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Coexpression cluster:C4530: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!2.88e-29!86;UBERON:0000119!3.42e-29!312;UBERON:0000073!1.02e-27!94;UBERON:0001016!1.02e-27!94;UBERON:0003075!1.02e-27!86;UBERON:0007284!1.02e-27!86;UBERON:0000483!1.40e-27!309;UBERON:0001017!4.51e-27!82;UBERON:0002346!5.01e-27!90;UBERON:0000477!1.07e-26!286;UBERON:0002616!1.12e-24!59;UBERON:0001049!2.85e-24!57;UBERON:0005068!2.85e-24!57;UBERON:0006241!2.85e-24!57;UBERON:0007135!2.85e-24!57;UBERON:0000025!4.14e-24!194;UBERON:0000955!4.59e-24!69;UBERON:0006238!4.59e-24!69;UBERON:0004111!4.67e-24!241;UBERON:0000475!2.30e-23!365;UBERON:0003056!2.69e-20!61;UBERON:0000481!3.47e-19!347;UBERON:0004121!7.55e-19!169;UBERON:0000924!9.37e-19!173;UBERON:0006601!9.37e-19!173;UBERON:0000033!1.57e-18!123;UBERON:0002780!9.85e-17!41;UBERON:0001890!9.85e-17!41;UBERON:0006240!9.85e-17!41;UBERON:0003080!1.01e-16!42;UBERON:0002020!1.39e-16!34;UBERON:0003528!1.39e-16!34;UBERON:0000153!1.45e-16!129;UBERON:0007811!1.45e-16!129;UBERON:0001893!1.91e-16!34;UBERON:0002791!5.14e-16!33;UBERON:0001869!8.20e-16!32;UBERON:0000064!4.15e-15!219;UBERON:0000468!2.00e-14!659;UBERON:0000956!7.12e-14!25;UBERON:0000203!7.12e-14!25;UBERON:0002619!9.01e-13!22;UBERON:0000922!1.95e-12!612;UBERON:0001950!1.43e-11!20;UBERON:0002050!4.91e-11!605;UBERON:0005423!4.91e-11!605;UBERON:0000923!8.63e-11!604;UBERON:0005291!8.63e-11!604;UBERON:0006598!8.63e-11!604;UBERON:0002532!8.63e-11!604;UBERON:0000467!1.31e-10!625;UBERON:0000480!2.08e-10!626;UBERON:0000062!7.32e-09!511;UBERON:0003076!7.38e-09!15;UBERON:0003057!7.38e-09!15;UBERON:0002049!3.10e-08!79;UBERON:0007798!3.10e-08!79;UBERON:0007023!7.94e-08!115;UBERON:0007625!1.75e-07!11;UBERON:0000063!2.19e-07!97;UBERON:0000490!2.62e-07!138;UBERON:0002100!2.78e-07!216;UBERON:0004733!2.98e-07!12;UBERON:0002028!2.98e-07!12;UBERON:0007277!2.98e-07!12;UBERON:0000487!3.38e-07!22;UBERON:0004732!3.65e-07!13;UBERON:0002200!4.26e-07!11;UBERON:0006876!4.26e-07!11;UBERON:0003914!7.69e-07!118
|ontology_enrichment_uberon=UBERON:0005743!2.88e-29!86;UBERON:0000119!3.42e-29!312;UBERON:0000073!1.02e-27!94;UBERON:0001016!1.02e-27!94;UBERON:0003075!1.02e-27!86;UBERON:0007284!1.02e-27!86;UBERON:0000483!1.40e-27!309;UBERON:0001017!4.51e-27!82;UBERON:0002346!5.01e-27!90;UBERON:0000477!1.07e-26!286;UBERON:0002616!1.12e-24!59;UBERON:0001049!2.85e-24!57;UBERON:0005068!2.85e-24!57;UBERON:0006241!2.85e-24!57;UBERON:0007135!2.85e-24!57;UBERON:0000025!4.14e-24!194;UBERON:0000955!4.59e-24!69;UBERON:0006238!4.59e-24!69;UBERON:0004111!4.67e-24!241;UBERON:0000475!2.30e-23!365;UBERON:0003056!2.69e-20!61;UBERON:0000481!3.47e-19!347;UBERON:0004121!7.55e-19!169;UBERON:0000924!9.37e-19!173;UBERON:0006601!9.37e-19!173;UBERON:0000033!1.57e-18!123;UBERON:0002780!9.85e-17!41;UBERON:0001890!9.85e-17!41;UBERON:0006240!9.85e-17!41;UBERON:0003080!1.01e-16!42;UBERON:0002020!1.39e-16!34;UBERON:0003528!1.39e-16!34;UBERON:0000153!1.45e-16!129;UBERON:0007811!1.45e-16!129;UBERON:0001893!1.91e-16!34;UBERON:0002791!5.14e-16!33;UBERON:0001869!8.20e-16!32;UBERON:0000064!4.15e-15!219;UBERON:0000468!2.00e-14!659;UBERON:0000956!7.12e-14!25;UBERON:0000203!7.12e-14!25;UBERON:0002619!9.01e-13!22;UBERON:0000922!1.95e-12!612;UBERON:0001950!1.43e-11!20;UBERON:0002050!4.91e-11!605;UBERON:0005423!4.91e-11!605;UBERON:0000923!8.63e-11!604;UBERON:0005291!8.63e-11!604;UBERON:0006598!8.63e-11!604;UBERON:0002532!8.63e-11!604;UBERON:0000467!1.31e-10!625;UBERON:0000480!2.08e-10!626;UBERON:0000062!7.32e-09!511;UBERON:0003076!7.38e-09!15;UBERON:0003057!7.38e-09!15;UBERON:0002049!3.10e-08!79;UBERON:0007798!3.10e-08!79;UBERON:0007023!7.94e-08!115;UBERON:0007625!1.75e-07!11;UBERON:0000063!2.19e-07!97;UBERON:0000490!2.62e-07!138;UBERON:0002100!2.78e-07!216;UBERON:0004733!2.98e-07!12;UBERON:0002028!2.98e-07!12;UBERON:0007277!2.98e-07!12;UBERON:0000487!3.38e-07!22;UBERON:0004732!3.65e-07!13;UBERON:0002200!4.26e-07!11;UBERON:0006876!4.26e-07!11;UBERON:0003914!7.69e-07!118
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}}
}}

