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Coexpression cluster:C2567: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0004672!protein kinase activity!0.0313840803320159!90134;4139$GO:0000155!two-component sensor activity!0.0313840803320159!90134$GO:0000160!two-component signal transduction system (phosphorelay)!0.0313840803320159!90134$GO:0004673!protein histidine kinase activity!0.0313840803320159!90134$GO:0016773!phosphotransferase activity, alcohol group as acceptor!0.0313840803320159!90134;4139$GO:0016775!phosphotransferase activity, nitrogenous group as acceptor!0.0313840803320159!90134$GO:0016301!kinase activity!0.035627077908378!90134;4139$GO:0016772!transferase activity, transferring phosphorus-containing groups!0.0416307496441538!90134;4139
|gostat_on_coexpression_clusters=GO:0004672!protein kinase activity!0.0313840803320159!90134;4139$GO:0000155!two-component sensor activity!0.0313840803320159!90134$GO:0000160!two-component signal transduction system (phosphorelay)!0.0313840803320159!90134$GO:0004673!protein histidine kinase activity!0.0313840803320159!90134$GO:0016773!phosphotransferase activity, alcohol group as acceptor!0.0313840803320159!90134;4139$GO:0016775!phosphotransferase activity, nitrogenous group as acceptor!0.0313840803320159!90134$GO:0016301!kinase activity!0.035627077908378!90134;4139$GO:0016772!transferase activity, transferring phosphorus-containing groups!0.0416307496441538!90134;4139
|id=C2567
|id=C2567
|ontology_enrichment_celltype=CL:0000221!4.99e-12!71;CL:0000133!2.92e-09!59;CL:0000066!4.90e-08!254;CL:0002319!6.56e-08!25;CL:0002077!2.71e-07!33
|ontology_enrichment_celltype=CL:0000047!2.30e-11!8;CL:0002319!5.29e-09!25;CL:0000540!1.10e-08!6;CL:0000031!1.10e-08!6;CL:0000404!1.10e-08!6;CL:0000133!2.15e-07!59
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!3.38e-38!169;UBERON:0000073!3.51e-37!94;UBERON:0001016!3.51e-37!94;UBERON:0000924!3.52e-37!173;UBERON:0006601!3.52e-37!173;UBERON:0005743!1.15e-35!86;UBERON:0001017!5.12e-35!82;UBERON:0001049!9.08e-31!57;UBERON:0005068!9.08e-31!57;UBERON:0006241!9.08e-31!57;UBERON:0007135!9.08e-31!57;UBERON:0000033!5.46e-30!123;UBERON:0003075!2.31e-29!86;UBERON:0007284!2.31e-29!86;UBERON:0000153!4.48e-29!129;UBERON:0007811!4.48e-29!129;UBERON:0000955!4.62e-28!69;UBERON:0006238!4.62e-28!69;UBERON:0002346!7.62e-28!90;UBERON:0007023!4.23e-27!115;UBERON:0002616!4.63e-26!59;UBERON:0003080!1.08e-24!42;UBERON:0002780!2.36e-24!41;UBERON:0001890!2.36e-24!41;UBERON:0006240!2.36e-24!41;UBERON:0003056!1.50e-23!61;UBERON:0002020!1.23e-20!34;UBERON:0003528!1.23e-20!34;UBERON:0001893!1.56e-20!34;UBERON:0001869!3.37e-20!32;UBERON:0002791!7.25e-20!33;UBERON:0000064!1.46e-18!219;UBERON:0000956!1.35e-16!25;UBERON:0000203!1.35e-16!25;UBERON:0000475!7.66e-16!365;UBERON:0002619!2.04e-15!22;UBERON:0000922!1.24e-14!612;UBERON:0001950!2.17e-14!20;UBERON:0000481!2.76e-14!347;UBERON:0000468!1.04e-13!659;UBERON:0000483!8.47e-13!309;UBERON:0000119!1.48e-12!312;UBERON:0002050!2.15e-12!605;UBERON:0005423!2.15e-12!605;UBERON:0000923!3.79e-12!604;UBERON:0005291!3.79e-12!604;UBERON:0006598!3.79e-12!604;UBERON:0002532!3.79e-12!604;UBERON:0000480!1.00e-11!626;UBERON:0000467!1.94e-11!625;UBERON:0000477!7.01e-11!286;UBERON:0004111!2.25e-10!241;UBERON:0000062!1.46e-08!511;UBERON:0000025!6.18e-08!194;UBERON:0003076!2.59e-07!15;UBERON:0003057!2.59e-07!15
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}}
}}

