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Coexpression cluster:C953: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000477!3.87e-20!373;UBERON:0000119!1.23e-18!309;UBERON:0000483!6.21e-18!306;UBERON:0000468!3.17e-16!656;UBERON:0000481!2.94e-14!342;UBERON:0000467!7.02e-14!624;UBERON:0000480!1.30e-13!625;UBERON:0004111!2.12e-13!240;UBERON:0010314!7.41e-12!132;UBERON:0000025!9.28e-12!192;UBERON:0000922!2.80e-11!592;UBERON:0002049!3.12e-11!78;UBERON:0007798!3.12e-11!78;UBERON:0003104!2.78e-10!160;UBERON:0009142!2.78e-10!160;UBERON:0001016!2.02e-09!89;UBERON:0001017!3.23e-09!81;UBERON:0005423!3.77e-09!581;UBERON:0007503!4.54e-09!78;UBERON:0007524!5.92e-09!73;UBERON:0003077!1.02e-08!72;UBERON:0007285!1.02e-08!72;UBERON:0000490!1.15e-08!148;UBERON:0003075!1.42e-08!82;UBERON:0007284!1.42e-08!82;UBERON:0000486!1.61e-08!83;UBERON:0002329!2.02e-08!71;UBERON:0003059!2.02e-08!71;UBERON:0007282!2.02e-08!71;UBERON:0004290!2.02e-08!71;UBERON:0009618!2.02e-08!71;UBERON:0000475!2.32e-08!264;UBERON:0000055!2.71e-08!68;UBERON:0002100!3.40e-08!199;UBERON:0002346!3.91e-08!86;UBERON:0002385!4.35e-08!64;UBERON:0001015!4.35e-08!64;UBERON:0000383!4.35e-08!64;UBERON:0005256!5.00e-08!122;UBERON:0000923!5.84e-08!560;UBERON:0010316!5.84e-08!560;UBERON:0005291!5.84e-08!560;UBERON:0006598!5.84e-08!560;UBERON:0010317!5.84e-08!560;UBERON:0002532!5.84e-08!560;UBERON:0001134!9.07e-08!62;UBERON:0002036!9.07e-08!62;UBERON:0003082!9.07e-08!62;UBERON:0002050!1.01e-07!564;UBERON:0007500!2.20e-07!59;UBERON:0001981!2.20e-07!59;UBERON:0004537!2.20e-07!59;UBERON:0006965!2.20e-07!59;UBERON:0000955!2.58e-07!68;UBERON:0006238!2.58e-07!68;UBERON:0004535!3.17e-07!109;UBERON:0001009!3.29e-07!112;UBERON:0003914!4.42e-07!117;UBERON:0001049!8.08e-07!56;UBERON:0005068!8.08e-07!56;UBERON:0006241!8.08e-07!56;UBERON:0007135!8.08e-07!56;UBERON:0004872!8.59e-07!83
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|tfbs_overrepresentation_for_novel_motifs=0.83884,0.0494815,0.305225,1.12193,0.267236,0.439064,0.511871,0.164003,0.487494,0.285547,0.410439,0.553754,0.127813,1.25117,0.266007,0.782718,0.728104,1.17081,0.842338,0.216842,0.823689,0.0355541,0.431698,0.262652,0.918075,0.575764,0.112018,0.429643,0.74357,0.329945,0.389837,0.764231,3.14828,0.406122,0.23642,4.22578,0.233607,0.440165,0.213144,0.451713,0.235191,0.374544,0.0412835,2.0705,0.149259,0.333541,0.51292,0.4002,0.0372068,0.270138,0.589559,0.524278,0.257164,0.839846,0.99088,0.503626,0.273964,0.472204,0.100358,0.47124,0.804523,0.5152,0.162346,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,0.0724994,0.988898,0.124338,0.114787,0.342172,0.684401,0.750836,0.341765,0.858505,0.699894,0.532172,0.963219,0.937974,0.0150019,0.0591186,0.096982,0.614883,1.54397,1.17124,0.911274,0.78075,0.571859,0.267904,2.49908,0.423564,0.82268,0.619373,0.606171,0.214313,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.252953,0.846745,0.814459,0.300169,0.41935,1.12352,2.66855,0.0867932,0.388709,0.664981,0.199081,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,0.39253,1.03718,1.33422,1.18405,0.636999,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,1.17257,0.641461,1.83907,0.37143,0.193834,0.50389,0.150327,0.912334,0.155464,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.323817,0.673453,0.531409,0.183544,1.27204,0.0121205
}}
}}

