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Coexpression cluster:C2463: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!2.39e-87!57;UBERON:0005068!2.39e-87!57;UBERON:0006241!2.39e-87!57;UBERON:0007135!2.39e-87!57;UBERON:0001017!3.41e-73!82;UBERON:0002616!1.33e-72!59;UBERON:0005743!6.37e-72!86;UBERON:0000955!5.82e-69!69;UBERON:0006238!5.82e-69!69;UBERON:0000073!8.41e-67!94;UBERON:0001016!8.41e-67!94;UBERON:0002780!9.06e-67!41;UBERON:0001890!9.06e-67!41;UBERON:0006240!9.06e-67!41;UBERON:0003080!5.77e-65!42;UBERON:0003075!2.84e-61!86;UBERON:0007284!2.84e-61!86;UBERON:0002346!5.98e-58!90;UBERON:0002020!1.84e-51!34;UBERON:0003528!1.84e-51!34;UBERON:0001893!2.07e-51!34;UBERON:0007023!1.37e-49!115;UBERON:0002791!4.01e-49!33;UBERON:0001869!1.43e-46!32;UBERON:0003056!2.90e-44!61;UBERON:0000033!8.90e-37!123;UBERON:0002619!4.44e-36!22;UBERON:0000153!1.85e-34!129;UBERON:0007811!1.85e-34!129;UBERON:0004121!1.88e-32!169;UBERON:0001950!1.38e-31!20;UBERON:0000924!2.28e-31!173;UBERON:0006601!2.28e-31!173;UBERON:0000956!2.91e-31!25;UBERON:0000203!2.91e-31!25;UBERON:0002308!8.97e-23!9;UBERON:0000125!8.97e-23!9;UBERON:0003076!2.91e-22!15;UBERON:0003057!2.91e-22!15;UBERON:0002420!3.47e-22!9;UBERON:0007245!3.47e-22!9;UBERON:0010009!3.47e-22!9;UBERON:0010011!3.47e-22!9;UBERON:0000454!3.47e-22!9;UBERON:0004732!3.03e-18!13;UBERON:0009663!7.57e-18!7;UBERON:0000025!1.24e-17!194;UBERON:0001894!7.86e-17!7;UBERON:0006222!7.86e-17!7;UBERON:0004733!6.44e-16!12;UBERON:0002028!6.44e-16!12;UBERON:0007277!6.44e-16!12;UBERON:0002298!6.49e-16!8;UBERON:0000200!3.25e-15!6;UBERON:0000349!5.17e-13!5;UBERON:0004111!1.70e-12!241;UBERON:0000483!6.86e-12!309;UBERON:0000119!1.21e-11!312;UBERON:0001871!3.55e-11!7;UBERON:0000477!1.56e-10!286;UBERON:0000369!1.83e-10!4;UBERON:0002435!1.83e-10!4;UBERON:0000204!1.83e-10!4;UBERON:0010082!1.83e-10!4;UBERON:0000475!2.61e-10!365;UBERON:0002680!9.28e-10!9;UBERON:0001895!9.28e-10!9;UBERON:0010092!9.28e-10!9;UBERON:0003296!1.40e-09!4;UBERON:0010133!1.40e-09!4;UBERON:0000064!3.53e-09!219;UBERON:0006331!4.23e-09!3;UBERON:0000988!4.46e-09!3;UBERON:0000062!7.67e-09!511;UBERON:0001872!8.58e-09!5;UBERON:0002771!1.35e-08!3;UBERON:0001896!1.57e-08!3;UBERON:0005290!1.57e-08!3;UBERON:0010096!1.57e-08!3;UBERON:0002021!1.71e-08!5;UBERON:0002240!2.12e-08!3;UBERON:0005383!4.23e-08!3;UBERON:0005382!4.23e-08!3;UBERON:0000922!7.44e-07!612;UBERON:0005162!8.78e-07!2;UBERON:0000122!8.78e-07!2
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}}
}}

