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Coexpression cluster:C2543: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!1.17e-54!81;UBERON:0001016!2.62e-51!89;UBERON:0001049!3.45e-51!56;UBERON:0005068!3.45e-51!56;UBERON:0006241!3.45e-51!56;UBERON:0007135!3.45e-51!56;UBERON:0000073!2.21e-46!53;UBERON:0002616!2.21e-46!53;UBERON:0000955!7.98e-41!68;UBERON:0006238!7.98e-41!68;UBERON:0002346!8.35e-41!86;UBERON:0002780!2.11e-40!41;UBERON:0001890!2.11e-40!41;UBERON:0003080!2.11e-40!41;UBERON:0006240!2.11e-40!41;UBERON:0003075!8.16e-36!82;UBERON:0007284!8.16e-36!82;UBERON:0001869!4.19e-35!32;UBERON:0001893!5.96e-35!34;UBERON:0003528!1.01e-34!34;UBERON:0002020!1.01e-34!34;UBERON:0004121!2.29e-33!171;UBERON:0000924!2.29e-33!171;UBERON:0006601!2.29e-33!171;UBERON:0002791!1.87e-32!32;UBERON:0010371!3.06e-31!104;UBERON:0011216!1.64e-29!223;UBERON:0003056!3.34e-27!61;UBERON:0000956!6.38e-25!25;UBERON:0000203!6.38e-25!25;UBERON:0010314!3.71e-24!132;UBERON:0002619!8.58e-24!22;UBERON:0001950!1.25e-23!20;UBERON:0007023!4.70e-22!114;UBERON:0000477!1.31e-12!373;UBERON:0003076!1.03e-11!15;UBERON:0003057!1.03e-11!15;UBERON:0000125!3.34e-11!9;UBERON:0002308!3.34e-11!9;UBERON:0000025!3.52e-10!192;UBERON:0000200!1.19e-09!6;UBERON:0002420!3.08e-09!9;UBERON:0007245!3.08e-09!9;UBERON:0010009!3.08e-09!9;UBERON:0010011!3.08e-09!9;UBERON:0000454!3.08e-09!9;UBERON:0002298!4.29e-09!6;UBERON:0009663!5.31e-09!7;UBERON:0001872!6.16e-09!5;UBERON:0001871!1.17e-08!6;UBERON:0002784!2.01e-08!4;UBERON:0000369!9.49e-08!4;UBERON:0002435!9.49e-08!4;UBERON:0000204!9.49e-08!4;UBERON:0010082!9.49e-08!4;UBERON:0004733!1.47e-07!12;UBERON:0002028!1.47e-07!12;UBERON:0007277!1.47e-07!12;UBERON:0000064!3.53e-07!218;UBERON:0004732!7.25e-07!13;UBERON:0001894!7.87e-07!7;UBERON:0006222!7.87e-07!7
|ontology_enrichment_uberon=UBERON:0001017!1.17e-54!81;UBERON:0001016!2.62e-51!89;UBERON:0001049!3.45e-51!56;UBERON:0005068!3.45e-51!56;UBERON:0006241!3.45e-51!56;UBERON:0007135!3.45e-51!56;UBERON:0000073!2.21e-46!53;UBERON:0002616!2.21e-46!53;UBERON:0000955!7.98e-41!68;UBERON:0006238!7.98e-41!68;UBERON:0002346!8.35e-41!86;UBERON:0002780!2.11e-40!41;UBERON:0001890!2.11e-40!41;UBERON:0003080!2.11e-40!41;UBERON:0006240!2.11e-40!41;UBERON:0003075!8.16e-36!82;UBERON:0007284!8.16e-36!82;UBERON:0001869!4.19e-35!32;UBERON:0001893!5.96e-35!34;UBERON:0003528!1.01e-34!34;UBERON:0002020!1.01e-34!34;UBERON:0004121!2.29e-33!171;UBERON:0000924!2.29e-33!171;UBERON:0006601!2.29e-33!171;UBERON:0002791!1.87e-32!32;UBERON:0010371!3.06e-31!104;UBERON:0011216!1.64e-29!223;UBERON:0003056!3.34e-27!61;UBERON:0000956!6.38e-25!25;UBERON:0000203!6.38e-25!25;UBERON:0010314!3.71e-24!132;UBERON:0002619!8.58e-24!22;UBERON:0001950!1.25e-23!20;UBERON:0007023!4.70e-22!114;UBERON:0000477!1.31e-12!373;UBERON:0003076!1.03e-11!15;UBERON:0003057!1.03e-11!15;UBERON:0000125!3.34e-11!9;UBERON:0002308!3.34e-11!9;UBERON:0000025!3.52e-10!192;UBERON:0000200!1.19e-09!6;UBERON:0002420!3.08e-09!9;UBERON:0007245!3.08e-09!9;UBERON:0010009!3.08e-09!9;UBERON:0010011!3.08e-09!9;UBERON:0000454!3.08e-09!9;UBERON:0002298!4.29e-09!6;UBERON:0009663!5.31e-09!7;UBERON:0001872!6.16e-09!5;UBERON:0001871!1.17e-08!6;UBERON:0002784!2.01e-08!4;UBERON:0000369!9.49e-08!4;UBERON:0002435!9.49e-08!4;UBERON:0000204!9.49e-08!4;UBERON:0010082!9.49e-08!4;UBERON:0004733!1.47e-07!12;UBERON:0002028!1.47e-07!12;UBERON:0007277!1.47e-07!12;UBERON:0000064!3.53e-07!218;UBERON:0004732!7.25e-07!13;UBERON:0001894!7.87e-07!7;UBERON:0006222!7.87e-07!7
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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,1.42265,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.462021,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.938585,0.635753,0.581762,0.169357,0.731221,1.3102,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,1.00622,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.314427,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.336329,0.321165,0.823598,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,1.82173,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.934671,1.15558,0.939507,0.749003,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.27972,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
}}
}}

