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Coexpression cluster:C4878: Difference between revisions

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|full_id=C4878_spleen_H9_HES3GFP_iPS_hippocampus_spinal_Neural
|full_id=C4878_spleen_H9_HES3GFP_iPS_hippocampus_spinal_Neural
|id=C4878
|id=C4878
|ontology_enrichment_celltype=CL:0000047!2.39e-16!8;CL:0002319!6.12e-13!25;CL:0000540!1.57e-12!6;CL:0000031!1.57e-12!6;CL:0000404!1.57e-12!6;CL:0000128!5.41e-12!7;CL:0000126!5.41e-12!7;CL:0000127!5.41e-12!7;CL:0002453!5.41e-12!7;CL:0002322!8.68e-12!5;CL:0000221!6.26e-08!71;CL:0000133!8.79e-08!59
|ontology_enrichment_celltype=CL:0000047!7.00e-17!8;CL:0002322!2.94e-15!5;CL:0000540!8.12e-12!6;CL:0000031!8.12e-12!6;CL:0000404!8.12e-12!6;CL:0002319!9.10e-12!25;CL:0000128!9.84e-09!7;CL:0000126!9.84e-09!7;CL:0000127!9.84e-09!7;CL:0002453!9.84e-09!7;CL:0000133!1.52e-08!59;CL:0002605!3.26e-08!3
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.16e-88!82;UBERON:0001049!1.80e-87!57;UBERON:0005068!1.80e-87!57;UBERON:0006241!1.80e-87!57;UBERON:0007135!1.80e-87!57;UBERON:0005743!1.37e-86!86;UBERON:0000073!1.01e-76!94;UBERON:0001016!1.01e-76!94;UBERON:0002616!7.53e-74!59;UBERON:0003075!2.43e-69!86;UBERON:0007284!2.43e-69!86;UBERON:0000955!7.06e-68!69;UBERON:0006238!7.06e-68!69;UBERON:0002346!1.72e-65!90;UBERON:0002780!1.30e-62!41;UBERON:0001890!1.30e-62!41;UBERON:0006240!1.30e-62!41;UBERON:0003080!7.31e-61!42;UBERON:0002020!1.28e-54!34;UBERON:0003528!1.28e-54!34;UBERON:0001893!1.78e-54!34;UBERON:0002791!7.49e-53!33;UBERON:0003056!1.72e-52!61;UBERON:0001869!8.42e-51!32;UBERON:0004121!6.53e-46!169;UBERON:0000033!9.18e-46!123;UBERON:0000153!1.89e-44!129;UBERON:0007811!1.89e-44!129;UBERON:0000924!2.13e-44!173;UBERON:0006601!2.13e-44!173;UBERON:0000956!2.78e-38!25;UBERON:0000203!2.78e-38!25;UBERON:0002619!2.61e-33!22;UBERON:0007023!1.11e-32!115;UBERON:0001950!8.00e-30!20;UBERON:0003076!1.50e-26!15;UBERON:0003057!1.50e-26!15;UBERON:0004733!1.65e-21!12;UBERON:0002028!1.65e-21!12;UBERON:0007277!1.65e-21!12;UBERON:0004732!1.30e-19!13;UBERON:0002308!1.30e-17!9;UBERON:0000125!1.30e-17!9;UBERON:0002420!1.69e-17!9;UBERON:0007245!1.69e-17!9;UBERON:0010009!1.69e-17!9;UBERON:0010011!1.69e-17!9;UBERON:0000454!1.69e-17!9;UBERON:0000064!1.52e-16!219;UBERON:0000025!1.64e-16!194;UBERON:0002680!8.01e-16!9;UBERON:0001895!8.01e-16!9;UBERON:0010092!8.01e-16!9;UBERON:0009663!6.09e-14!7;UBERON:0004111!2.62e-12!241;UBERON:0002298!2.94e-12!8;UBERON:0001871!5.73e-12!7;UBERON:0000477!1.01e-11!286;UBERON:0000200!1.65e-11!6;UBERON:0000483!3.37e-11!309;UBERON:0000119!6.21e-11!312;UBERON:0002037!1.32e-10!6;UBERON:0006215!1.32e-10!6;UBERON:0000349!1.68e-10!5;UBERON:0001872!8.61e-10!5;UBERON:0000475!1.15e-09!365;UBERON:0001894!1.97e-09!7;UBERON:0006222!1.97e-09!7;UBERON:0000922!3.66e-09!612;UBERON:0000369!1.21e-08!4;UBERON:0002435!1.21e-08!4;UBERON:0000204!1.21e-08!4;UBERON:0010082!1.21e-08!4;UBERON:0000062!1.88e-07!511;UBERON:0001896!2.19e-07!3;UBERON:0005290!2.19e-07!3;UBERON:0010096!2.19e-07!3;UBERON:0000468!2.39e-07!659;UBERON:0006331!6.48e-07!3;UBERON:0000988!6.75e-07!3;UBERON:0005383!7.61e-07!3;UBERON:0005382!7.61e-07!3;UBERON:0002771!9.46e-07!3
