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Coexpression cluster:C2689: Difference between revisions

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|full_id=C2689_merkel_occipital_parietal_pineal_cerebellum_temporal_amygdala
|full_id=C2689_merkel_occipital_parietal_pineal_cerebellum_temporal_amygdala
|id=C2689
|id=C2689
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0000242!4.37e-07!2
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!3.06e-81!57;UBERON:0005068!3.06e-81!57;UBERON:0006241!3.06e-81!57;UBERON:0007135!3.06e-81!57;UBERON:0001017!7.11e-79!82;UBERON:0005743!4.80e-77!86;UBERON:0000073!1.90e-75!94;UBERON:0001016!1.90e-75!94;UBERON:0002616!1.99e-68!59;UBERON:0002780!5.72e-67!41;UBERON:0001890!5.72e-67!41;UBERON:0006240!5.72e-67!41;UBERON:0000955!4.36e-66!69;UBERON:0006238!4.36e-66!69;UBERON:0003080!4.22e-65!42;UBERON:0003075!1.08e-59!86;UBERON:0007284!1.08e-59!86;UBERON:0002346!2.72e-56!90;UBERON:0002020!6.31e-54!34;UBERON:0003528!6.31e-54!34;UBERON:0001893!6.78e-54!34;UBERON:0002791!4.26e-52!33;UBERON:0001869!7.90e-51!32;UBERON:0003056!1.07e-45!61;UBERON:0004121!1.29e-42!169;UBERON:0007023!8.46e-42!115;UBERON:0000924!3.56e-41!173;UBERON:0006601!3.56e-41!173;UBERON:0002619!2.30e-40!22;UBERON:0000956!6.56e-38!25;UBERON:0000203!6.56e-38!25;UBERON:0001950!1.31e-36!20;UBERON:0000033!2.12e-36!123;UBERON:0000153!5.97e-34!129;UBERON:0007811!5.97e-34!129;UBERON:0000025!9.21e-20!194;UBERON:0002420!7.60e-18!9;UBERON:0007245!7.60e-18!9;UBERON:0010009!7.60e-18!9;UBERON:0010011!7.60e-18!9;UBERON:0000454!7.60e-18!9;UBERON:0002308!2.76e-17!9;UBERON:0000125!2.76e-17!9;UBERON:0003076!1.04e-16!15;UBERON:0003057!1.04e-16!15;UBERON:0001894!3.41e-14!7;UBERON:0006222!3.41e-14!7;UBERON:0009663!4.96e-14!7;UBERON:0004111!1.77e-13!241;UBERON:0001871!1.03e-12!7;UBERON:0000200!1.70e-12!6;UBERON:0004733!3.50e-12!12;UBERON:0002028!3.50e-12!12;UBERON:0007277!3.50e-12!12;UBERON:0000064!4.58e-12!219;UBERON:0004732!4.35e-11!13;UBERON:0000483!4.43e-11!309;UBERON:0000349!4.46e-11!5;UBERON:0001872!5.92e-11!5;UBERON:0000119!8.18e-11!312;UBERON:0002021!9.20e-11!5;UBERON:0002298!9.57e-11!8;UBERON:0000477!4.09e-10!286;UBERON:0000369!2.00e-09!4;UBERON:0002435!2.00e-09!4;UBERON:0000204!2.00e-09!4;UBERON:0010082!2.00e-09!4;UBERON:0003296!3.14e-09!4;UBERON:0010133!3.14e-09!4;UBERON:0002680!5.86e-08!9;UBERON:0001895!5.86e-08!9;UBERON:0010092!5.86e-08!9;UBERON:0000475!6.60e-08!365;UBERON:0005383!1.55e-07!3;UBERON:0005382!1.55e-07!3;UBERON:0002771!3.19e-07!3
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}}
}}

