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Coexpression cluster:C1428: Difference between revisions

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|id=C1428
|id=C1428
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:171!3.31e-08!10
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.24e-62!115;UBERON:0001049!7.44e-60!57;UBERON:0005068!7.44e-60!57;UBERON:0006241!7.44e-60!57;UBERON:0007135!7.44e-60!57;UBERON:0000073!2.69e-58!94;UBERON:0001016!2.69e-58!94;UBERON:0001017!6.12e-57!82;UBERON:0005743!5.54e-55!86;UBERON:0002616!2.49e-49!59;UBERON:0000955!6.37e-46!69;UBERON:0006238!6.37e-46!69;UBERON:0002780!3.16e-45!41;UBERON:0001890!3.16e-45!41;UBERON:0006240!3.16e-45!41;UBERON:0002346!6.40e-45!90;UBERON:0003080!8.70e-44!42;UBERON:0003075!1.13e-41!86;UBERON:0007284!1.13e-41!86;UBERON:0002020!2.28e-38!34;UBERON:0003528!2.28e-38!34;UBERON:0001893!4.74e-38!34;UBERON:0002791!5.78e-37!33;UBERON:0001869!1.69e-35!32;UBERON:0000924!6.21e-34!173;UBERON:0006601!6.21e-34!173;UBERON:0004121!2.84e-31!169;UBERON:0000956!4.13e-27!25;UBERON:0000203!4.13e-27!25;UBERON:0003056!6.20e-27!61;UBERON:0000153!3.69e-26!129;UBERON:0007811!3.69e-26!129;UBERON:0000033!1.42e-25!123;UBERON:0002619!4.66e-24!22;UBERON:0001950!1.55e-21!20;UBERON:0003076!1.53e-16!15;UBERON:0003057!1.53e-16!15;UBERON:0004732!1.53e-13!13;UBERON:0004733!1.02e-12!12;UBERON:0002028!1.02e-12!12;UBERON:0007277!1.02e-12!12;UBERON:0002308!1.15e-12!9;UBERON:0000125!1.15e-12!9;UBERON:0000025!1.36e-12!194;UBERON:0002420!2.23e-12!9;UBERON:0007245!2.23e-12!9;UBERON:0010009!2.23e-12!9;UBERON:0010011!2.23e-12!9;UBERON:0000454!2.23e-12!9;UBERON:0000922!9.36e-12!612;UBERON:0000468!2.09e-11!659;UBERON:0000064!6.27e-11!219;UBERON:0004111!7.00e-11!241;UBERON:0000475!1.17e-10!365;UBERON:0001871!1.61e-10!7;UBERON:0009663!4.63e-10!7;UBERON:0002050!1.20e-09!605;UBERON:0005423!1.20e-09!605;UBERON:0000477!2.51e-09!286;UBERON:0000923!3.04e-09!604;UBERON:0005291!3.04e-09!604;UBERON:0006598!3.04e-09!604;UBERON:0002532!3.04e-09!604;UBERON:0000481!4.70e-09!347;UBERON:0002298!5.03e-09!8;UBERON:0002680!5.89e-09!9;UBERON:0001895!5.89e-09!9;UBERON:0010092!5.89e-09!9;UBERON:0001894!1.89e-08!7;UBERON:0006222!1.89e-08!7;UBERON:0000200!4.50e-08!6;UBERON:0000349!1.21e-07!5;UBERON:0000467!1.52e-07!625;UBERON:0000480!1.80e-07!626;UBERON:0000483!4.03e-07!309;UBERON:0001872!6.98e-07!5;UBERON:0000119!7.36e-07!312
