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Coexpression cluster:C2853: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.89e-82!115;UBERON:0001049!1.81e-45!57;UBERON:0005068!1.81e-45!57;UBERON:0006241!1.81e-45!57;UBERON:0007135!1.81e-45!57;UBERON:0002616!3.61e-37!59;UBERON:0003080!7.75e-35!42;UBERON:0003075!8.48e-35!86;UBERON:0007284!8.48e-35!86;UBERON:0002780!8.60e-34!41;UBERON:0001890!8.60e-34!41;UBERON:0006240!8.60e-34!41;UBERON:0002346!1.33e-33!90;UBERON:0005743!2.46e-32!86;UBERON:0001017!3.31e-32!82;UBERON:0000955!1.28e-31!69;UBERON:0006238!1.28e-31!69;UBERON:0000073!4.55e-30!94;UBERON:0001016!4.55e-30!94;UBERON:0002020!1.32e-26!34;UBERON:0003528!1.32e-26!34;UBERON:0001893!3.54e-26!34;UBERON:0002791!3.81e-25!33;UBERON:0001869!4.49e-24!32;UBERON:0003056!1.92e-23!61;UBERON:0000153!6.44e-23!129;UBERON:0007811!6.44e-23!129;UBERON:0000033!9.07e-22!123;UBERON:0002619!1.54e-19!22;UBERON:0004121!1.87e-19!169;UBERON:0000924!3.34e-19!173;UBERON:0006601!3.34e-19!173;UBERON:0004111!1.48e-17!241;UBERON:0001950!4.06e-17!20;UBERON:0000956!1.85e-16!25;UBERON:0000203!1.85e-16!25;UBERON:0000477!3.97e-15!286;UBERON:0000025!1.21e-14!194;UBERON:0002308!2.62e-12!9;UBERON:0000125!2.62e-12!9;UBERON:0000062!3.23e-12!511;UBERON:0003076!1.75e-11!15;UBERON:0003057!1.75e-11!15;UBERON:0002298!8.46e-11!8;UBERON:0000481!3.98e-10!347;UBERON:0009663!7.10e-10!7;UBERON:0004732!1.09e-09!13;UBERON:0002420!1.13e-09!9;UBERON:0007245!1.13e-09!9;UBERON:0010009!1.13e-09!9;UBERON:0010011!1.13e-09!9;UBERON:0000454!1.13e-09!9;UBERON:0001894!3.25e-09!7;UBERON:0006222!3.25e-09!7;UBERON:0000483!5.81e-09!309;UBERON:0000119!1.16e-08!312;UBERON:0000475!1.33e-08!365;UBERON:0000200!1.67e-08!6;UBERON:0004733!1.74e-08!12;UBERON:0002028!1.74e-08!12;UBERON:0007277!1.74e-08!12;UBERON:0000064!4.47e-08!219;UBERON:0001044!1.00e-07!6;UBERON:0003293!1.00e-07!6;UBERON:0003294!1.00e-07!6;UBERON:0010047!1.00e-07!6;UBERON:0000167!1.00e-07!6;UBERON:0003408!1.58e-07!10;UBERON:0000468!2.14e-07!659;UBERON:0000467!2.21e-07!625;UBERON:0000480!2.61e-07!626;UBERON:0002050!4.39e-07!605;UBERON:0005423!4.39e-07!605;UBERON:0000922!5.66e-07!612;UBERON:0000923!8.64e-07!604;UBERON:0005291!8.64e-07!604;UBERON:0006598!8.64e-07!604;UBERON:0002532!8.64e-07!604