Revision as of 14:35, 26 November 2012


Full id: C953_Synoviocyte_Olfactory_Lens_embryonic_eye_rectum_tenocyte



Phase1 CAGE Peaks

Hg19::chr6:151670237..151670275,-p@chr6:151670237..151670275
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Hg19::chr6:151670325..151670388,-p@chr6:151670325..151670388
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Hg19::chr6:151670495..151670565,-p@chr6:151670495..151670565
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Hg19::chr6:151671044..151671077,-p@chr6:151671044..151671077
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Hg19::chr6:151671119..151671166,-p@chr6:151671119..151671166
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Hg19::chr6:151671321..151671355,-p@chr6:151671321..151671355
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Hg19::chr6:151671408..151671451,-p@chr6:151671408..151671451
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Hg19::chr6:151671486..151671529,-p@chr6:151671486..151671529
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Hg19::chr6:151678864..151678868,+p6@AKAP12


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
anatomical cluster3.87e-20373
cell layer1.23e-18309
epithelium6.21e-18306
multi-cellular organism3.17e-16656
multi-tissue structure2.94e-14342
anatomical system7.02e-14624
anatomical group1.30e-13625
anatomical conduit2.12e-13240
structure with developmental contribution from neural crest7.41e-12132
tube9.28e-12192
embryo2.80e-11592
vasculature3.12e-1178
vascular system3.12e-1178
mesenchyme2.78e-10160
entire embryonic mesenchyme2.78e-10160
nervous system2.02e-0989
central nervous system3.23e-0981
developing anatomical structure3.77e-09581
epithelial vesicle4.54e-0978
dense mesenchyme tissue5.92e-0973
paraxial mesoderm1.02e-0872
presumptive paraxial mesoderm1.02e-0872
unilaminar epithelium1.15e-08148
neural plate1.42e-0882
presumptive neural plate1.42e-0882
multilaminar epithelium1.61e-0883
somite2.02e-0871
presomitic mesoderm2.02e-0871
presumptive segmental plate2.02e-0871
dermomyotome2.02e-0871
trunk paraxial mesoderm2.02e-0871
organism subdivision2.32e-08264
vessel2.71e-0868
trunk3.40e-08199
neurectoderm3.91e-0886
muscle tissue4.35e-0864
musculature4.35e-0864
musculature of body4.35e-0864
trunk mesenchyme5.00e-08122
germ layer5.84e-08560
germ layer / neural crest5.84e-08560
embryonic tissue5.84e-08560
presumptive structure5.84e-08560
germ layer / neural crest derived structure5.84e-08560
epiblast (generic)5.84e-08560
skeletal muscle tissue9.07e-0862
striated muscle tissue9.07e-0862
myotome9.07e-0862
embryonic structure1.01e-07564
epithelial tube open at both ends2.20e-0759
blood vessel2.20e-0759
blood vasculature2.20e-0759
vascular cord2.20e-0759
brain2.58e-0768
future brain2.58e-0768
cardiovascular system3.17e-07109
circulatory system3.29e-07112
epithelial tube4.42e-07117
neural tube8.08e-0756
neural rod8.08e-0756
future spinal cord8.08e-0756
neural keel8.08e-0756
splanchnic layer of lateral plate mesoderm8.59e-0783


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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