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Coexpression cluster:C3009: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004121!2.09e-26!171;UBERON:0000924!2.09e-26!171;UBERON:0006601!2.09e-26!171;UBERON:0001049!2.65e-26!56;UBERON:0005068!2.65e-26!56;UBERON:0006241!2.65e-26!56;UBERON:0007135!2.65e-26!56;UBERON:0001016!1.96e-25!89;UBERON:0001017!2.59e-25!81;UBERON:0000073!1.97e-24!53;UBERON:0002616!1.97e-24!53;UBERON:0000955!3.40e-23!68;UBERON:0006238!3.40e-23!68;UBERON:0000468!3.26e-22!656;UBERON:0002780!8.66e-22!41;UBERON:0001890!8.66e-22!41;UBERON:0003080!8.66e-22!41;UBERON:0006240!8.66e-22!41;UBERON:0010314!1.36e-21!132;UBERON:0007023!1.49e-21!114;UBERON:0003528!2.90e-21!34;UBERON:0002020!2.90e-21!34;UBERON:0001893!3.46e-21!34;UBERON:0002791!6.11e-20!32;UBERON:0001869!8.17e-20!32;UBERON:0003075!1.72e-19!82;UBERON:0007284!1.72e-19!82;UBERON:0000467!1.88e-19!624;UBERON:0002346!3.16e-19!86;UBERON:0000480!5.15e-19!625;UBERON:0010371!2.41e-18!104;UBERON:0000956!1.10e-15!25;UBERON:0000203!1.10e-15!25;UBERON:0002050!1.24e-15!564;UBERON:0000062!4.99e-15!503;UBERON:0011216!5.85e-15!223;UBERON:0000923!8.72e-15!560;UBERON:0010316!8.72e-15!560;UBERON:0005291!8.72e-15!560;UBERON:0006598!8.72e-15!560;UBERON:0010317!8.72e-15!560;UBERON:0002532!8.72e-15!560;UBERON:0002619!1.98e-14!22;UBERON:0005423!4.09e-14!581;UBERON:0003056!1.51e-13!61;UBERON:0001950!3.22e-13!20;UBERON:0000922!7.09e-13!592;UBERON:0000477!5.94e-12!373;UBERON:0000481!8.57e-11!342;UBERON:0004111!7.91e-10!240;UBERON:0000064!7.68e-09!218;UBERON:0000119!1.24e-07!309;UBERON:0000483!1.25e-07!306;UBERON:0000479!2.88e-07!773;UBERON:0000125!4.77e-07!9;UBERON:0002308!4.77e-07!9;UBERON:0002420!6.09e-07!9;UBERON:0007245!6.09e-07!9;UBERON:0010009!6.09e-07!9;UBERON:0010011!6.09e-07!9;UBERON:0000454!6.09e-07!9;UBERON:0000025!6.94e-07!192
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}}
}}

Revision as of 15:52, 26 November 2012


Full id: C3009_optic_substantia_thalamus_globus_spinal_mature_Mast



Phase1 CAGE Peaks

Hg19::chr10:24914220..24914234,-p@chr10:24914220..24914234
-
Hg19::chr10:25012800..25012822,-p1@ARHGAP21
Hg19::chr10:25012828..25012860,-p2@ARHGAP21


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
fibroblast3.74e-0876
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure2.09e-26171
ectoderm2.09e-26171
presumptive ectoderm2.09e-26171
neural tube2.65e-2656
neural rod2.65e-2656
future spinal cord2.65e-2656
neural keel2.65e-2656
nervous system1.96e-2589
central nervous system2.59e-2581
regional part of nervous system1.97e-2453
regional part of brain1.97e-2453
brain3.40e-2368
future brain3.40e-2368
multi-cellular organism3.26e-22656
regional part of forebrain8.66e-2241
forebrain8.66e-2241
anterior neural tube8.66e-2241
future forebrain8.66e-2241
structure with developmental contribution from neural crest1.36e-21132
adult organism1.49e-21114
brain grey matter2.90e-2134
gray matter2.90e-2134
telencephalon3.46e-2134
regional part of telencephalon6.11e-2032
cerebral hemisphere8.17e-2032
neural plate1.72e-1982
presumptive neural plate1.72e-1982
anatomical system1.88e-19624
neurectoderm3.16e-1986
anatomical group5.15e-19625
ecto-epithelium2.41e-18104
cerebral cortex1.10e-1525
pallium1.10e-1525
embryonic structure1.24e-15564
organ4.99e-15503
organ system subdivision5.85e-15223
germ layer8.72e-15560
germ layer / neural crest8.72e-15560
embryonic tissue8.72e-15560
presumptive structure8.72e-15560
germ layer / neural crest derived structure8.72e-15560
epiblast (generic)8.72e-15560
regional part of cerebral cortex1.98e-1422
developing anatomical structure4.09e-14581
pre-chordal neural plate1.51e-1361
neocortex3.22e-1320
embryo7.09e-13592
anatomical cluster5.94e-12373
multi-tissue structure8.57e-11342
anatomical conduit7.91e-10240
organ part7.68e-09218
cell layer1.24e-07309
epithelium1.25e-07306
tissue2.88e-07773
neural nucleus4.77e-079
nucleus of brain4.77e-079
basal ganglion6.09e-079
nuclear complex of neuraxis6.09e-079
aggregate regional part of brain6.09e-079
collection of basal ganglia6.09e-079
cerebral subcortex6.09e-079
tube6.94e-07192


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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