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Coexpression cluster:C2983: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!1.59e-31!56;UBERON:0005068!1.59e-31!56;UBERON:0006241!1.59e-31!56;UBERON:0007135!1.59e-31!56;UBERON:0001017!9.15e-29!81;UBERON:0000073!1.88e-27!53;UBERON:0002616!1.88e-27!53;UBERON:0002780!2.68e-26!41;UBERON:0001890!2.68e-26!41;UBERON:0003080!2.68e-26!41;UBERON:0006240!2.68e-26!41;UBERON:0001016!3.08e-26!89;UBERON:0003528!1.32e-25!34;UBERON:0002020!1.32e-25!34;UBERON:0001893!1.80e-25!34;UBERON:0000955!1.58e-23!68;UBERON:0006238!1.58e-23!68;UBERON:0002791!8.72e-23!32;UBERON:0001869!1.92e-22!32;UBERON:0003075!2.98e-22!82;UBERON:0007284!2.98e-22!82;UBERON:0002346!1.09e-20!86;UBERON:0003056!2.43e-19!61;UBERON:0010371!1.11e-18!104;UBERON:0002619!3.72e-18!22;UBERON:0007023!5.09e-18!114;UBERON:0000956!1.69e-15!25;UBERON:0000203!1.69e-15!25;UBERON:0001950!3.42e-15!20;UBERON:0004121!7.04e-13!171;UBERON:0000924!7.04e-13!171;UBERON:0006601!7.04e-13!171;UBERON:0010314!7.28e-13!132;UBERON:0000125!2.05e-12!9;UBERON:0002308!2.05e-12!9;UBERON:0002420!1.36e-09!9;UBERON:0007245!1.36e-09!9;UBERON:0010009!1.36e-09!9;UBERON:0010011!1.36e-09!9;UBERON:0000454!1.36e-09!9;UBERON:0009663!2.45e-09!7;UBERON:0011216!9.13e-08!223;UBERON:0002298!1.53e-07!6;UBERON:0000200!5.04e-07!6
|ontology_enrichment_uberon=UBERON:0001049!1.59e-31!56;UBERON:0005068!1.59e-31!56;UBERON:0006241!1.59e-31!56;UBERON:0007135!1.59e-31!56;UBERON:0001017!9.15e-29!81;UBERON:0000073!1.88e-27!53;UBERON:0002616!1.88e-27!53;UBERON:0002780!2.68e-26!41;UBERON:0001890!2.68e-26!41;UBERON:0003080!2.68e-26!41;UBERON:0006240!2.68e-26!41;UBERON:0001016!3.08e-26!89;UBERON:0003528!1.32e-25!34;UBERON:0002020!1.32e-25!34;UBERON:0001893!1.80e-25!34;UBERON:0000955!1.58e-23!68;UBERON:0006238!1.58e-23!68;UBERON:0002791!8.72e-23!32;UBERON:0001869!1.92e-22!32;UBERON:0003075!2.98e-22!82;UBERON:0007284!2.98e-22!82;UBERON:0002346!1.09e-20!86;UBERON:0003056!2.43e-19!61;UBERON:0010371!1.11e-18!104;UBERON:0002619!3.72e-18!22;UBERON:0007023!5.09e-18!114;UBERON:0000956!1.69e-15!25;UBERON:0000203!1.69e-15!25;UBERON:0001950!3.42e-15!20;UBERON:0004121!7.04e-13!171;UBERON:0000924!7.04e-13!171;UBERON:0006601!7.04e-13!171;UBERON:0010314!7.28e-13!132;UBERON:0000125!2.05e-12!9;UBERON:0002308!2.05e-12!9;UBERON:0002420!1.36e-09!9;UBERON:0007245!1.36e-09!9;UBERON:0010009!1.36e-09!9;UBERON:0010011!1.36e-09!9;UBERON:0000454!1.36e-09!9;UBERON:0009663!2.45e-09!7;UBERON:0011216!9.13e-08!223;UBERON:0002298!1.53e-07!6;UBERON:0000200!5.04e-07!6
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}}
}}

Revision as of 15:51, 26 November 2012


Full id: C2983_Melanocyte_astrocytoma_melanoma_Macrophage_Monocytederived_Dendritic_substantia



Phase1 CAGE Peaks

Hg19::chr10:118719680..118719720,-p10@KIAA1598
Hg19::chr10:118719724..118719735,-p14@KIAA1598
Hg19::chr10:118719743..118719755,-p13@KIAA1598


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
macrophage3.53e-126
melanocyte7.61e-0710
melanoblast7.61e-0710
Uber Anatomy
Ontology termp-valuen
neural tube1.59e-3156
neural rod1.59e-3156
future spinal cord1.59e-3156
neural keel1.59e-3156
central nervous system9.15e-2981
regional part of nervous system1.88e-2753
regional part of brain1.88e-2753
regional part of forebrain2.68e-2641
forebrain2.68e-2641
anterior neural tube2.68e-2641
future forebrain2.68e-2641
nervous system3.08e-2689
brain grey matter1.32e-2534
gray matter1.32e-2534
telencephalon1.80e-2534
brain1.58e-2368
future brain1.58e-2368
regional part of telencephalon8.72e-2332
cerebral hemisphere1.92e-2232
neural plate2.98e-2282
presumptive neural plate2.98e-2282
neurectoderm1.09e-2086
pre-chordal neural plate2.43e-1961
ecto-epithelium1.11e-18104
regional part of cerebral cortex3.72e-1822
adult organism5.09e-18114
cerebral cortex1.69e-1525
pallium1.69e-1525
neocortex3.42e-1520
ectoderm-derived structure7.04e-13171
ectoderm7.04e-13171
presumptive ectoderm7.04e-13171
structure with developmental contribution from neural crest7.28e-13132
neural nucleus2.05e-129
nucleus of brain2.05e-129
basal ganglion1.36e-099
nuclear complex of neuraxis1.36e-099
aggregate regional part of brain1.36e-099
collection of basal ganglia1.36e-099
cerebral subcortex1.36e-099
telencephalic nucleus2.45e-097
organ system subdivision9.13e-08223
brainstem1.53e-076
gyrus5.04e-076


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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