|ontology_enrichment_uberon=UBERON:0007023!8.78e-92!114;UBERON:0001049!4.29e-48!56;UBERON:0005068!4.29e-48!56;UBERON:0006241!4.29e-48!56;UBERON:0007135!4.29e-48!56;UBERON:0000073!1.63e-43!53;UBERON:0002616!1.63e-43!53;UBERON:0003075!1.74e-38!82;UBERON:0007284!1.74e-38!82;UBERON:0002346!4.54e-36!86;UBERON:0002780!3.55e-34!41;UBERON:0001890!3.55e-34!41;UBERON:0003080!3.55e-34!41;UBERON:0006240!3.55e-34!41;UBERON:0000955!6.87e-33!68;UBERON:0006238!6.87e-33!68;UBERON:0001017!1.27e-32!81;UBERON:0003528!1.69e-30!34;UBERON:0002020!1.69e-30!34;UBERON:0010371!2.13e-30!104;UBERON:0001893!3.13e-30!34;UBERON:0001016!5.46e-30!89;UBERON:0002791!2.69e-27!32;UBERON:0001869!3.65e-27!32;UBERON:0003056!1.34e-23!61;UBERON:0010314!1.50e-23!132;UBERON:0002619!5.72e-22!22;UBERON:0011216!1.10e-20!223;UBERON:0004121!2.34e-19!171;UBERON:0000924!2.34e-19!171;UBERON:0006601!2.34e-19!171;UBERON:0000956!7.49e-19!25;UBERON:0000203!7.49e-19!25;UBERON:0001950!1.68e-18!20;UBERON:0004111!5.11e-15!240;UBERON:0003076!1.11e-14!15;UBERON:0003057!1.11e-14!15;UBERON:0000025!1.80e-14!192;UBERON:0000125!7.57e-14!9;UBERON:0002308!7.57e-14!9;UBERON:0000477!2.47e-13!373;UBERON:0000481!5.20e-13!342;UBERON:0000200!3.22e-12!6;UBERON:0004732!4.23e-12!13;UBERON:0000062!2.92e-11!503;UBERON:0002420!7.83e-11!9;UBERON:0007245!7.83e-11!9;UBERON:0010009!7.83e-11!9;UBERON:0010011!7.83e-11!9;UBERON:0000454!7.83e-11!9;UBERON:0009663!1.99e-10!7;UBERON:0004733!2.49e-10!12;UBERON:0002028!2.49e-10!12;UBERON:0007277!2.49e-10!12;UBERON:0000483!4.24e-10!306;UBERON:0000064!4.95e-10!218;UBERON:0000119!7.53e-10!309;UBERON:0002298!6.11e-09!6;UBERON:0002680!4.82e-08!9;UBERON:0001895!4.82e-08!9;UBERON:0010092!4.82e-08!9;UBERON:0000468!1.65e-07!656;UBERON:0000349!2.90e-07!5;UBERON:0001870!3.46e-07!3;UBERON:0005423!4.67e-07!581;UBERON:0000467!5.09e-07!624;UBERON:0000988!5.52e-07!3;UBERON:0000480!5.68e-07!625;UBERON:0000922!5.82e-07!592;UBERON:0003978!7.31e-07!3;UBERON:0009751!7.31e-07!3;UBERON:0000946!7.31e-07!3;UBERON:0002523!7.31e-07!3;UBERON:0005983!7.31e-07!3;UBERON:0002165!7.31e-07!3;UBERON:0002062!7.31e-07!3;UBERON:0007280!7.31e-07!3;UBERON:0000923!9.03e-07!560;UBERON:0010316!9.03e-07!560;UBERON:0005291!9.03e-07!560;UBERON:0006598!9.03e-07!560;UBERON:0010317!9.03e-07!560;UBERON:0002532!9.03e-07!560;UBERON:0001872!9.70e-07!5
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00819506397884537!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.00107311083660896!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000724163048648433!GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.78915265216316e-05!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000444364109240078!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129855747553998!REST#5978;4:9.65002871612802:0.000115282561421917:0.0015748849486388
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}}
}}

