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Coexpression cluster:C2861: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003075!7.03e-38!86;UBERON:0007284!7.03e-38!86;UBERON:0001049!1.04e-37!57;UBERON:0005068!1.04e-37!57;UBERON:0006241!1.04e-37!57;UBERON:0007135!1.04e-37!57;UBERON:0001017!5.93e-36!82;UBERON:0005743!9.53e-36!86;UBERON:0002616!8.82e-35!59;UBERON:0002346!1.86e-34!90;UBERON:0000955!8.58e-33!69;UBERON:0006238!8.58e-33!69;UBERON:0000073!3.40e-32!94;UBERON:0001016!3.40e-32!94;UBERON:0003056!2.12e-29!61;UBERON:0007023!1.13e-28!115;UBERON:0003080!4.59e-28!42;UBERON:0002780!6.69e-28!41;UBERON:0001890!6.69e-28!41;UBERON:0006240!6.69e-28!41;UBERON:0002020!7.16e-24!34;UBERON:0003528!7.16e-24!34;UBERON:0001893!7.16e-24!34;UBERON:0002791!4.83e-23!33;UBERON:0000153!1.31e-22!129;UBERON:0007811!1.31e-22!129;UBERON:0001869!1.50e-22!32;UBERON:0000033!2.79e-21!123;UBERON:0000956!1.08e-17!25;UBERON:0000203!1.08e-17!25;UBERON:0004121!8.54e-17!169;UBERON:0002619!5.37e-16!22;UBERON:0000924!1.56e-15!173;UBERON:0006601!1.56e-15!173;UBERON:0001950!1.19e-14!20;UBERON:0000475!6.30e-12!365;UBERON:0003076!1.35e-10!15;UBERON:0003057!1.35e-10!15;UBERON:0004732!2.79e-09!13;UBERON:0004733!1.02e-08!12;UBERON:0002028!1.02e-08!12;UBERON:0007277!1.02e-08!12;UBERON:0002308!1.26e-07!9;UBERON:0000125!1.26e-07!9;UBERON:0000483!1.92e-07!309;UBERON:0000119!1.92e-07!312;UBERON:0002420!1.96e-07!9;UBERON:0007245!1.96e-07!9;UBERON:0010009!1.96e-07!9;UBERON:0010011!1.96e-07!9;UBERON:0000454!1.96e-07!9;UBERON:0002680!9.88e-07!9;UBERON:0001895!9.88e-07!9;UBERON:0010092!9.88e-07!9
|ontology_enrichment_uberon=UBERON:0003075!7.03e-38!86;UBERON:0007284!7.03e-38!86;UBERON:0001049!1.04e-37!57;UBERON:0005068!1.04e-37!57;UBERON:0006241!1.04e-37!57;UBERON:0007135!1.04e-37!57;UBERON:0001017!5.93e-36!82;UBERON:0005743!9.53e-36!86;UBERON:0002616!8.82e-35!59;UBERON:0002346!1.86e-34!90;UBERON:0000955!8.58e-33!69;UBERON:0006238!8.58e-33!69;UBERON:0000073!3.40e-32!94;UBERON:0001016!3.40e-32!94;UBERON:0003056!2.12e-29!61;UBERON:0007023!1.13e-28!115;UBERON:0003080!4.59e-28!42;UBERON:0002780!6.69e-28!41;UBERON:0001890!6.69e-28!41;UBERON:0006240!6.69e-28!41;UBERON:0002020!7.16e-24!34;UBERON:0003528!7.16e-24!34;UBERON:0001893!7.16e-24!34;UBERON:0002791!4.83e-23!33;UBERON:0000153!1.31e-22!129;UBERON:0007811!1.31e-22!129;UBERON:0001869!1.50e-22!32;UBERON:0000033!2.79e-21!123;UBERON:0000956!1.08e-17!25;UBERON:0000203!1.08e-17!25;UBERON:0004121!8.54e-17!169;UBERON:0002619!5.37e-16!22;UBERON:0000924!1.56e-15!173;UBERON:0006601!1.56e-15!173;UBERON:0001950!1.19e-14!20;UBERON:0000475!6.30e-12!365;UBERON:0003076!1.35e-10!15;UBERON:0003057!1.35e-10!15;UBERON:0004732!2.79e-09!13;UBERON:0004733!1.02e-08!12;UBERON:0002028!1.02e-08!12;UBERON:0007277!1.02e-08!12;UBERON:0002308!1.26e-07!9;UBERON:0000125!1.26e-07!9;UBERON:0000483!1.92e-07!309;UBERON:0000119!1.92e-07!312;UBERON:0002420!1.96e-07!9;UBERON:0007245!1.96e-07!9;UBERON:0010009!1.96e-07!9;UBERON:0010011!1.96e-07!9;UBERON:0000454!1.96e-07!9;UBERON:0002680!9.88e-07!9;UBERON:0001895!9.88e-07!9;UBERON:0010092!9.88e-07!9
|tf_chipseq_enrich=JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392535967108384!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123478171965367!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000230877796903666
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}}
}}

Revision as of 13:13, 5 September 2012


Full id: C2861_Ciliary_anaplastic_paracentral_pons_parietal_postcentral_medial



Phase1 CAGE Peaks

Hg19::chr6:46293212..46293228,-p15@RCAN2
Hg19::chr6:46293378..46293415,-p1@RCAN2
Hg19::chr6:46293429..46293442,-p8@RCAN2
Hg19::chr6:46293461..46293464,-p13@RCAN2


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 plate7.03e-3886
presumptive neural plate7.03e-3886
neural tube1.04e-3757
neural rod1.04e-3757
future spinal cord1.04e-3757
neural keel1.04e-3757
central nervous system5.93e-3682
regional part of brain8.82e-3559
neurectoderm1.86e-3490
brain8.58e-3369
future brain8.58e-3369
regional part of nervous system3.40e-3294
nervous system3.40e-3294
pre-chordal neural plate2.12e-2961
adult organism1.13e-28115
anterior neural tube4.59e-2842
regional part of forebrain6.69e-2841
forebrain6.69e-2841
future forebrain6.69e-2841
gray matter7.16e-2434
brain grey matter7.16e-2434
telencephalon7.16e-2434
regional part of telencephalon4.83e-2333
anterior region of body1.31e-22129
craniocervical region1.31e-22129
cerebral hemisphere1.50e-2232
head2.79e-21123
cerebral cortex1.08e-1725
pallium1.08e-1725
ectoderm-derived structure8.54e-17169
regional part of cerebral cortex5.37e-1622
ectoderm1.56e-15173
presumptive ectoderm1.56e-15173
neocortex1.19e-1420
organism subdivision6.30e-12365
posterior neural tube1.35e-1015
chordal neural plate1.35e-1015
segmental subdivision of nervous system2.79e-0913
segmental subdivision of hindbrain1.02e-0812
hindbrain1.02e-0812
presumptive hindbrain1.02e-0812
nucleus of brain1.26e-079
neural nucleus1.26e-079
epithelium1.92e-07309
cell layer1.92e-07312
basal ganglion1.96e-079
nuclear complex of neuraxis1.96e-079
aggregate regional part of brain1.96e-079
collection of basal ganglia1.96e-079
cerebral subcortex1.96e-079
regional part of metencephalon9.88e-079
metencephalon9.88e-079
future metencephalon9.88e-079


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

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

TF#promotersEnrichmentp-valueq-value
JUND#372746.994663941871030.000417684217818580.00392535967108384
STAT3#6774410.51946499715428.16377768286615e-050.00123478171965367
TRIM28#10155418.59052504526258.36730015875654e-060.000230877796903666



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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