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Coexpression cluster:C3463: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0007023!1.20e-78!115;UBERON:0001049!1.31e-39!57;UBERON:0005068!1.31e-39!57;UBERON:0006241!1.31e-39!57;UBERON:0007135!1.31e-39!57;UBERON:0001017!1.91e-34!82;UBERON:0005743!1.81e-33!86;UBERON:0000073!2.22e-33!94;UBERON:0001016!2.22e-33!94;UBERON:0002616!1.23e-31!59;UBERON:0000955!9.18e-31!69;UBERON:0006238!9.18e-31!69;UBERON:0003080!1.47e-28!42;UBERON:0003075!1.88e-28!86;UBERON:0007284!1.88e-28!86;UBERON:0002780!8.61e-28!41;UBERON:0001890!8.61e-28!41;UBERON:0006240!8.61e-28!41;UBERON:0002346!1.97e-27!90;UBERON:0002020!9.23e-25!34;UBERON:0003528!9.23e-25!34;UBERON:0001893!1.58e-24!34;UBERON:0002791!1.22e-23!33;UBERON:0001869!2.74e-22!32;UBERON:0004121!2.25e-18!169;UBERON:0000924!4.23e-18!173;UBERON:0006601!4.23e-18!173;UBERON:0003056!5.69e-18!61;UBERON:0000153!1.15e-17!129;UBERON:0007811!1.15e-17!129;UBERON:0000033!5.28e-17!123;UBERON:0002619!1.17e-15!22;UBERON:0000956!1.62e-15!25;UBERON:0000203!1.62e-15!25;UBERON:0001950!5.74e-14!20;UBERON:0003076!5.71e-12!15;UBERON:0003057!5.71e-12!15;UBERON:0002308!2.64e-11!9;UBERON:0000125!2.64e-11!9;UBERON:0002298!2.33e-10!8;UBERON:0002420!2.60e-10!9;UBERON:0007245!2.60e-10!9;UBERON:0010009!2.60e-10!9;UBERON:0010011!2.60e-10!9;UBERON:0000454!2.60e-10!9;UBERON:0000025!5.22e-10!194;UBERON:0004732!7.10e-10!13;UBERON:0004111!7.35e-10!241;UBERON:0000062!7.71e-10!511;UBERON:0000922!1.34e-09!612;UBERON:0000468!2.00e-09!659;UBERON:0009663!5.57e-09!7;UBERON:0004733!9.19e-09!12;UBERON:0002028!9.19e-09!12;UBERON:0007277!9.19e-09!12;UBERON:0000481!2.34e-08!347;UBERON:0000477!1.36e-07!286;UBERON:0000064!1.66e-07!219;UBERON:0002050!2.17e-07!605;UBERON:0005423!2.17e-07!605;UBERON:0000200!4.19e-07!6;UBERON:0000923!4.87e-07!604;UBERON:0005291!4.87e-07!604;UBERON:0006598!4.87e-07!604;UBERON:0002532!4.87e-07!604;UBERON:0000475!9.05e-07!365
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}}
}}

Revision as of 13:13, 5 September 2012


Full id: C3463_pineal_optic_colon_spinal_substantia_globus_locus



Phase1 CAGE Peaks

Hg19::chr14:94254821..94254836,-p2@PRIMA1
Hg19::chr14:94255332..94255348,-p@chr14:94255332..94255348
-
Hg19::chr14:94255350..94255382,-p@chr14:94255350..94255382
-


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><br>


Uber Anatomy
Ontology termp-valuen
adult organism1.20e-78115
neural tube1.31e-3957
neural rod1.31e-3957
future spinal cord1.31e-3957
neural keel1.31e-3957
central nervous system1.91e-3482
regional part of nervous system2.22e-3394
nervous system2.22e-3394
regional part of brain1.23e-3159
brain9.18e-3169
future brain9.18e-3169
anterior neural tube1.47e-2842
neural plate1.88e-2886
presumptive neural plate1.88e-2886
regional part of forebrain8.61e-2841
forebrain8.61e-2841
future forebrain8.61e-2841
neurectoderm1.97e-2790
gray matter9.23e-2534
brain grey matter9.23e-2534
telencephalon1.58e-2434
regional part of telencephalon1.22e-2333
cerebral hemisphere2.74e-2232
ectoderm-derived structure2.25e-18169
ectoderm4.23e-18173
presumptive ectoderm4.23e-18173
pre-chordal neural plate5.69e-1861
anterior region of body1.15e-17129
craniocervical region1.15e-17129
head5.28e-17123
regional part of cerebral cortex1.17e-1522
cerebral cortex1.62e-1525
pallium1.62e-1525
neocortex5.74e-1420
posterior neural tube5.71e-1215
chordal neural plate5.71e-1215
nucleus of brain2.64e-119
neural nucleus2.64e-119
brainstem2.33e-108
basal ganglion2.60e-109
nuclear complex of neuraxis2.60e-109
aggregate regional part of brain2.60e-109
collection of basal ganglia2.60e-109
cerebral subcortex2.60e-109
tube5.22e-10194
segmental subdivision of nervous system7.10e-1013
anatomical conduit7.35e-10241
organ7.71e-10511
embryo1.34e-09612
multi-cellular organism2.00e-09659
telencephalic nucleus5.57e-097
segmental subdivision of hindbrain9.19e-0912
hindbrain9.19e-0912
presumptive hindbrain9.19e-0912
multi-tissue structure2.34e-08347
anatomical cluster1.36e-07286
organ part1.66e-07219
embryonic structure2.17e-07605
developing anatomical structure2.17e-07605
gyrus4.19e-076
germ layer4.87e-07604
embryonic tissue4.87e-07604
presumptive structure4.87e-07604
epiblast (generic)4.87e-07604
organism subdivision9.05e-07365


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
E2F1#186934.907389214879320.008460985347239390.0324444429681427



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.