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Coexpression cluster:C1503: Difference between revisions

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|full_id=C1503_cerebellum_heart_small_left_hippocampus_skeletal_occipital
|full_id=C1503_cerebellum_heart_small_left_hippocampus_skeletal_occipital
|id=C1503
|id=C1503
|ontology_enrichment_celltype=CL:0000047!3.01e-07!8
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!9.37e-59!115;UBERON:0001017!3.99e-49!82;UBERON:0001049!7.01e-48!57;UBERON:0005068!7.01e-48!57;UBERON:0006241!7.01e-48!57;UBERON:0007135!7.01e-48!57;UBERON:0005743!1.10e-47!86;UBERON:0002346!5.40e-47!90;UBERON:0000073!2.30e-46!94;UBERON:0001016!2.30e-46!94;UBERON:0003075!3.81e-42!86;UBERON:0007284!3.81e-42!86;UBERON:0002616!2.06e-39!59;UBERON:0000955!1.24e-37!69;UBERON:0006238!1.24e-37!69;UBERON:0002780!5.93e-36!41;UBERON:0001890!5.93e-36!41;UBERON:0006240!5.93e-36!41;UBERON:0000924!7.63e-35!173;UBERON:0006601!7.63e-35!173;UBERON:0003080!8.42e-35!42;UBERON:0001893!6.78e-33!34;UBERON:0002020!8.38e-33!34;UBERON:0003528!8.38e-33!34;UBERON:0002791!1.36e-31!33;UBERON:0004121!3.77e-31!169;UBERON:0001869!7.96e-31!32;UBERON:0003056!4.93e-28!61;UBERON:0002619!4.99e-27!22;UBERON:0000153!5.70e-26!129;UBERON:0007811!5.70e-26!129;UBERON:0000033!6.45e-25!123;UBERON:0001950!2.55e-24!20;UBERON:0000956!5.80e-23!25;UBERON:0000203!5.80e-23!25;UBERON:0003076!8.10e-14!15;UBERON:0003057!8.10e-14!15;UBERON:0000025!2.10e-13!194;UBERON:0000468!7.93e-13!659;UBERON:0000064!1.13e-12!219;UBERON:0000477!1.84e-12!286;UBERON:0004111!4.22e-12!241;UBERON:0004732!8.13e-12!13;UBERON:0002420!1.19e-11!9;UBERON:0007245!1.19e-11!9;UBERON:0010009!1.19e-11!9;UBERON:0010011!1.19e-11!9;UBERON:0000454!1.19e-11!9;UBERON:0000062!1.84e-11!511;UBERON:0002308!2.51e-11!9;UBERON:0000125!2.51e-11!9;UBERON:0000922!3.65e-11!612;UBERON:0000483!3.75e-11!309;UBERON:0000119!8.03e-11!312;UBERON:0004733!9.92e-11!12;UBERON:0002028!9.92e-11!12;UBERON:0007277!9.92e-11!12;UBERON:0000923!3.03e-10!604;UBERON:0005291!3.03e-10!604;UBERON:0006598!3.03e-10!604;UBERON:0002532!3.03e-10!604;UBERON:0002050!3.63e-10!605;UBERON:0005423!3.63e-10!605;UBERON:0000475!3.90e-10!365;UBERON:0000481!6.24e-10!347;UBERON:0000467!6.54e-10!625;UBERON:0000480!7.81e-10!626;UBERON:0002680!1.33e-09!9;UBERON:0001895!1.33e-09!9;UBERON:0010092!1.33e-09!9;UBERON:0009663!5.63e-09!7;UBERON:0001871!7.90e-09!7;UBERON:0000200!8.09e-09!6;UBERON:0000349!2.59e-08!5;UBERON:0001872!1.28e-07!5;UBERON:0002021!2.16e-07!5
|ontology_enrichment_uberon=UBERON:0001049!5.91e-65!56;UBERON:0005068!5.91e-65!56;UBERON:0006241!5.91e-65!56;UBERON:0007135!5.91e-65!56;UBERON:0000073!9.15e-60!53;UBERON:0002616!9.15e-60!53;UBERON:0001017!1.79e-59!81;UBERON:0002346!3.25e-59!86;UBERON:0001016!4.11e-57!89;UBERON:0007023!7.12e-53!114;UBERON:0003075!6.83e-52!82;UBERON:0007284!6.83e-52!82;UBERON:0002780!2.54e-49!41;UBERON:0001890!2.54e-49!41;UBERON:0003080!2.54e-49!41;UBERON:0006240!2.54e-49!41;UBERON:0000955!2.22e-48!68;UBERON:0006238!2.22e-48!68;UBERON:0001893!8.45e-47!34;UBERON:0003528!1.23e-46!34;UBERON:0002020!1.23e-46!34;UBERON:0001869!2.08e-43!32;UBERON:0002791!6.85e-43!32;UBERON:0004121!4.68e-41!171;UBERON:0000924!4.68e-41!171;UBERON:0006601!4.68e-41!171;UBERON:0010371!8.64e-40!104;UBERON:0002619!4.55e-39!22;UBERON:0010314!1.60e-36!132;UBERON:0003056!2.09e-36!61;UBERON:0001950!8.11e-35!20;UBERON:0000956!8.23e-34!25;UBERON:0000203!8.23e-34!25;UBERON:0011216!1.33e-22!223;UBERON:0000025!1.30e-17!192;UBERON:0003076!4.14e-16!15;UBERON:0003057!4.14e-16!15;UBERON:0002420!1.55e-14!9;UBERON:0007245!1.55e-14!9;UBERON:0010009!1.55e-14!9;UBERON:0010011!1.55e-14!9;UBERON:0000454!1.55e-14!9;UBERON:0000125!4.40e-14!9;UBERON:0002308!4.40e-14!9;UBERON:0004111!1.34e-13!240;UBERON:0000477!1.96e-13!373;UBERON:0000200!3.26e-13!6;UBERON:0004732!4.82e-13!13;UBERON:0000064!8.34e-13!218;UBERON:0000349!3.05e-12!5;UBERON:0001871!1.15e-11!6;UBERON:0001872!2.00e-11!5;UBERON:0004733!2.01e-11!12;UBERON:0002028!2.01e-11!12;UBERON:0007277!2.01e-11!12;UBERON:0000483!1.52e-10!306;UBERON:0009663!1.94e-10!7;UBERON:0000119!2.66e-10!309;UBERON:0002298!3.73e-09!6;UBERON:0000481!4.45e-09!342;UBERON:0002680!4.54e-09!9;UBERON:0001895!4.54e-09!9;UBERON:0010092!4.54e-09!9;UBERON:0000369!5.01e-09!4;UBERON:0002435!5.01e-09!4;UBERON:0000204!5.01e-09!4;UBERON:0010082!5.01e-09!4;UBERON:0000062!2.86e-08!503;UBERON:0000922!3.25e-08!592;UBERON:0000923!3.57e-08!560;UBERON:0010316!3.57e-08!560;UBERON:0005291!3.57e-08!560;UBERON:0006598!3.57e-08!560;UBERON:0010317!3.57e-08!560;UBERON:0002532!3.57e-08!560;UBERON:0000468!4.24e-08!656;UBERON:0002050!5.62e-08!564;UBERON:0005423!1.15e-07!581;UBERON:0001870!1.93e-07!3;UBERON:0002021!2.04e-07!5;UBERON:0000988!3.88e-07!3;UBERON:0005383!5.46e-07!3;UBERON:0005382!5.46e-07!3
|tf_chipseq_enrich=SUZ12#23512;5:41.7631507592191:1.86145137032345e-08:1.33613827948598e-06
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}}
}}

