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Coexpression cluster:C1965: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!6.93e-52!53;UBERON:0002616!6.93e-52!53;UBERON:0001049!3.67e-51!56;UBERON:0005068!3.67e-51!56;UBERON:0006241!3.67e-51!56;UBERON:0007135!3.67e-51!56;UBERON:0001893!7.74e-50!34;UBERON:0003528!1.75e-49!34;UBERON:0002020!1.75e-49!34;UBERON:0002780!4.76e-49!41;UBERON:0001890!4.76e-49!41;UBERON:0003080!4.76e-49!41;UBERON:0006240!4.76e-49!41;UBERON:0001869!6.18e-46!32;UBERON:0002791!9.07e-46!32;UBERON:0000955!1.84e-44!68;UBERON:0006238!1.84e-44!68;UBERON:0001017!1.97e-43!81;UBERON:0003075!2.13e-43!82;UBERON:0007284!2.13e-43!82;UBERON:0007023!5.59e-43!114;UBERON:0003056!3.36e-41!61;UBERON:0002346!8.92e-41!86;UBERON:0000956!2.48e-40!25;UBERON:0000203!2.48e-40!25;UBERON:0001016!7.44e-38!89;UBERON:0002619!9.18e-35!22;UBERON:0010314!1.49e-31!132;UBERON:0010371!1.76e-31!104;UBERON:0001950!2.81e-31!20;UBERON:0004121!8.82e-21!171;UBERON:0000924!8.82e-21!171;UBERON:0006601!8.82e-21!171;UBERON:0000025!1.13e-16!192;UBERON:0011216!2.70e-15!223;UBERON:0000200!1.67e-13!6;UBERON:0000477!1.22e-12!373;UBERON:0002298!2.42e-12!6;UBERON:0004111!5.17e-12!240;UBERON:0000064!2.26e-11!218;UBERON:0001871!2.28e-11!6;UBERON:0000349!2.75e-11!5;UBERON:0002420!6.12e-11!9;UBERON:0007245!6.12e-11!9;UBERON:0010009!6.12e-11!9;UBERON:0010011!6.12e-11!9;UBERON:0000454!6.12e-11!9;UBERON:0000125!1.10e-10!9;UBERON:0002308!1.10e-10!9;UBERON:0000481!2.97e-10!342;UBERON:0000483!5.81e-10!306;UBERON:0000119!9.97e-10!309;UBERON:0001872!1.02e-07!5;UBERON:0001870!1.23e-07!3;UBERON:0002021!1.58e-07!5;UBERON:0009663!2.53e-07!7;UBERON:0000062!3.03e-07!503;UBERON:0000988!3.09e-07!3;UBERON:0001896!9.30e-07!3;UBERON:0005290!9.30e-07!3;UBERON:0010096!9.30e-07!3
|ontology_enrichment_uberon=UBERON:0000073!6.93e-52!53;UBERON:0002616!6.93e-52!53;UBERON:0001049!3.67e-51!56;UBERON:0005068!3.67e-51!56;UBERON:0006241!3.67e-51!56;UBERON:0007135!3.67e-51!56;UBERON:0001893!7.74e-50!34;UBERON:0003528!1.75e-49!34;UBERON:0002020!1.75e-49!34;UBERON:0002780!4.76e-49!41;UBERON:0001890!4.76e-49!41;UBERON:0003080!4.76e-49!41;UBERON:0006240!4.76e-49!41;UBERON:0001869!6.18e-46!32;UBERON:0002791!9.07e-46!32;UBERON:0000955!1.84e-44!68;UBERON:0006238!1.84e-44!68;UBERON:0001017!1.97e-43!81;UBERON:0003075!2.13e-43!82;UBERON:0007284!2.13e-43!82;UBERON:0007023!5.59e-43!114;UBERON:0003056!3.36e-41!61;UBERON:0002346!8.92e-41!86;UBERON:0000956!2.48e-40!25;UBERON:0000203!2.48e-40!25;UBERON:0001016!7.44e-38!89;UBERON:0002619!9.18e-35!22;UBERON:0010314!1.49e-31!132;UBERON:0010371!1.76e-31!104;UBERON:0001950!2.81e-31!20;UBERON:0004121!8.82e-21!171;UBERON:0000924!8.82e-21!171;UBERON:0006601!8.82e-21!171;UBERON:0000025!1.13e-16!192;UBERON:0011216!2.70e-15!223;UBERON:0000200!1.67e-13!6;UBERON:0000477!1.22e-12!373;UBERON:0002298!2.42e-12!6;UBERON:0004111!5.17e-12!240;UBERON:0000064!2.26e-11!218;UBERON:0001871!2.28e-11!6;UBERON:0000349!2.75e-11!5;UBERON:0002420!6.12e-11!9;UBERON:0007245!6.12e-11!9;UBERON:0010009!6.12e-11!9;UBERON:0010011!6.12e-11!9;UBERON:0000454!6.12e-11!9;UBERON:0000125!1.10e-10!9;UBERON:0002308!1.10e-10!9;UBERON:0000481!2.97e-10!342;UBERON:0000483!5.81e-10!306;UBERON:0000119!9.97e-10!309;UBERON:0001872!1.02e-07!5;UBERON:0001870!1.23e-07!3;UBERON:0002021!1.58e-07!5;UBERON:0009663!2.53e-07!7;UBERON:0000062!3.03e-07!503;UBERON:0000988!3.09e-07!3;UBERON:0001896!9.30e-07!3;UBERON:0005290!9.30e-07!3;UBERON:0010096!9.30e-07!3
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}}
}}