|ontology_enrichment_uberon=UBERON:0001049!4.34e-86!56;UBERON:0005068!4.34e-86!56;UBERON:0006241!4.34e-86!56;UBERON:0007135!4.34e-86!56;UBERON:0000073!6.67e-78!53;UBERON:0002616!6.67e-78!53;UBERON:0001016!1.04e-67!89;UBERON:0001017!6.04e-67!81;UBERON:0003075!1.46e-63!82;UBERON:0007284!1.46e-63!82;UBERON:0000955!1.07e-60!68;UBERON:0006238!1.07e-60!68;UBERON:0002346!4.80e-60!86;UBERON:0002780!7.95e-60!41;UBERON:0001890!7.95e-60!41;UBERON:0003080!7.95e-60!41;UBERON:0006240!7.95e-60!41;UBERON:0003528!9.49e-56!34;UBERON:0002020!9.49e-56!34;UBERON:0001893!3.58e-55!34;UBERON:0002791!2.18e-50!32;UBERON:0010371!5.97e-50!104;UBERON:0001869!6.04e-50!32;UBERON:0007023!7.26e-49!114;UBERON:0003056!5.60e-40!61;UBERON:0010314!2.50e-38!132;UBERON:0004121!1.87e-35!171;UBERON:0000924!1.87e-35!171;UBERON:0006601!1.87e-35!171;UBERON:0011216!3.38e-34!223;UBERON:0000956!1.98e-33!25;UBERON:0000203!1.98e-33!25;UBERON:0002619!9.71e-31!22;UBERON:0003076!3.13e-26!15;UBERON:0003057!3.13e-26!15;UBERON:0001950!6.39e-26!20;UBERON:0000125!4.02e-25!9;UBERON:0002308!4.02e-25!9;UBERON:0002420!1.16e-24!9;UBERON:0007245!1.16e-24!9;UBERON:0010009!1.16e-24!9;UBERON:0010011!1.16e-24!9;UBERON:0000454!1.16e-24!9;UBERON:0000025!1.69e-22!192;UBERON:0009663!1.48e-19!7;UBERON:0000477!1.03e-18!373;UBERON:0004733!1.95e-18!12;UBERON:0002028!1.95e-18!12;UBERON:0007277!1.95e-18!12;UBERON:0002298!3.63e-18!6;UBERON:0004732!7.25e-17!13;UBERON:0004111!2.06e-16!240;UBERON:0000349!1.55e-14!5;UBERON:0001871!1.00e-13!6;UBERON:0000064!5.59e-13!218;UBERON:0000481!8.33e-13!342;UBERON:0000483!2.53e-12!306;UBERON:0000119!4.44e-12!309;UBERON:0000369!1.68e-11!4;UBERON:0002435!1.68e-11!4;UBERON:0000204!1.68e-11!4;UBERON:0010082!1.68e-11!4;UBERON:0000200!3.33e-11!6;UBERON:0002680!4.75e-11!9;UBERON:0001895!4.75e-11!9;UBERON:0010092!4.75e-11!9;UBERON:0002240!4.99e-10!3;UBERON:0005174!4.99e-10!3;UBERON:0001137!4.99e-10!3;UBERON:0001896!5.45e-10!3;UBERON:0005290!5.45e-10!3;UBERON:0010096!5.45e-10!3;UBERON:0000988!6.86e-10!3;UBERON:0005383!4.29e-09!3;UBERON:0005382!4.29e-09!3;UBERON:0002050!8.32e-09!564;UBERON:0002108!1.27e-08!4;UBERON:0000923!2.22e-08!560;UBERON:0010316!2.22e-08!560;UBERON:0005291!2.22e-08!560;UBERON:0006598!2.22e-08!560;UBERON:0010317!2.22e-08!560;UBERON:0002532!2.22e-08!560;UBERON:0000922!3.35e-08!592;UBERON:0005423!4.45e-08!581;UBERON:0002148!2.87e-07!2;UBERON:0006331!2.87e-07!2;UBERON:0009662!2.87e-07!2;UBERON:0001897!4.45e-07!2;UBERON:0010225!4.45e-07!2;UBERON:0001875!4.85e-07!2;UBERON:0006514!4.85e-07!2;UBERON:0002784!5.00e-07!4;UBERON:0001954!5.29e-07!2;UBERON:0003022!5.29e-07!2;UBERON:0002421!5.29e-07!2;UBERON:0002600!5.29e-07!2;UBERON:0001876!8.60e-07!2;UBERON:0001873!9.62e-07!2;UBERON:0010122!9.62e-07!2
|tf_chipseq_enrich=CTBP2#1488;3:31.3585001696641:7.81255347077474e-05:0.00120326688089403
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}}
}}

