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Coexpression cluster:C2452: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!1.69e-32!114;UBERON:0001049!1.12e-25!56;UBERON:0005068!1.12e-25!56;UBERON:0006241!1.12e-25!56;UBERON:0007135!1.12e-25!56;UBERON:0000073!1.23e-24!53;UBERON:0002616!1.23e-24!53;UBERON:0002346!2.09e-22!86;UBERON:0004121!4.14e-20!171;UBERON:0000924!4.14e-20!171;UBERON:0006601!4.14e-20!171;UBERON:0002780!7.82e-20!41;UBERON:0001890!7.82e-20!41;UBERON:0003080!7.82e-20!41;UBERON:0006240!7.82e-20!41;UBERON:0010314!1.55e-19!132;UBERON:0003075!2.77e-19!82;UBERON:0007284!2.77e-19!82;UBERON:0003528!3.09e-19!34;UBERON:0002020!3.09e-19!34;UBERON:0001893!3.98e-19!34;UBERON:0001017!1.00e-18!81;UBERON:0000955!5.41e-18!68;UBERON:0006238!5.41e-18!68;UBERON:0002791!7.66e-18!32;UBERON:0001869!1.03e-17!32;UBERON:0001016!3.57e-17!89;UBERON:0010371!2.01e-15!104;UBERON:0011216!1.77e-13!223;UBERON:0003056!2.29e-13!61;UBERON:0000956!4.98e-13!25;UBERON:0000203!4.98e-13!25;UBERON:0000064!2.48e-12!218;UBERON:0002619!1.56e-11!22;UBERON:0001950!1.88e-11!20;UBERON:0000468!4.58e-11!656;UBERON:0000481!4.46e-10!342;UBERON:0002420!2.59e-08!9;UBERON:0007245!2.59e-08!9;UBERON:0010009!2.59e-08!9;UBERON:0010011!2.59e-08!9;UBERON:0000454!2.59e-08!9;UBERON:0000477!4.31e-08!373;UBERON:0000125!7.04e-08!9;UBERON:0002308!7.04e-08!9;UBERON:0000062!7.06e-08!503;UBERON:0003076!4.64e-07!15;UBERON:0003057!4.64e-07!15;UBERON:0000480!5.56e-07!625;UBERON:0000467!8.58e-07!624
|ontology_enrichment_uberon=UBERON:0007023!1.69e-32!114;UBERON:0001049!1.12e-25!56;UBERON:0005068!1.12e-25!56;UBERON:0006241!1.12e-25!56;UBERON:0007135!1.12e-25!56;UBERON:0000073!1.23e-24!53;UBERON:0002616!1.23e-24!53;UBERON:0002346!2.09e-22!86;UBERON:0004121!4.14e-20!171;UBERON:0000924!4.14e-20!171;UBERON:0006601!4.14e-20!171;UBERON:0002780!7.82e-20!41;UBERON:0001890!7.82e-20!41;UBERON:0003080!7.82e-20!41;UBERON:0006240!7.82e-20!41;UBERON:0010314!1.55e-19!132;UBERON:0003075!2.77e-19!82;UBERON:0007284!2.77e-19!82;UBERON:0003528!3.09e-19!34;UBERON:0002020!3.09e-19!34;UBERON:0001893!3.98e-19!34;UBERON:0001017!1.00e-18!81;UBERON:0000955!5.41e-18!68;UBERON:0006238!5.41e-18!68;UBERON:0002791!7.66e-18!32;UBERON:0001869!1.03e-17!32;UBERON:0001016!3.57e-17!89;UBERON:0010371!2.01e-15!104;UBERON:0011216!1.77e-13!223;UBERON:0003056!2.29e-13!61;UBERON:0000956!4.98e-13!25;UBERON:0000203!4.98e-13!25;UBERON:0000064!2.48e-12!218;UBERON:0002619!1.56e-11!22;UBERON:0001950!1.88e-11!20;UBERON:0000468!4.58e-11!656;UBERON:0000481!4.46e-10!342;UBERON:0002420!2.59e-08!9;UBERON:0007245!2.59e-08!9;UBERON:0010009!2.59e-08!9;UBERON:0010011!2.59e-08!9;UBERON:0000454!2.59e-08!9;UBERON:0000477!4.31e-08!373;UBERON:0000125!7.04e-08!9;UBERON:0002308!7.04e-08!9;UBERON:0000062!7.06e-08!503;UBERON:0003076!4.64e-07!15;UBERON:0003057!4.64e-07!15;UBERON:0000480!5.56e-07!625;UBERON:0000467!8.58e-07!624
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7,0.122782,0.0991993,0.289049,0.00396262,0.125746,0.112897,0.398354,0.222091,0.00172179,0.34423,0.0936726,0.343425,0.132374,0.000404905,0.22741,0.203996,0.276721,0.0585101,0.264707,0.450113
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.938585,0.635753,0.581762,0.975621,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,2.05579,0.491074,0.740899,0.463978,0.371755,1.23481,0.66492,0.183156,2.26333,0.0946706,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,1.94963,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.749003,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,1.23342,0.175846,1.24902,0.383416,0.824835,5.75089,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.4289
}}
}}

Revision as of 15:30, 26 November 2012


Full id: C2452_Mesenchymal_small_neuroepithelioma_colon_Adipocyte_neuroectodermal_mature



Phase1 CAGE Peaks

Hg19::chr18:10454594..10454645,+p1@APCDD1
Hg19::chr18:10471655..10471667,+p@chr18:10471655..10471667
+
Hg19::chr18:10471813..10471824,+p@chr18:10471813..10471824
+
Hg19::chr18:10471826..10471841,+p@chr18:10471826..10471841
+


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
fat cell5.42e-0815
Uber Anatomy
Ontology termp-valuen
adult organism1.69e-32114
neural tube1.12e-2556
neural rod1.12e-2556
future spinal cord1.12e-2556
neural keel1.12e-2556
regional part of nervous system1.23e-2453
regional part of brain1.23e-2453
neurectoderm2.09e-2286
ectoderm-derived structure4.14e-20171
ectoderm4.14e-20171
presumptive ectoderm4.14e-20171
regional part of forebrain7.82e-2041
forebrain7.82e-2041
anterior neural tube7.82e-2041
future forebrain7.82e-2041
structure with developmental contribution from neural crest1.55e-19132
neural plate2.77e-1982
presumptive neural plate2.77e-1982
brain grey matter3.09e-1934
gray matter3.09e-1934
telencephalon3.98e-1934
central nervous system1.00e-1881
brain5.41e-1868
future brain5.41e-1868
regional part of telencephalon7.66e-1832
cerebral hemisphere1.03e-1732
nervous system3.57e-1789
ecto-epithelium2.01e-15104
organ system subdivision1.77e-13223
pre-chordal neural plate2.29e-1361
cerebral cortex4.98e-1325
pallium4.98e-1325
organ part2.48e-12218
regional part of cerebral cortex1.56e-1122
neocortex1.88e-1120
multi-cellular organism4.58e-11656
multi-tissue structure4.46e-10342
basal ganglion2.59e-089
nuclear complex of neuraxis2.59e-089
aggregate regional part of brain2.59e-089
collection of basal ganglia2.59e-089
cerebral subcortex2.59e-089
anatomical cluster4.31e-08373
neural nucleus7.04e-089
nucleus of brain7.04e-089
organ7.06e-08503
posterior neural tube4.64e-0715
chordal neural plate4.64e-0715
anatomical group5.56e-07625
anatomical system8.58e-07624


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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