Revision as of 15:13, 26 November 2012


Full id: C1965_Hepatocyte_liver_CD133_CD34_mesenchymal_placenta_kidney



Phase1 CAGE Peaks

Hg19::chr5:76248681..76248690,+p5@CRHBP
Hg19::chr5:76248797..76248808,+p3@CRHBP
Hg19::chr5:76248833..76248836,+p9@CRHBP
Hg19::chr5:76248861..76248877,+p1@CRHBP
Hg19::chr5:76248878..76248889,+p4@CRHBP


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
astrocyte of the cerebral cortex3.52e-073
Uber Anatomy
Ontology termp-valuen
regional part of nervous system6.93e-5253
regional part of brain6.93e-5253
neural tube3.67e-5156
neural rod3.67e-5156
future spinal cord3.67e-5156
neural keel3.67e-5156
telencephalon7.74e-5034
brain grey matter1.75e-4934
gray matter1.75e-4934
regional part of forebrain4.76e-4941
forebrain4.76e-4941
anterior neural tube4.76e-4941
future forebrain4.76e-4941
cerebral hemisphere6.18e-4632
regional part of telencephalon9.07e-4632
brain1.84e-4468
future brain1.84e-4468
central nervous system1.97e-4381
neural plate2.13e-4382
presumptive neural plate2.13e-4382
adult organism5.59e-43114
pre-chordal neural plate3.36e-4161
neurectoderm8.92e-4186
cerebral cortex2.48e-4025
pallium2.48e-4025
nervous system7.44e-3889
regional part of cerebral cortex9.18e-3522
structure with developmental contribution from neural crest1.49e-31132
ecto-epithelium1.76e-31104
neocortex2.81e-3120
ectoderm-derived structure8.82e-21171
ectoderm8.82e-21171
presumptive ectoderm8.82e-21171
tube1.13e-16192
organ system subdivision2.70e-15223
gyrus1.67e-136
anatomical cluster1.22e-12373
brainstem2.42e-126
anatomical conduit5.17e-12240
organ part2.26e-11218
temporal lobe2.28e-116
limbic system2.75e-115
basal ganglion6.12e-119
nuclear complex of neuraxis6.12e-119
aggregate regional part of brain6.12e-119
collection of basal ganglia6.12e-119
cerebral subcortex6.12e-119
neural nucleus1.10e-109
nucleus of brain1.10e-109
multi-tissue structure2.97e-10342
epithelium5.81e-10306
cell layer9.97e-10309
parietal lobe1.02e-075
frontal cortex1.23e-073
occipital lobe1.58e-075
telencephalic nucleus2.53e-077
organ3.03e-07503
pons3.09e-073
medulla oblongata9.30e-073
myelencephalon9.30e-073
future myelencephalon9.30e-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.

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