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Coexpression cluster:C4186: Difference between revisions

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|full_id=C4186_retina_corpus_Retinal_medulla_eye_pons_spinal
|full_id=C4186_retina_corpus_Retinal_medulla_eye_pons_spinal
|id=C4186
|id=C4186
|ontology_enrichment_celltype=CL:0000147!1.96e-08!14;CL:0000149!4.32e-07!4
|ontology_enrichment_celltype=CL:0000149!2.40e-10!4;CL:0002586!2.17e-08!3
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!5.81e-57!57;UBERON:0005068!5.81e-57!57;UBERON:0006241!5.81e-57!57;UBERON:0007135!5.81e-57!57;UBERON:0005743!1.61e-54!86;UBERON:0000073!1.50e-49!94;UBERON:0001016!1.50e-49!94;UBERON:0001017!6.17e-49!82;UBERON:0003075!5.82e-47!86;UBERON:0007284!5.82e-47!86;UBERON:0002616!8.56e-47!59;UBERON:0000955!4.62e-45!69;UBERON:0006238!4.62e-45!69;UBERON:0002780!8.93e-45!41;UBERON:0001890!8.93e-45!41;UBERON:0006240!8.93e-45!41;UBERON:0002346!4.99e-44!90;UBERON:0001893!1.82e-43!34;UBERON:0003080!2.02e-43!42;UBERON:0002020!3.40e-43!34;UBERON:0003528!3.40e-43!34;UBERON:0002791!7.10e-42!33;UBERON:0007023!7.55e-41!115;UBERON:0001869!2.98e-40!32;UBERON:0003056!5.35e-36!61;UBERON:0004121!1.74e-34!169;UBERON:0000033!4.77e-34!123;UBERON:0000924!3.72e-33!173;UBERON:0006601!3.72e-33!173;UBERON:0000153!9.24e-33!129;UBERON:0007811!9.24e-33!129;UBERON:0000956!4.35e-30!25;UBERON:0000203!4.35e-30!25;UBERON:0002619!6.78e-27!22;UBERON:0001950!3.38e-24!20;UBERON:0000025!5.64e-20!194;UBERON:0004111!5.19e-16!241;UBERON:0002308!1.60e-14!9;UBERON:0000125!1.60e-14!9;UBERON:0002420!2.30e-14!9;UBERON:0007245!2.30e-14!9;UBERON:0010009!2.30e-14!9;UBERON:0010011!2.30e-14!9;UBERON:0000454!2.30e-14!9;UBERON:0003076!3.70e-14!15;UBERON:0003057!3.70e-14!15;UBERON:0000483!3.24e-12!309;UBERON:0000119!6.82e-12!312;UBERON:0000475!8.64e-12!365;UBERON:0009663!1.25e-11!7;UBERON:0004732!1.61e-11!13;UBERON:0000064!1.84e-11!219;UBERON:0000477!1.86e-11!286;UBERON:0002298!1.50e-10!8;UBERON:0004733!3.59e-10!12;UBERON:0002028!3.59e-10!12;UBERON:0007277!3.59e-10!12;UBERON:0000062!4.16e-10!511;UBERON:0000200!5.24e-10!6;UBERON:0001871!1.83e-09!7;UBERON:0000481!1.92e-09!347;UBERON:0000349!1.28e-08!5;UBERON:0001872!1.67e-08!5;UBERON:0000922!7.63e-08!612;UBERON:0000369!2.06e-07!4;UBERON:0002435!2.06e-07!4;UBERON:0000204!2.06e-07!4;UBERON:0010082!2.06e-07!4
