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Coexpression cluster:C1056: Difference between revisions

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|full_id=C1056_small_Neural_Astrocyte_teratocarcinoma_H9_hippocampus_testicular
|full_id=C1056_small_Neural_Astrocyte_teratocarcinoma_H9_hippocampus_testicular
|id=C1056
|id=C1056
|ontology_enrichment_celltype=CL:0002319!4.62e-12!25;CL:0000133!8.05e-09!59;CL:0000047!2.77e-08!8;CL:0000221!4.14e-08!71;CL:0002076!4.69e-07!43
|ontology_enrichment_celltype=CL:0002319!2.91e-20!25;CL:0000047!2.44e-12!8;CL:0000133!3.54e-12!59;CL:0000095!1.13e-10!17;CL:0000123!1.13e-10!17;CL:0000128!7.92e-10!7;CL:0000126!7.92e-10!7;CL:0000127!7.92e-10!7;CL:0002453!7.92e-10!7;CL:0000540!9.66e-10!6;CL:0000031!9.66e-10!6;CL:0000404!9.66e-10!6;CL:0000221!3.20e-09!72;CL:0000243!1.35e-08!15;CL:0000125!1.35e-08!15;CL:0000030!1.35e-08!15;CL:0000339!1.35e-08!15;CL:0002322!5.95e-08!5
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!8.32e-48!82;UBERON:0000073!2.89e-46!94;UBERON:0001016!2.89e-46!94;UBERON:0005743!1.96e-45!86;UBERON:0001049!6.80e-41!57;UBERON:0005068!6.80e-41!57;UBERON:0006241!6.80e-41!57;UBERON:0007135!6.80e-41!57;UBERON:0000924!6.99e-40!173;UBERON:0006601!6.99e-40!173;UBERON:0004121!1.43e-38!169;UBERON:0000955!2.79e-37!69;UBERON:0006238!2.79e-37!69;UBERON:0002616!3.68e-37!59;UBERON:0002346!7.49e-35!90;UBERON:0003075!9.95e-34!86;UBERON:0007284!9.95e-34!86;UBERON:0007023!1.63e-33!115;UBERON:0000153!6.28e-32!129;UBERON:0007811!6.28e-32!129;UBERON:0002780!7.93e-31!41;UBERON:0001890!7.93e-31!41;UBERON:0006240!7.93e-31!41;UBERON:0000033!8.06e-31!123;UBERON:0003080!1.23e-29!42;UBERON:0001893!2.80e-26!34;UBERON:0002020!2.82e-26!34;UBERON:0003528!2.82e-26!34;UBERON:0002791!1.36e-25!33;UBERON:0001869!1.33e-24!32;UBERON:0003056!4.44e-24!61;UBERON:0000956!1.88e-19!25;UBERON:0000203!1.88e-19!25;UBERON:0002619!8.49e-17!22;UBERON:0000064!1.39e-15!219;UBERON:0001950!3.66e-15!20;UBERON:0000475!9.03e-13!365;UBERON:0000922!2.57e-12!612;UBERON:0003076!3.81e-12!15;UBERON:0003057!3.81e-12!15;UBERON:0000468!1.30e-11!659;UBERON:0004732!3.38e-10!13;UBERON:0004111!7.85e-10!241;UBERON:0004733!8.75e-10!12;UBERON:0002028!8.75e-10!12;UBERON:0007277!8.75e-10!12;UBERON:0002050!1.31e-09!605;UBERON:0005423!1.31e-09!605;UBERON:0000923!2.26e-09!604;UBERON:0005291!2.26e-09!604;UBERON:0006598!2.26e-09!604;UBERON:0002532!2.26e-09!604;UBERON:0000481!4.37e-09!347;UBERON:0000477!4.85e-09!286;UBERON:0000025!8.25e-09!194;UBERON:0000062!9.14e-09!511;UBERON:0002420!2.26e-08!9;UBERON:0007245!2.26e-08!9;UBERON:0010009!2.26e-08!9;UBERON:0010011!2.26e-08!9;UBERON:0000454!2.26e-08!9;UBERON:0002308!2.95e-08!9;UBERON:0000125!2.95e-08!9;UBERON:0000480!3.15e-08!626;UBERON:0000483!3.84e-08!309;UBERON:0000467!5.01e-08!625;UBERON:0000119!9.33e-08!312;UBERON:0002680!1.49e-07!9;UBERON:0001895!1.49e-07!9;UBERON:0010092!1.49e-07!9;UBERON:0009663!8.94e-07!7