Revision as of 14:18, 19 October 2012


Full id: C2689_merkel_occipital_parietal_pineal_cerebellum_temporal_amygdala



Phase1 CAGE Peaks

Hg19::chr2:226264401..226264438,+p1@ENST00000431435
Hg19::chr2:226265133..226265158,+p2@NYAP2
Hg19::chr2:226265161..226265212,+p1@NYAP2
Hg19::chr2:226276996..226277000,+p@chr2:226276996..226277000
+


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
Merkel cell4.37e-072
Uber Anatomy
Ontology termp-valuen
neural tube3.86e-10356
neural rod3.86e-10356
future spinal cord3.86e-10356
neural keel3.86e-10356
regional part of nervous system2.74e-9653
regional part of brain2.74e-9653
central nervous system3.77e-9681
nervous system7.08e-9289
brain6.89e-8268
future brain6.89e-8268
regional part of forebrain9.23e-8141
forebrain9.23e-8141
anterior neural tube9.23e-8141
future forebrain9.23e-8141
neural plate2.67e-7282
presumptive neural plate2.67e-7282
neurectoderm2.46e-6886
brain grey matter2.15e-6334
gray matter2.15e-6334
cerebral hemisphere2.22e-6332
telencephalon2.47e-6334
ecto-epithelium1.10e-59104
regional part of telencephalon7.37e-5932
pre-chordal neural plate6.30e-5761
regional part of cerebral cortex3.13e-5322
ectoderm-derived structure2.11e-50171
ectoderm2.11e-50171
presumptive ectoderm2.11e-50171
neocortex1.98e-4820
cerebral cortex2.54e-4625
pallium2.54e-4625
adult organism5.19e-46114
structure with developmental contribution from neural crest1.12e-43132
organ system subdivision3.70e-36223
tube1.89e-24192
posterior neural tube2.20e-2215
chordal neural plate2.20e-2215
diencephalon1.35e-187
future diencephalon1.35e-187
basal ganglion1.48e-189
nuclear complex of neuraxis1.48e-189
aggregate regional part of brain1.48e-189
collection of basal ganglia1.48e-189
cerebral subcortex1.48e-189
neural nucleus4.00e-189
nucleus of brain4.00e-189
anatomical cluster5.30e-17373
anatomical conduit6.55e-17240
segmental subdivision of hindbrain2.65e-1612
hindbrain2.65e-1612
presumptive hindbrain2.65e-1612
gyrus3.10e-166
segmental subdivision of nervous system6.59e-1513
brainstem2.20e-146
parietal lobe3.18e-145
temporal lobe6.15e-146
limbic system8.35e-145
telencephalic nucleus9.22e-147
occipital lobe9.53e-145
epithelium1.73e-13306
cell layer3.16e-13309
organ part6.75e-13218
gland of diencephalon5.12e-124
neuroendocrine gland5.12e-124
corpus striatum5.71e-124
striatum5.71e-124
ventral part of telencephalon5.71e-124
future corpus striatum5.71e-124
regional part of diencephalon1.83e-114
regional part of metencephalon1.44e-109
metencephalon1.44e-109
future metencephalon1.44e-109
caudate-putamen1.89e-093
dorsal striatum1.89e-093
multi-tissue structure3.03e-09342
frontal cortex4.07e-093
germ layer2.78e-08560
germ layer / neural crest2.78e-08560
embryonic tissue2.78e-08560
presumptive structure2.78e-08560
germ layer / neural crest derived structure2.78e-08560
epiblast (generic)2.78e-08560
pons3.08e-083
embryonic structure4.17e-08564
spinal cord4.98e-083
dorsal region element4.98e-083
dorsum4.98e-083
medulla oblongata7.99e-083
myelencephalon7.99e-083
future myelencephalon7.99e-083
embryo1.78e-07592
organ1.92e-07503
developing anatomical structure2.18e-07581
pineal body4.62e-072
regional part of epithalamus4.62e-072
secretory circumventricular organ4.62e-072
circumventricular organ4.62e-072
epithalamus4.62e-072
caudate nucleus8.35e-072


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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