Revision as of 13:04, 5 September 2012


Full id: C4530_duodenum_temporal_Mesenchymal_breast_Neurons_Fibroblast_Lens



Phase1 CAGE Peaks

Hg19::chr5:92918768..92918783,+p8@NR2F1
Hg19::chr5:92918789..92918800,+p12@NR2F1
Hg19::chr5:92918860..92918871,+p10@NR2F1


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
mesodermal cell4.10e-08119
lining cell5.73e-0757
barrier cell5.73e-0757
Uber Anatomy
Ontology termp-valuen
cell layer3.42e-29312
regional part of nervous system1.02e-2794
nervous system1.02e-2794
neural plate1.02e-2786
presumptive neural plate1.02e-2786
epithelium1.40e-27309
central nervous system4.51e-2782
neurectoderm5.01e-2790
anatomical cluster1.07e-26286
regional part of brain1.12e-2459
neural tube2.85e-2457
neural rod2.85e-2457
future spinal cord2.85e-2457
neural keel2.85e-2457
tube4.14e-24194
brain4.59e-2469
future brain4.59e-2469
anatomical conduit4.67e-24241
organism subdivision2.30e-23365
pre-chordal neural plate2.69e-2061
multi-tissue structure3.47e-19347
ectoderm-derived structure7.55e-19169
ectoderm9.37e-19173
presumptive ectoderm9.37e-19173
head1.57e-18123
regional part of forebrain9.85e-1741
forebrain9.85e-1741
future forebrain9.85e-1741
anterior neural tube1.01e-1642
gray matter1.39e-1634
brain grey matter1.39e-1634
anterior region of body1.45e-16129
craniocervical region1.45e-16129
telencephalon1.91e-1634
regional part of telencephalon5.14e-1633
cerebral hemisphere8.20e-1632
organ part4.15e-15219
multi-cellular organism2.00e-14659
cerebral cortex7.12e-1425
pallium7.12e-1425
regional part of cerebral cortex9.01e-1322
embryo1.95e-12612
neocortex1.43e-1120
embryonic structure4.91e-11605
developing anatomical structure4.91e-11605
germ layer8.63e-11604
embryonic tissue8.63e-11604
presumptive structure8.63e-11604
epiblast (generic)8.63e-11604
anatomical system1.31e-10625
anatomical group2.08e-10626
organ7.32e-09511
posterior neural tube7.38e-0915
chordal neural plate7.38e-0915
vasculature3.10e-0879
vascular system3.10e-0879
adult organism7.94e-08115
pigment epithelium of eye1.75e-0711
organ segment2.19e-0797
unilaminar epithelium2.62e-07138
trunk2.78e-07216
segmental subdivision of hindbrain2.98e-0712
hindbrain2.98e-0712
presumptive hindbrain2.98e-0712
simple squamous epithelium3.38e-0722
segmental subdivision of nervous system3.65e-0713
vasculature of head4.26e-0711
vasculature of organ4.26e-0711
epithelial tube7.69e-07118


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#203336.77394172622320.003216880500103790.0168210976092895
FOXA1#3169311.08141974938550.000734755275698670.00583463399016829
FOXA2#3170324.63046375266526.68983856509345e-050.00107605120883997
GATA1#2623313.56030814380040.0004009615963782630.00389218590613899
GATA2#2624312.7449317335540.0004829527704283790.0043867719943268
GTF2F1#2962312.73966087675770.0004835525047438590.00435660283324223
HDAC2#3066313.41562023662630.0004140761399857210.00393035517440414
HNF4A#3172323.13229036295378.07584663437677e-050.00123326999071162
HNF4G#3174328.75342252644684.20470658818262e-050.000759881210180316
JUND#372736.994663941871030.002921845042734990.0157482878886412
NANOG#79923329.24477848101273.99627955670032e-050.000740407026117128
PRDM1#6393131.8309557774614.35536935195671e-072.08464903642991e-05
RAD21#5885310.35503389545630.0009004912073565420.00667753487681836
REST#597839.650028716128020.001112636247114590.00770625485857157
RFX5#5993312.04791082719510.0005717246050312580.00486359420256248
RXRA#6256320.07461713913330.0001235730348432220.00165863567484787
SIN3A#2594235.408884726815140.006318961977991520.0278000787741462
SP1#666735.69838137814090.005403962701712170.0247667395385342
SRF#6722313.79717826216780.0003806615025800190.00376120214455578
TAL1#6886329.86861667744023.75103522793067e-050.00072199478099862
TCF7L2#6934310.77017656313730.0008003181298398380.00616859226290353
TRIM28#10155318.59052504526250.0001555969297255280.00197789529498593
ZNF263#1012738.221841637010680.001799043925565870.0109967428621195
ZZZ3#260093239.4132124352337.25894005043406e-084.38471046805831e-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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