Revision as of 14:10, 19 October 2012


Full id: C2567_merkel_neuroblastoma_parietal_occipital_duodenum_temporal_brain



Phase1 CAGE Peaks

Hg19::chr1:220701456..220701574,+p1@MARK1
Hg19::chr2:163645495..163645498,-p@chr2:163645495..163645498
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Hg19::chr2:163695238..163695258,-p2@KCNH7
Hg19::chr2:163695260..163695301,-p1@KCNH7


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

GO IDGO nameFDR corrected p-value
GO:0004672protein kinase activity0.0313840803320159
GO:0000155two-component sensor activity0.0313840803320159
GO:0000160two-component signal transduction system (phosphorelay)0.0313840803320159
GO:0004673protein histidine kinase activity0.0313840803320159
GO:0016773phosphotransferase activity, alcohol group as acceptor0.0313840803320159
GO:0016775phosphotransferase activity, nitrogenous group as acceptor0.0313840803320159
GO:0016301kinase activity0.035627077908378
GO:0016772transferase activity, transferring phosphorus-containing groups0.0416307496441538



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
neuronal stem cell2.30e-118
neural cell5.29e-0925
neuron1.10e-086
neuroblast1.10e-086
electrically signaling cell1.10e-086
neurectodermal cell2.15e-0759
Uber Anatomy
Ontology termp-valuen
nervous system3.29e-7189
central nervous system4.64e-7181
neural tube1.34e-7056
neural rod1.34e-7056
future spinal cord1.34e-7056
neural keel1.34e-7056
regional part of nervous system1.03e-6653
regional part of brain1.03e-6653
neurectoderm3.88e-6086
neural plate8.83e-6082
presumptive neural plate8.83e-6082
regional part of forebrain1.24e-5641
forebrain1.24e-5641
anterior neural tube1.24e-5641
future forebrain1.24e-5641
brain2.05e-5468
future brain2.05e-5468
cerebral hemisphere7.64e-4832
pre-chordal neural plate3.79e-4761
telencephalon3.88e-4734
brain grey matter4.95e-4734
gray matter4.95e-4734
ecto-epithelium7.51e-47104
regional part of telencephalon1.77e-4432
ectoderm-derived structure2.00e-43171
ectoderm2.00e-43171
presumptive ectoderm2.00e-43171
cerebral cortex1.33e-3825
pallium1.33e-3825
structure with developmental contribution from neural crest2.42e-37132
regional part of cerebral cortex2.56e-3522
adult organism2.89e-35114
neocortex6.38e-3320
organ system subdivision2.28e-30223
anatomical cluster3.72e-16373
posterior neural tube9.21e-1515
chordal neural plate9.21e-1515
tube2.47e-14192
segmental subdivision of nervous system1.99e-1213
temporal lobe8.18e-126
segmental subdivision of hindbrain2.75e-1112
hindbrain2.75e-1112
presumptive hindbrain2.75e-1112
organ part3.44e-11218
diencephalon1.17e-107
future diencephalon1.17e-107
basal ganglion2.48e-109
nuclear complex of neuraxis2.48e-109
aggregate regional part of brain2.48e-109
collection of basal ganglia2.48e-109
cerebral subcortex2.48e-109
gyrus3.08e-106
anatomical conduit3.21e-10240
regional part of metencephalon3.39e-109
metencephalon3.39e-109
future metencephalon3.39e-109
neural nucleus5.14e-109
nucleus of brain5.14e-109
parietal lobe3.36e-095
occipital lobe3.42e-095
embryo9.50e-09592
multi-tissue structure1.53e-08342
limbic system2.47e-085
epithelium6.57e-08306
cell layer1.15e-07309
telencephalic nucleus1.30e-077
gland of diencephalon2.39e-074
neuroendocrine gland2.39e-074
corpus striatum5.54e-074
striatum5.54e-074
ventral part of telencephalon5.54e-074
future corpus striatum5.54e-074
embryonic structure9.09e-07564


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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