Revision as of 11:22, 19 October 2012


Full id: C1503_cerebellum_heart_small_left_hippocampus_skeletal_occipital



Phase1 CAGE Peaks

Hg19::chr2:229046330..229046346,-p4@SPHKAP
Hg19::chr2:229046362..229046373,-p6@SPHKAP
Hg19::chr2:229046385..229046408,-p1@SPHKAP
Hg19::chr2:229046419..229046438,-p2@SPHKAP
Hg19::chr2:229046447..229046465,-p3@SPHKAP
Hg19::chr2:229046721..229046736,-p7@SPHKAP


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 tube5.91e-6556
neural rod5.91e-6556
future spinal cord5.91e-6556
neural keel5.91e-6556
regional part of nervous system9.15e-6053
regional part of brain9.15e-6053
central nervous system1.79e-5981
neurectoderm3.25e-5986
nervous system4.11e-5789
adult organism7.12e-53114
neural plate6.83e-5282
presumptive neural plate6.83e-5282
regional part of forebrain2.54e-4941
forebrain2.54e-4941
anterior neural tube2.54e-4941
future forebrain2.54e-4941
brain2.22e-4868
future brain2.22e-4868
telencephalon8.45e-4734
brain grey matter1.23e-4634
gray matter1.23e-4634
cerebral hemisphere2.08e-4332
regional part of telencephalon6.85e-4332
ectoderm-derived structure4.68e-41171
ectoderm4.68e-41171
presumptive ectoderm4.68e-41171
ecto-epithelium8.64e-40104
regional part of cerebral cortex4.55e-3922
structure with developmental contribution from neural crest1.60e-36132
pre-chordal neural plate2.09e-3661
neocortex8.11e-3520
cerebral cortex8.23e-3425
pallium8.23e-3425
organ system subdivision1.33e-22223
tube1.30e-17192
posterior neural tube4.14e-1615
chordal neural plate4.14e-1615
basal ganglion1.55e-149
nuclear complex of neuraxis1.55e-149
aggregate regional part of brain1.55e-149
collection of basal ganglia1.55e-149
cerebral subcortex1.55e-149
neural nucleus4.40e-149
nucleus of brain4.40e-149
anatomical conduit1.34e-13240
anatomical cluster1.96e-13373
gyrus3.26e-136
segmental subdivision of nervous system4.82e-1313
organ part8.34e-13218
limbic system3.05e-125
temporal lobe1.15e-116
parietal lobe2.00e-115
segmental subdivision of hindbrain2.01e-1112
hindbrain2.01e-1112
presumptive hindbrain2.01e-1112
epithelium1.52e-10306
telencephalic nucleus1.94e-107
cell layer2.66e-10309
brainstem3.73e-096
multi-tissue structure4.45e-09342
regional part of metencephalon4.54e-099
metencephalon4.54e-099
future metencephalon4.54e-099
corpus striatum5.01e-094
striatum5.01e-094
ventral part of telencephalon5.01e-094
future corpus striatum5.01e-094
organ2.86e-08503
embryo3.25e-08592
germ layer3.57e-08560
germ layer / neural crest3.57e-08560
embryonic tissue3.57e-08560
presumptive structure3.57e-08560
germ layer / neural crest derived structure3.57e-08560
epiblast (generic)3.57e-08560
multi-cellular organism4.24e-08656
embryonic structure5.62e-08564
developing anatomical structure1.15e-07581
frontal cortex1.93e-073
occipital lobe2.04e-075
pons3.88e-073
caudate-putamen5.46e-073
dorsal striatum5.46e-073


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
SUZ12#23512541.76315075921911.86145137032345e-081.33613827948598e-06



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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