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Coexpression cluster:C2210: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!1.22e-53!56;UBERON:0005068!1.22e-53!56;UBERON:0006241!1.22e-53!56;UBERON:0007135!1.22e-53!56;UBERON:0000073!1.03e-49!53;UBERON:0002616!1.03e-49!53;UBERON:0001017!2.92e-49!81;UBERON:0001016!5.16e-47!89;UBERON:0002780!7.00e-43!41;UBERON:0001890!7.00e-43!41;UBERON:0003080!7.00e-43!41;UBERON:0006240!7.00e-43!41;UBERON:0002346!2.35e-42!86;UBERON:0003075!2.50e-42!82;UBERON:0007284!2.50e-42!82;UBERON:0000955!2.16e-41!68;UBERON:0006238!2.16e-41!68;UBERON:0003528!9.81e-38!34;UBERON:0002020!9.81e-38!34;UBERON:0001893!2.22e-37!34;UBERON:0007023!1.82e-35!114;UBERON:0002791!3.21e-35!32;UBERON:0001869!3.75e-35!32;UBERON:0003056!5.22e-33!61;UBERON:0010371!1.82e-31!104;UBERON:0010314!2.91e-30!132;UBERON:0000956!7.90e-27!25;UBERON:0000203!7.90e-27!25;UBERON:0002619!1.24e-26!22;UBERON:0001950!4.70e-24!20;UBERON:0004121!4.78e-24!171;UBERON:0000924!4.78e-24!171;UBERON:0006601!4.78e-24!171;UBERON:0011216!2.70e-15!223;UBERON:0000125!2.66e-12!9;UBERON:0002308!2.66e-12!9;UBERON:0002420!2.87e-12!9;UBERON:0007245!2.87e-12!9;UBERON:0010009!2.87e-12!9;UBERON:0010011!2.87e-12!9;UBERON:0000454!2.87e-12!9;UBERON:0003076!9.64e-12!15;UBERON:0003057!9.64e-12!15;UBERON:0000025!2.05e-11!192;UBERON:0009663!7.34e-10!7;UBERON:0004732!1.74e-09!13;UBERON:0000200!7.52e-09!6;UBERON:0004111!1.39e-08!240;UBERON:0002298!1.48e-08!6;UBERON:0004733!2.65e-08!12;UBERON:0002028!2.65e-08!12;UBERON:0007277!2.65e-08!12;UBERON:0000477!3.83e-08!373;UBERON:0002021!9.76e-08!5;UBERON:0000349!1.09e-07!5;UBERON:0001871!1.49e-07!6;UBERON:0001872!1.74e-07!5;UBERON:0000483!5.38e-07!306;UBERON:0001894!6.65e-07!7;UBERON:0006222!6.65e-07!7;UBERON:0000119!9.71e-07!309
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}}
}}

Revision as of 15:22, 26 November 2012


Full id: C2210_medial_occipital_duodenum_spinal_hippocampus_cerebral_optic



Phase1 CAGE Peaks

Hg19::chr12:50291331..50291372,-p6@FAIM2
Hg19::chr19:6495958..6495977,-p@chr19:6495958..6495977
-
Hg19::chr4:89618393..89618411,-p5@NAP1L5
Hg19::chrX:102470619..102470632,+p2@BEX4


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
neural tube1.22e-5356
neural rod1.22e-5356
future spinal cord1.22e-5356
neural keel1.22e-5356
regional part of nervous system1.03e-4953
regional part of brain1.03e-4953
central nervous system2.92e-4981
nervous system5.16e-4789
regional part of forebrain7.00e-4341
forebrain7.00e-4341
anterior neural tube7.00e-4341
future forebrain7.00e-4341
neurectoderm2.35e-4286
neural plate2.50e-4282
presumptive neural plate2.50e-4282
brain2.16e-4168
future brain2.16e-4168
brain grey matter9.81e-3834
gray matter9.81e-3834
telencephalon2.22e-3734
adult organism1.82e-35114
regional part of telencephalon3.21e-3532
cerebral hemisphere3.75e-3532
pre-chordal neural plate5.22e-3361
ecto-epithelium1.82e-31104
structure with developmental contribution from neural crest2.91e-30132
cerebral cortex7.90e-2725
pallium7.90e-2725
regional part of cerebral cortex1.24e-2622
neocortex4.70e-2420
ectoderm-derived structure4.78e-24171
ectoderm4.78e-24171
presumptive ectoderm4.78e-24171
organ system subdivision2.70e-15223
neural nucleus2.66e-129
nucleus of brain2.66e-129
basal ganglion2.87e-129
nuclear complex of neuraxis2.87e-129
aggregate regional part of brain2.87e-129
collection of basal ganglia2.87e-129
cerebral subcortex2.87e-129
posterior neural tube9.64e-1215
chordal neural plate9.64e-1215
tube2.05e-11192
telencephalic nucleus7.34e-107
segmental subdivision of nervous system1.74e-0913
gyrus7.52e-096
anatomical conduit1.39e-08240
brainstem1.48e-086
segmental subdivision of hindbrain2.65e-0812
hindbrain2.65e-0812
presumptive hindbrain2.65e-0812
anatomical cluster3.83e-08373
occipital lobe9.76e-085
limbic system1.09e-075
temporal lobe1.49e-076
parietal lobe1.74e-075
epithelium5.38e-07306
diencephalon6.65e-077
future diencephalon6.65e-077
cell layer9.71e-07309


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)

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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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