Revision as of 11:16, 19 October 2012


Full id: C1428_neuroblastoma_medulla_locus_spinal_hippocampus_thalamus_globus



Phase1 CAGE Peaks

Hg19::chr17:10741337..10741344,-p3@PIRT
Hg19::chr17:10741366..10741377,-p2@PIRT
Hg19::chr17:10741392..10741423,-p1@PIRT
Hg19::chr3:28617858..28617911,+p1@ENST00000443912
Hg19::chr3:28617928..28617938,+p1@ENST00000445077
Hg19::chr3:28617949..28617957,+p2@ENST00000445077


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 tube4.34e-8656
neural rod4.34e-8656
future spinal cord4.34e-8656
neural keel4.34e-8656
regional part of nervous system6.67e-7853
regional part of brain6.67e-7853
nervous system1.04e-6789
central nervous system6.04e-6781
neural plate1.46e-6382
presumptive neural plate1.46e-6382
brain1.07e-6068
future brain1.07e-6068
neurectoderm4.80e-6086
regional part of forebrain7.95e-6041
forebrain7.95e-6041
anterior neural tube7.95e-6041
future forebrain7.95e-6041
brain grey matter9.49e-5634
gray matter9.49e-5634
telencephalon3.58e-5534
regional part of telencephalon2.18e-5032
ecto-epithelium5.97e-50104
cerebral hemisphere6.04e-5032
adult organism7.26e-49114
pre-chordal neural plate5.60e-4061
structure with developmental contribution from neural crest2.50e-38132
ectoderm-derived structure1.87e-35171
ectoderm1.87e-35171
presumptive ectoderm1.87e-35171
organ system subdivision3.38e-34223
cerebral cortex1.98e-3325
pallium1.98e-3325
regional part of cerebral cortex9.71e-3122
posterior neural tube3.13e-2615
chordal neural plate3.13e-2615
neocortex6.39e-2620
neural nucleus4.02e-259
nucleus of brain4.02e-259
basal ganglion1.16e-249
nuclear complex of neuraxis1.16e-249
aggregate regional part of brain1.16e-249
collection of basal ganglia1.16e-249
cerebral subcortex1.16e-249
tube1.69e-22192
telencephalic nucleus1.48e-197
anatomical cluster1.03e-18373
segmental subdivision of hindbrain1.95e-1812
hindbrain1.95e-1812
presumptive hindbrain1.95e-1812
brainstem3.63e-186
segmental subdivision of nervous system7.25e-1713
anatomical conduit2.06e-16240
limbic system1.55e-145
temporal lobe1.00e-136
organ part5.59e-13218
multi-tissue structure8.33e-13342
epithelium2.53e-12306
cell layer4.44e-12309
corpus striatum1.68e-114
striatum1.68e-114
ventral part of telencephalon1.68e-114
future corpus striatum1.68e-114
gyrus3.33e-116
regional part of metencephalon4.75e-119
metencephalon4.75e-119
future metencephalon4.75e-119
spinal cord4.99e-103
dorsal region element4.99e-103
dorsum4.99e-103
medulla oblongata5.45e-103
myelencephalon5.45e-103
future myelencephalon5.45e-103
pons6.86e-103
caudate-putamen4.29e-093
dorsal striatum4.29e-093
embryonic structure8.32e-09564
small intestine1.27e-084
germ layer2.22e-08560
germ layer / neural crest2.22e-08560
embryonic tissue2.22e-08560
presumptive structure2.22e-08560
germ layer / neural crest derived structure2.22e-08560
epiblast (generic)2.22e-08560
embryo3.35e-08592
developing anatomical structure4.45e-08581
locus ceruleus2.87e-072
brainstem nucleus2.87e-072
hindbrain nucleus2.87e-072
dorsal plus ventral thalamus4.45e-072
thalamic complex4.45e-072
globus pallidus4.85e-072
pallidum4.85e-072
regional part of diencephalon5.00e-074
Ammon's horn5.29e-072
lobe parts of cerebral cortex5.29e-072
hippocampal formation5.29e-072
limbic lobe5.29e-072
amygdala8.60e-072
caudate nucleus9.62e-072
future caudate nucleus9.62e-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

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

TF#promotersEnrichmentp-valueq-value
CTBP2#1488331.35850016966417.81255347077474e-050.00120326688089403



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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