|ontology_enrichment_uberon=UBERON:0001049!9.29e-79!56;UBERON:0005068!9.29e-79!56;UBERON:0006241!9.29e-79!56;UBERON:0007135!9.29e-79!56;UBERON:0000073!7.26e-72!53;UBERON:0002616!7.26e-72!53;UBERON:0003075!5.92e-67!82;UBERON:0007284!5.92e-67!82;UBERON:0001017!5.03e-66!81;UBERON:0002346!3.29e-63!86;UBERON:0000955!3.00e-61!68;UBERON:0006238!3.00e-61!68;UBERON:0001016!7.81e-61!89;UBERON:0002780!2.64e-60!41;UBERON:0001890!2.64e-60!41;UBERON:0003080!2.64e-60!41;UBERON:0006240!2.64e-60!41;UBERON:0001893!7.79e-57!34;UBERON:0010371!1.13e-56!104;UBERON:0003528!2.26e-56!34;UBERON:0002020!2.26e-56!34;UBERON:0003056!1.08e-54!61;UBERON:0002791!5.91e-52!32;UBERON:0001869!6.29e-52!32;UBERON:0010314!1.84e-43!132;UBERON:0004121!3.31e-40!171;UBERON:0000924!3.31e-40!171;UBERON:0006601!3.31e-40!171;UBERON:0007023!8.11e-39!114;UBERON:0000956!1.94e-36!25;UBERON:0000203!1.94e-36!25;UBERON:0002619!2.48e-34!22;UBERON:0001950!2.69e-30!20;UBERON:0011216!1.58e-23!223;UBERON:0000125!8.65e-22!9;UBERON:0002308!8.65e-22!9;UBERON:0000025!1.32e-21!192;UBERON:0002420!1.41e-21!9;UBERON:0007245!1.41e-21!9;UBERON:0010009!1.41e-21!9;UBERON:0010011!1.41e-21!9;UBERON:0000454!1.41e-21!9;UBERON:0003076!1.06e-18!15;UBERON:0003057!1.06e-18!15;UBERON:0009663!2.00e-17!7;UBERON:0000483!6.16e-16!306;UBERON:0002298!1.23e-15!6;UBERON:0000119!1.24e-15!309;UBERON:0004111!1.96e-15!240;UBERON:0004732!1.63e-14!13;UBERON:0000477!1.33e-13!373;UBERON:0000064!9.69e-13!218;UBERON:0004733!1.40e-12!12;UBERON:0002028!1.40e-12!12;UBERON:0007277!1.40e-12!12;UBERON:0001872!2.15e-12!5;UBERON:0000349!2.15e-12!5;UBERON:0000481!3.88e-11!342;UBERON:0000369!5.68e-11!4;UBERON:0002435!5.68e-11!4;UBERON:0000204!5.68e-11!4;UBERON:0010082!5.68e-11!4;UBERON:0000966!7.27e-11!6;UBERON:0005388!7.27e-11!6;UBERON:0001802!7.27e-11!6;UBERON:0001781!1.43e-10!4;UBERON:0000200!1.51e-10!6;UBERON:0001871!7.26e-09!6;UBERON:0001896!8.74e-09!3;UBERON:0005290!8.74e-09!3;UBERON:0010096!8.74e-09!3;UBERON:0000062!1.43e-08!503;UBERON:0000988!1.53e-08!3;UBERON:0002240!1.61e-08!3;UBERON:0005174!1.61e-08!3;UBERON:0001137!1.61e-08!3;UBERON:0005383!1.65e-08!3;UBERON:0005382!1.65e-08!3;UBERON:0001782!2.17e-08!3;UBERON:0005424!2.17e-08!3;UBERON:0002021!4.22e-08!5;UBERON:0000923!1.89e-07!560;UBERON:0010316!1.89e-07!560;UBERON:0005291!1.89e-07!560;UBERON:0006598!1.89e-07!560;UBERON:0010317!1.89e-07!560;UBERON:0002532!1.89e-07!560;UBERON:0002050!2.83e-07!564;UBERON:0002680!8.39e-07!9;UBERON:0001895!8.39e-07!9;UBERON:0010092!8.39e-07!9
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.016781607519997!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00243505279166128!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392144522886912!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00123039146119282!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000758175675696141!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00665768095746212!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247103529161172!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00615224681012387
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}}
}}