|ontology_enrichment_uberon=UBERON:0001017!3.82e-76!81;UBERON:0001016!1.18e-74!89;UBERON:0001049!4.00e-68!56;UBERON:0005068!4.00e-68!56;UBERON:0006241!4.00e-68!56;UBERON:0007135!4.00e-68!56;UBERON:0000073!4.80e-64!53;UBERON:0002616!4.80e-64!53;UBERON:0000955!6.31e-61!68;UBERON:0006238!6.31e-61!68;UBERON:0002346!4.92e-51!86;UBERON:0002780!1.17e-49!41;UBERON:0001890!1.17e-49!41;UBERON:0003080!1.17e-49!41;UBERON:0006240!1.17e-49!41;UBERON:0003075!5.84e-49!82;UBERON:0007284!5.84e-49!82;UBERON:0004121!1.04e-46!171;UBERON:0000924!1.04e-46!171;UBERON:0006601!1.04e-46!171;UBERON:0003528!1.67e-42!34;UBERON:0002020!1.67e-42!34;UBERON:0001893!1.94e-42!34;UBERON:0002791!5.11e-40!32;UBERON:0001869!1.02e-39!32;UBERON:0010371!1.98e-37!104;UBERON:0003056!3.92e-37!61;UBERON:0011216!4.18e-37!223;UBERON:0000956!1.95e-31!25;UBERON:0000203!1.95e-31!25;UBERON:0010314!3.04e-27!132;UBERON:0002619!3.89e-27!22;UBERON:0007023!2.10e-26!114;UBERON:0001950!1.99e-24!20;UBERON:0003076!8.99e-19!15;UBERON:0003057!8.99e-19!15;UBERON:0000477!6.02e-18!373;UBERON:0004733!5.13e-15!12;UBERON:0002028!5.13e-15!12;UBERON:0007277!5.13e-15!12;UBERON:0004732!1.37e-13!13;UBERON:0002420!1.29e-12!9;UBERON:0007245!1.29e-12!9;UBERON:0010009!1.29e-12!9;UBERON:0010011!1.29e-12!9;UBERON:0000454!1.29e-12!9;UBERON:0000064!1.46e-12!218;UBERON:0000125!2.38e-12!9;UBERON:0002308!2.38e-12!9;UBERON:0000025!2.47e-12!192;UBERON:0000922!1.36e-11!592;UBERON:0002680!1.77e-11!9;UBERON:0001895!1.77e-11!9;UBERON:0010092!1.77e-11!9;UBERON:0004111!4.75e-11!240;UBERON:0009663!5.77e-10!7;UBERON:0000923!1.72e-09!560;UBERON:0010316!1.72e-09!560;UBERON:0005291!1.72e-09!560;UBERON:0006598!1.72e-09!560;UBERON:0010317!1.72e-09!560;UBERON:0002532!1.72e-09!560;UBERON:0000468!3.19e-09!656;UBERON:0000200!3.39e-09!6;UBERON:0002050!3.41e-09!564;UBERON:0005423!9.46e-09!581;UBERON:0002298!1.42e-08!6;UBERON:0001894!1.70e-08!7;UBERON:0006222!1.70e-08!7;UBERON:0000481!3.43e-08!342;UBERON:0000349!3.70e-08!5;UBERON:0002037!4.38e-08!6;UBERON:0006215!4.38e-08!6;UBERON:0001871!5.56e-08!6;UBERON:0001872!1.33e-07!5;UBERON:0002021!3.80e-07!5
|tf_chipseq_enrich=NANOG#79923;4:14.6223892405063:8.55931368384764e-05:0.00128345464727547
|tf_chipseq_enrich=NANOG#79923;4:14.6223892405063:8.55931368384764e-05:0.00128345464727547
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}}
}}