Revision as of 15:34, 26 November 2012


Full id: C2543_pineal_parietal_occipital_temporal_hippocampus_duodenum_brain



Phase1 CAGE Peaks

Hg19::chr1:181286826..181286889,+p@chr1:181286826..181286889
+
Hg19::chr3:77088989..77088997,+p10@ROBO2
Hg19::chr3:77185657..77185661,+p@chr3:77185657..77185661
+
Hg19::chr3:77596949..77596954,+p@chr3:77596949..77596954
+


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 cell5.27e-088
Uber Anatomy
Ontology termp-valuen
central nervous system1.17e-5481
nervous system2.62e-5189
neural tube3.45e-5156
neural rod3.45e-5156
future spinal cord3.45e-5156
neural keel3.45e-5156
regional part of nervous system2.21e-4653
regional part of brain2.21e-4653
brain7.98e-4168
future brain7.98e-4168
neurectoderm8.35e-4186
regional part of forebrain2.11e-4041
forebrain2.11e-4041
anterior neural tube2.11e-4041
future forebrain2.11e-4041
neural plate8.16e-3682
presumptive neural plate8.16e-3682
cerebral hemisphere4.19e-3532
telencephalon5.96e-3534
brain grey matter1.01e-3434
gray matter1.01e-3434
ectoderm-derived structure2.29e-33171
ectoderm2.29e-33171
presumptive ectoderm2.29e-33171
regional part of telencephalon1.87e-3232
ecto-epithelium3.06e-31104
organ system subdivision1.64e-29223
pre-chordal neural plate3.34e-2761
cerebral cortex6.38e-2525
pallium6.38e-2525
structure with developmental contribution from neural crest3.71e-24132
regional part of cerebral cortex8.58e-2422
neocortex1.25e-2320
adult organism4.70e-22114
anatomical cluster1.31e-12373
posterior neural tube1.03e-1115
chordal neural plate1.03e-1115
neural nucleus3.34e-119
nucleus of brain3.34e-119
tube3.52e-10192
gyrus1.19e-096
basal ganglion3.08e-099
nuclear complex of neuraxis3.08e-099
aggregate regional part of brain3.08e-099
collection of basal ganglia3.08e-099
cerebral subcortex3.08e-099
brainstem4.29e-096
telencephalic nucleus5.31e-097
parietal lobe6.16e-095
temporal lobe1.17e-086
regional part of diencephalon2.01e-084
corpus striatum9.49e-084
striatum9.49e-084
ventral part of telencephalon9.49e-084
future corpus striatum9.49e-084
segmental subdivision of hindbrain1.47e-0712
hindbrain1.47e-0712
presumptive hindbrain1.47e-0712
organ part3.53e-07218
segmental subdivision of nervous system7.25e-0713
diencephalon7.87e-077
future diencephalon7.87e-077


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

No analysis results for this cluster

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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