Revision as of 15:44, 19 October 2012


Full id: C4186_retina_corpus_Retinal_medulla_eye_pons_spinal



Phase1 CAGE Peaks

Hg19::chr2:219610834..219610846,+p11@TTLL4
Hg19::chr2:219610848..219610865,+p6@TTLL4
Hg19::chr2:219610868..219610888,+p9@TTLL4


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
visual pigment cell2.40e-104
retinal pigment epithelial cell2.17e-083
Uber Anatomy
Ontology termp-valuen
neural tube9.29e-7956
neural rod9.29e-7956
future spinal cord9.29e-7956
neural keel9.29e-7956
regional part of nervous system7.26e-7253
regional part of brain7.26e-7253
neural plate5.92e-6782
presumptive neural plate5.92e-6782
central nervous system5.03e-6681
neurectoderm3.29e-6386
brain3.00e-6168
future brain3.00e-6168
nervous system7.81e-6189
regional part of forebrain2.64e-6041
forebrain2.64e-6041
anterior neural tube2.64e-6041
future forebrain2.64e-6041
telencephalon7.79e-5734
ecto-epithelium1.13e-56104
brain grey matter2.26e-5634
gray matter2.26e-5634
pre-chordal neural plate1.08e-5461
regional part of telencephalon5.91e-5232
cerebral hemisphere6.29e-5232
structure with developmental contribution from neural crest1.84e-43132
ectoderm-derived structure3.31e-40171
ectoderm3.31e-40171
presumptive ectoderm3.31e-40171
adult organism8.11e-39114
cerebral cortex1.94e-3625
pallium1.94e-3625
regional part of cerebral cortex2.48e-3422
neocortex2.69e-3020
organ system subdivision1.58e-23223
neural nucleus8.65e-229
nucleus of brain8.65e-229
tube1.32e-21192
basal ganglion1.41e-219
nuclear complex of neuraxis1.41e-219
aggregate regional part of brain1.41e-219
collection of basal ganglia1.41e-219
cerebral subcortex1.41e-219
posterior neural tube1.06e-1815
chordal neural plate1.06e-1815
telencephalic nucleus2.00e-177
epithelium6.16e-16306
brainstem1.23e-156
cell layer1.24e-15309
anatomical conduit1.96e-15240
segmental subdivision of nervous system1.63e-1413
anatomical cluster1.33e-13373
organ part9.69e-13218
segmental subdivision of hindbrain1.40e-1212
hindbrain1.40e-1212
presumptive hindbrain1.40e-1212
parietal lobe2.15e-125
limbic system2.15e-125
multi-tissue structure3.88e-11342
corpus striatum5.68e-114
striatum5.68e-114
ventral part of telencephalon5.68e-114
future corpus striatum5.68e-114
retina7.27e-116
photoreceptor array7.27e-116
posterior segment of eyeball7.27e-116
layer of retina1.43e-104
gyrus1.51e-106
temporal lobe7.26e-096
medulla oblongata8.74e-093
myelencephalon8.74e-093
future myelencephalon8.74e-093
organ1.43e-08503
pons1.53e-083
spinal cord1.61e-083
dorsal region element1.61e-083
dorsum1.61e-083
caudate-putamen1.65e-083
dorsal striatum1.65e-083
pigmented layer of retina2.17e-083
presumptive retinal pigmented epithelium2.17e-083
occipital lobe4.22e-085
germ layer1.89e-07560
germ layer / neural crest1.89e-07560
embryonic tissue1.89e-07560
presumptive structure1.89e-07560
germ layer / neural crest derived structure1.89e-07560
epiblast (generic)1.89e-07560
embryonic structure2.83e-07564
regional part of metencephalon8.39e-079
metencephalon8.39e-079
future metencephalon8.39e-079


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
EP300#203336.77394172622320.003216880500103790.016781607519997
FOSL2#2355316.93020060456170.0002060162053171620.00243505279166128
HDAC2#3066313.41562023662630.0004140761399857210.00392144522886912
HNF4A#3172323.13229036295378.07584663437677e-050.00123039146119282
HNF4G#3174328.75342252644684.20470658818262e-050.000758175675696141
RAD21#5885310.35503389545630.0009004912073565420.00665768095746212
SP1#666735.69838137814090.005403962701712170.0247103529161172
TCF7L2#6934310.77017656313730.0008003181298398380.00615224681012387



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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