|ontology_enrichment_uberon=UBERON:0001049!1.55e-72!56;UBERON:0005068!1.55e-72!56;UBERON:0006241!1.55e-72!56;UBERON:0007135!1.55e-72!56;UBERON:0001017!1.96e-72!81;UBERON:0000073!3.16e-69!53;UBERON:0002616!3.16e-69!53;UBERON:0001016!5.11e-64!89;UBERON:0003075!2.08e-56!82;UBERON:0007284!2.08e-56!82;UBERON:0000955!1.17e-53!68;UBERON:0006238!1.17e-53!68;UBERON:0002346!3.07e-53!86;UBERON:0002780!1.34e-49!41;UBERON:0001890!1.34e-49!41;UBERON:0003080!1.34e-49!41;UBERON:0006240!1.34e-49!41;UBERON:0001893!9.40e-49!34;UBERON:0003528!1.04e-48!34;UBERON:0002020!1.04e-48!34;UBERON:0001869!3.74e-44!32;UBERON:0002791!4.47e-44!32;UBERON:0010371!5.64e-42!104;UBERON:0003056!1.58e-40!61;UBERON:0004121!2.98e-33!171;UBERON:0000924!2.98e-33!171;UBERON:0006601!2.98e-33!171;UBERON:0010314!2.65e-32!132;UBERON:0000956!5.29e-32!25;UBERON:0000203!5.29e-32!25;UBERON:0011216!5.30e-26!223;UBERON:0002619!6.60e-26!22;UBERON:0001950!7.03e-25!20;UBERON:0007023!4.73e-24!114;UBERON:0003076!2.74e-23!15;UBERON:0003057!2.74e-23!15;UBERON:0004733!2.11e-20!12;UBERON:0002028!2.11e-20!12;UBERON:0007277!2.11e-20!12;UBERON:0004732!1.15e-18!13;UBERON:0000125!1.95e-18!9;UBERON:0002308!1.95e-18!9;UBERON:0002298!2.43e-16!6;UBERON:0002420!3.23e-14!9;UBERON:0007245!3.23e-14!9;UBERON:0010009!3.23e-14!9;UBERON:0010011!3.23e-14!9;UBERON:0000454!3.23e-14!9;UBERON:0000064!8.92e-14!218;UBERON:0009663!1.04e-13!7;UBERON:0000025!1.67e-13!192;UBERON:0002680!4.41e-13!9;UBERON:0001895!4.41e-13!9;UBERON:0010092!4.41e-13!9;UBERON:0000477!9.44e-13!373;UBERON:0000200!9.05e-11!6;UBERON:0001896!1.51e-09!3;UBERON:0005290!1.51e-09!3;UBERON:0010096!1.51e-09!3;UBERON:0001871!1.73e-09!6;UBERON:0002021!5.88e-09!5;UBERON:0004111!8.59e-09!240;UBERON:0000988!1.66e-08!3;UBERON:0000483!1.94e-08!306;UBERON:0000119!3.00e-08!309;UBERON:0000922!3.26e-08!592;UBERON:0000481!1.64e-07!342;UBERON:0002037!7.00e-07!6;UBERON:0006215!7.00e-07!6;UBERON:0000369!7.45e-07!4;UBERON:0002435!7.45e-07!4;UBERON:0000204!7.45e-07!4;UBERON:0010082!7.45e-07!4
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.028186023770617!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00669893875668565!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00311252330807245!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110335515028583
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.028186023770617!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00669893875668565!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00311252330807245!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110335515028583
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}}
}}