Revision as of 14:03, 19 October 2012


Full id: C2463_endometrial_optic_corpus_globus_astrocytoma_thalamus_spinal



Phase1 CAGE Peaks

Hg19::chr18:48918403..48918418,+p1@LOC100287225
Hg19::chr18:48918420..48918432,+p3@LOC100287225
Hg19::chr18:48918435..48918444,+p4@LOC100287225
Hg19::chr18:48918447..48918475,+p2@LOC100287225


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 tube1.85e-10656
neural rod1.85e-10656
future spinal cord1.85e-10656
neural keel1.85e-10656
regional part of nervous system2.92e-9753
regional part of brain2.92e-9753
central nervous system4.23e-8881
brain7.06e-8568
future brain7.06e-8568
nervous system3.45e-8289
regional part of forebrain9.94e-8141
forebrain9.94e-8141
anterior neural tube9.94e-8141
future forebrain9.94e-8141
neural plate6.76e-7782
presumptive neural plate6.76e-7782
neurectoderm7.47e-7386
brain grey matter6.93e-7034
gray matter6.93e-7034
telencephalon7.32e-7034
regional part of telencephalon2.10e-6332
cerebral hemisphere2.33e-6332
adult organism4.55e-61114
pre-chordal neural plate6.20e-5961
ecto-epithelium1.81e-58104
structure with developmental contribution from neural crest1.31e-50132
regional part of cerebral cortex1.22e-4822
neocortex1.63e-4220
cerebral cortex1.93e-4225
pallium1.93e-4225
ectoderm-derived structure8.77e-40171
ectoderm8.77e-40171
presumptive ectoderm8.77e-40171
neural nucleus3.42e-309
nucleus of brain3.42e-309
basal ganglion1.37e-299
nuclear complex of neuraxis1.37e-299
aggregate regional part of brain1.37e-299
collection of basal ganglia1.37e-299
cerebral subcortex1.37e-299
organ system subdivision2.75e-29223
posterior neural tube2.42e-2515
chordal neural plate2.42e-2515
tube3.16e-25192
telencephalic nucleus1.50e-237
brainstem5.20e-216
segmental subdivision of nervous system4.07e-2013
gyrus7.29e-206
anatomical conduit4.72e-18240
limbic system3.37e-175
segmental subdivision of hindbrain3.92e-1712
hindbrain3.92e-1712
presumptive hindbrain3.92e-1712
anatomical cluster1.93e-15373
epithelium2.18e-15306
cell layer3.96e-15309
corpus striatum1.38e-134
striatum1.38e-134
ventral part of telencephalon1.38e-134
future corpus striatum1.38e-134
organ part4.74e-13218
temporal lobe4.88e-126
diencephalon5.36e-127
future diencephalon5.36e-127
pons1.09e-113
parietal lobe3.70e-115
occipital lobe4.57e-115
medulla oblongata4.64e-113
myelencephalon4.64e-113
future myelencephalon4.64e-113
multi-tissue structure6.32e-11342
frontal cortex9.43e-113
spinal cord9.43e-113
dorsal region element9.43e-113
dorsum9.43e-113
caudate-putamen2.02e-103
dorsal striatum2.02e-103
organ1.16e-09503
regional part of metencephalon2.43e-099
metencephalon2.43e-099
future metencephalon2.43e-099
germ layer1.11e-08560
germ layer / neural crest1.11e-08560
embryonic tissue1.11e-08560
presumptive structure1.11e-08560
germ layer / neural crest derived structure1.11e-08560
epiblast (generic)1.11e-08560
multi cell component structure1.32e-082
neuron projection bundle1.32e-082
embryonic structure1.57e-08564
globus pallidus1.82e-082
pallidum1.82e-082
locus ceruleus2.33e-082
brainstem nucleus2.33e-082
hindbrain nucleus2.33e-082
dorsal plus ventral thalamus3.32e-082
thalamic complex3.32e-082
embryo3.76e-08592
Ammon's horn5.59e-082
lobe parts of cerebral cortex5.59e-082


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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