Revision as of 10:45, 19 October 2012


Full id: C1056_small_Neural_Astrocyte_teratocarcinoma_H9_hippocampus_testicular



Phase1 CAGE Peaks

Hg19::chr18:53019208..53019223,-p@chr18:53019208..53019223
-
Hg19::chr3:181429641..181429650,+p3@SOX2
Hg19::chr3:181429704..181429722,+p1@SOX2
Hg19::chr3:181429741..181429767,+p2@SOX2
Hg19::chr3:181431050..181431079,+p@chr3:181431050..181431079
+
Hg19::chr3:181431124..181431130,+p@chr3:181431124..181431130
+
Hg19::chr3:181431210..181431225,-p@chr3:181431210..181431225
-
Hg19::chr3:181431401..181431408,+p@chr3:181431401..181431408
+


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>

Uber Anatomy
Ontology termp-valuen
central nervous system3.82e-7681
nervous system1.18e-7489
neural tube4.00e-6856
neural rod4.00e-6856
future spinal cord4.00e-6856
neural keel4.00e-6856
regional part of nervous system4.80e-6453
regional part of brain4.80e-6453
brain6.31e-6168
future brain6.31e-6168
neurectoderm4.92e-5186
regional part of forebrain1.17e-4941
forebrain1.17e-4941
anterior neural tube1.17e-4941
future forebrain1.17e-4941
neural plate5.84e-4982
presumptive neural plate5.84e-4982
ectoderm-derived structure1.04e-46171
ectoderm1.04e-46171
presumptive ectoderm1.04e-46171
brain grey matter1.67e-4234
gray matter1.67e-4234
telencephalon1.94e-4234
regional part of telencephalon5.11e-4032
cerebral hemisphere1.02e-3932
ecto-epithelium1.98e-37104
pre-chordal neural plate3.92e-3761
organ system subdivision4.18e-37223
cerebral cortex1.95e-3125
pallium1.95e-3125
structure with developmental contribution from neural crest3.04e-27132
regional part of cerebral cortex3.89e-2722
adult organism2.10e-26114
neocortex1.99e-2420
posterior neural tube8.99e-1915
chordal neural plate8.99e-1915
anatomical cluster6.02e-18373
segmental subdivision of hindbrain5.13e-1512
hindbrain5.13e-1512
presumptive hindbrain5.13e-1512
segmental subdivision of nervous system1.37e-1313
basal ganglion1.29e-129
nuclear complex of neuraxis1.29e-129
aggregate regional part of brain1.29e-129
collection of basal ganglia1.29e-129
cerebral subcortex1.29e-129
organ part1.46e-12218
neural nucleus2.38e-129
nucleus of brain2.38e-129
tube2.47e-12192
embryo1.36e-11592
regional part of metencephalon1.77e-119
metencephalon1.77e-119
future metencephalon1.77e-119
anatomical conduit4.75e-11240
telencephalic nucleus5.77e-107
germ layer1.72e-09560
germ layer / neural crest1.72e-09560
embryonic tissue1.72e-09560
presumptive structure1.72e-09560
germ layer / neural crest derived structure1.72e-09560
epiblast (generic)1.72e-09560
multi-cellular organism3.19e-09656
gyrus3.39e-096
embryonic structure3.41e-09564
developing anatomical structure9.46e-09581
brainstem1.42e-086
diencephalon1.70e-087
future diencephalon1.70e-087
multi-tissue structure3.43e-08342
limbic system3.70e-085
cerebellum4.38e-086
rhombic lip4.38e-086
temporal lobe5.56e-086
parietal lobe1.33e-075
occipital lobe3.80e-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
NANOG#79923414.62238924050638.55931368384764e-050.00128345464727547



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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