Revision as of 16:19, 19 October 2012


Full id: C4878_spleen_H9_HES3GFP_iPS_hippocampus_spinal_Neural



Phase1 CAGE Peaks

Hg19::chrX:69642952..69642968,+p3@GDPD2
Hg19::chrX:69643029..69643035,+p6@GDPD2
Hg19::chrX:69643047..69643060,+p2@GDPD2


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
neuronal stem cell7.00e-178
embryonic stem cell2.94e-155
neuron8.12e-126
neuroblast8.12e-126
electrically signaling cell8.12e-126
neural cell9.10e-1225
oligodendrocyte9.84e-097
macroglial cell9.84e-097
astrocyte9.84e-097
oligodendrocyte precursor cell9.84e-097
neurectodermal cell1.52e-0859
astrocyte of the cerebral cortex3.26e-083
Uber Anatomy
Ontology termp-valuen
neural tube1.55e-7256
neural rod1.55e-7256
future spinal cord1.55e-7256
neural keel1.55e-7256
central nervous system1.96e-7281
regional part of nervous system3.16e-6953
regional part of brain3.16e-6953
nervous system5.11e-6489
neural plate2.08e-5682
presumptive neural plate2.08e-5682
brain1.17e-5368
future brain1.17e-5368
neurectoderm3.07e-5386
regional part of forebrain1.34e-4941
forebrain1.34e-4941
anterior neural tube1.34e-4941
future forebrain1.34e-4941
telencephalon9.40e-4934
brain grey matter1.04e-4834
gray matter1.04e-4834
cerebral hemisphere3.74e-4432
regional part of telencephalon4.47e-4432
ecto-epithelium5.64e-42104
pre-chordal neural plate1.58e-4061
ectoderm-derived structure2.98e-33171
ectoderm2.98e-33171
presumptive ectoderm2.98e-33171
structure with developmental contribution from neural crest2.65e-32132
cerebral cortex5.29e-3225
pallium5.29e-3225
organ system subdivision5.30e-26223
regional part of cerebral cortex6.60e-2622
neocortex7.03e-2520
adult organism4.73e-24114
posterior neural tube2.74e-2315
chordal neural plate2.74e-2315
segmental subdivision of hindbrain2.11e-2012
hindbrain2.11e-2012
presumptive hindbrain2.11e-2012
segmental subdivision of nervous system1.15e-1813
neural nucleus1.95e-189
nucleus of brain1.95e-189
brainstem2.43e-166
basal ganglion3.23e-149
nuclear complex of neuraxis3.23e-149
aggregate regional part of brain3.23e-149
collection of basal ganglia3.23e-149
cerebral subcortex3.23e-149
organ part8.92e-14218
telencephalic nucleus1.04e-137
tube1.67e-13192
regional part of metencephalon4.41e-139
metencephalon4.41e-139
future metencephalon4.41e-139
anatomical cluster9.44e-13373
gyrus9.05e-116
medulla oblongata1.51e-093
myelencephalon1.51e-093
future myelencephalon1.51e-093
temporal lobe1.73e-096
occipital lobe5.88e-095
anatomical conduit8.59e-09240
pons1.66e-083
epithelium1.94e-08306
cell layer3.00e-08309
embryo3.26e-08592
multi-tissue structure1.64e-07342
cerebellum7.00e-076
rhombic lip7.00e-076
corpus striatum7.45e-074
striatum7.45e-074
ventral part of telencephalon7.45e-074
future corpus striatum7.45e-074


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)

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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
CTCF#1066435.360256373075030.0064925092527670.028186023770617
RAD21#5885310.35503389545630.0009004912073565420.00669893875668565
SMC3#9126315.04493284493280.0002935825420371870.00311252330807245
ZNF263#1012738.221841637010680.001799043925565870.0110335515028583



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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