28e-089
caudate-putamen7.48e-083
dorsal striatum7.48e-083
parietal lobe1.17e-075
pons1.79e-073
limbic system3.05e-075
occipital lobe4.79e-075
epithelium5.48e-07309
medulla oblongata6.80e-073
myelencephalon6.80e-073
future myelencephalon6.80e-073
cell layer8.35e-07312
middle temporal gyrus9.50e-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.