Revision as of 14:29, 19 October 2012


Full id: C2853_lung_pituitary_optic_locus_occipital_adipose_parietal



Phase1 CAGE Peaks

Hg19::chr6:168307760..168307775,+p@chr6:168307760..168307775
+
Hg19::chr6:168307783..168307796,+p@chr6:168307783..168307796
+
Hg19::chr6:168307841..168307856,+p@chr6:168307841..168307856
+
Hg19::chr6:168307867..168307880,+p@chr6:168307867..168307880
+


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
adult organism8.78e-92114
neural tube4.29e-4856
neural rod4.29e-4856
future spinal cord4.29e-4856
neural keel4.29e-4856
regional part of nervous system1.63e-4353
regional part of brain1.63e-4353
neural plate1.74e-3882
presumptive neural plate1.74e-3882
neurectoderm4.54e-3686
regional part of forebrain3.55e-3441
forebrain3.55e-3441
anterior neural tube3.55e-3441
future forebrain3.55e-3441
brain6.87e-3368
future brain6.87e-3368
central nervous system1.27e-3281
brain grey matter1.69e-3034
gray matter1.69e-3034
ecto-epithelium2.13e-30104
telencephalon3.13e-3034
nervous system5.46e-3089
regional part of telencephalon2.69e-2732
cerebral hemisphere3.65e-2732
pre-chordal neural plate1.34e-2361
structure with developmental contribution from neural crest1.50e-23132
regional part of cerebral cortex5.72e-2222
organ system subdivision1.10e-20223
ectoderm-derived structure2.34e-19171
ectoderm2.34e-19171
presumptive ectoderm2.34e-19171
cerebral cortex7.49e-1925
pallium7.49e-1925
neocortex1.68e-1820
anatomical conduit5.11e-15240
posterior neural tube1.11e-1415
chordal neural plate1.11e-1415
tube1.80e-14192
neural nucleus7.57e-149
nucleus of brain7.57e-149
anatomical cluster2.47e-13373
multi-tissue structure5.20e-13342
gyrus3.22e-126
segmental subdivision of nervous system4.23e-1213
organ2.92e-11503
basal ganglion7.83e-119
nuclear complex of neuraxis7.83e-119
aggregate regional part of brain7.83e-119
collection of basal ganglia7.83e-119
cerebral subcortex7.83e-119
telencephalic nucleus1.99e-107
segmental subdivision of hindbrain2.49e-1012
hindbrain2.49e-1012
presumptive hindbrain2.49e-1012
epithelium4.24e-10306
organ part4.95e-10218
cell layer7.53e-10309
brainstem6.11e-096
regional part of metencephalon4.82e-089
metencephalon4.82e-089
future metencephalon4.82e-089
multi-cellular organism1.65e-07656
limbic system2.90e-075
frontal cortex3.46e-073
developing anatomical structure4.67e-07581
anatomical system5.09e-07624
pons5.52e-073
anatomical group5.68e-07625
embryo5.82e-07592
valve7.31e-073
cardiac mesenchyme7.31e-073
cardial valve7.31e-073
tunica intima7.31e-073
heart layer7.31e-073
endocardium7.31e-073
endocardial cushion7.31e-073
presumptive endocardium7.31e-073
germ layer9.03e-07560
germ layer / neural crest9.03e-07560
embryonic tissue9.03e-07560
presumptive structure9.03e-07560
germ layer / neural crest derived structure9.03e-07560
epiblast (generic)9.03e-07560
parietal lobe9.70e-075


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
CTCF#1066445.360256373075030.001211145381643620.00819506397884537
FOXA1#3169411.08141974938556.62943068949433e-050.00107311083660896
GATA2#2624412.7449317335543.78864877853583e-050.000724163048648433
GATA3#2625427.2365163572061.81561517799785e-066.78915265216316e-05
NR3C1#2908414.9730233311731.98868032687801e-050.000444364109240078
RAD21#5885410.35503389545638.6948481184721e-050.00129855747553998
REST#597849.650028716128020.0001152825614219170.0015748849486388



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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