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Coexpression cluster:C4320: Difference between revisions

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|ontology_enrichment_disease=DOID:3095!5.33e-07!22;DOID:2994!5.33e-07!22
|ontology_enrichment_disease=DOID:3095!5.33e-07!22;DOID:2994!5.33e-07!22
|ontology_enrichment_uberon=UBERON:0007023!4.36e-58!115;UBERON:0001049!3.77e-39!57;UBERON:0005068!3.77e-39!57;UBERON:0006241!3.77e-39!57;UBERON:0007135!3.77e-39!57;UBERON:0002346!8.74e-39!90;UBERON:0005743!7.00e-38!86;UBERON:0000073!3.04e-37!94;UBERON:0001016!3.04e-37!94;UBERON:0003075!3.25e-36!86;UBERON:0007284!3.25e-36!86;UBERON:0001017!1.07e-35!82;UBERON:0002616!2.15e-33!59;UBERON:0000955!1.42e-32!69;UBERON:0006238!1.42e-32!69;UBERON:0000924!6.67e-30!173;UBERON:0006601!6.67e-30!173;UBERON:0003080!2.09e-29!42;UBERON:0002780!6.40e-29!41;UBERON:0001890!6.40e-29!41;UBERON:0006240!6.40e-29!41;UBERON:0000153!1.79e-28!129;UBERON:0007811!1.79e-28!129;UBERON:0003056!3.23e-28!61;UBERON:0004121!9.64e-28!169;UBERON:0000033!7.15e-27!123;UBERON:0001893!1.85e-24!34;UBERON:0002020!3.67e-24!34;UBERON:0003528!3.67e-24!34;UBERON:0001869!7.67e-24!32;UBERON:0002791!1.87e-23!33;UBERON:0002619!2.89e-21!22;UBERON:0001950!4.46e-20!20;UBERON:0000956!5.74e-19!25;UBERON:0000203!5.74e-19!25;UBERON:0000062!8.50e-15!511;UBERON:0000922!3.18e-14!612;UBERON:0000481!6.85e-13!347;UBERON:0000064!1.44e-12!219;UBERON:0002050!3.26e-12!605;UBERON:0005423!3.26e-12!605;UBERON:0000468!6.13e-12!659;UBERON:0000923!9.71e-12!604;UBERON:0005291!9.71e-12!604;UBERON:0006598!9.71e-12!604;UBERON:0002532!9.71e-12!604;UBERON:0003076!1.13e-10!15;UBERON:0003057!1.13e-10!15;UBERON:0000483!2.59e-10!309;UBERON:0000475!4.89e-10!365;UBERON:0000119!6.42e-10!312;UBERON:0000467!1.52e-09!625;UBERON:0000480!1.92e-09!626;UBERON:0000025!2.37e-09!194;UBERON:0000477!3.28e-09!286;UBERON:0004111!4.32e-09!241;UBERON:0004733!7.08e-09!12;UBERON:0002028!7.08e-09!12;UBERON:0007277!7.08e-09!12;UBERON:0001871!4.62e-08!7;UBERON:0004732!6.51e-08!13;UBERON:0002680!1.80e-07!9;UBERON:0001895!1.80e-07!9;UBERON:0010092!1.80e-07!9;UBERON:0000200!4.47e-07!6;UBERON:0002420!4.77e-07!9;UBERON:0007245!4.77e-07!9;UBERON:0010009!4.77e-07!9;UBERON:0010011!4.77e-07!9;UBERON:0000454!4.77e-07!9
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}}
}}

Revision as of 19:55, 8 August 2012


Full id: C4320_cerebellum_occipital_aorta_parietal_rectum_extraskeletal_brain



Phase1 CAGE Peaks

Hg19::chr3:2140514..2140525,+p7@CNTN4
Hg19::chr3:2140530..2140557,+p2@CNTN4
Hg19::chr3:2140565..2140621,+p1@CNTN4


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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism4.36e-58115
neural tube3.77e-3957
neural rod3.77e-3957
future spinal cord3.77e-3957
neural keel3.77e-3957
neurectoderm8.74e-3990
regional part of nervous system3.04e-3794
nervous system3.04e-3794
neural plate3.25e-3686
presumptive neural plate3.25e-3686
central nervous system1.07e-3582
regional part of brain2.15e-3359
brain1.42e-3269
future brain1.42e-3269
ectoderm6.67e-30173
presumptive ectoderm6.67e-30173
anterior neural tube2.09e-2942
regional part of forebrain6.40e-2941
forebrain6.40e-2941
future forebrain6.40e-2941
anterior region of body1.79e-28129
craniocervical region1.79e-28129
pre-chordal neural plate3.23e-2861
ectoderm-derived structure9.64e-28169
head7.15e-27123
telencephalon1.85e-2434
gray matter3.67e-2434
brain grey matter3.67e-2434
cerebral hemisphere7.67e-2432
regional part of telencephalon1.87e-2333
regional part of cerebral cortex2.89e-2122
neocortex4.46e-2020
cerebral cortex5.74e-1925
pallium5.74e-1925
organ8.50e-15511
embryo3.18e-14612
multi-tissue structure6.85e-13347
organ part1.44e-12219
embryonic structure3.26e-12605
developing anatomical structure3.26e-12605
multi-cellular organism6.13e-12659
germ layer9.71e-12604
embryonic tissue9.71e-12604
presumptive structure9.71e-12604
epiblast (generic)9.71e-12604
posterior neural tube1.13e-1015
chordal neural plate1.13e-1015
epithelium2.59e-10309
organism subdivision4.89e-10365
cell layer6.42e-10312
anatomical system1.52e-09625
anatomical group1.92e-09626
tube2.37e-09194
anatomical cluster3.28e-09286
anatomical conduit4.32e-09241
segmental subdivision of hindbrain7.08e-0912
hindbrain7.08e-0912
presumptive hindbrain7.08e-0912
temporal lobe4.62e-087
segmental subdivision of nervous system6.51e-0813
regional part of metencephalon1.80e-079
metencephalon1.80e-079
future metencephalon1.80e-079
gyrus4.47e-076
basal ganglion4.77e-079
nuclear complex of neuraxis4.77e-079
aggregate regional part of brain4.77e-079
collection of basal ganglia4.77e-079
cerebral subcortex4.77e-079
Disease
Ontology termp-valuen
germ cell and embryonal cancer5.33e-0722
germ cell cancer5.33e-0722


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.