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Coexpression cluster:C2549: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0006876!4.26e-17!11;UBERON:0002203!8.32e-13!6;UBERON:0001768!8.32e-13!6;UBERON:0002200!8.32e-13!6;UBERON:0000488!1.11e-12!4;UBERON:0001778!7.77e-10!3;UBERON:0001775!7.77e-10!3;UBERON:0000310!9.55e-10!10;UBERON:0001801!1.31e-09!14;UBERON:0007625!2.99e-09!11;UBERON:0003075!3.02e-09!82;UBERON:0007284!3.02e-09!82;UBERON:0010314!4.28e-09!132;UBERON:0001443!8.58e-09!11;UBERON:0002346!1.35e-08!86;UBERON:0000019!4.11e-08!20;UBERON:0000047!4.11e-08!20;UBERON:0010312!4.11e-08!20;UBERON:0004088!4.11e-08!20;UBERON:0010230!4.11e-08!20;UBERON:0003072!4.11e-08!20;UBERON:0004128!4.11e-08!20;UBERON:0003071!4.11e-08!20;UBERON:0000970!1.17e-07!21;UBERON:0002104!1.17e-07!21;UBERON:0005629!1.42e-07!2;UBERON:0005358!1.42e-07!2;UBERON:0001886!1.42e-07!2;UBERON:0004086!1.42e-07!2;UBERON:0005282!1.42e-07!2;UBERON:0005281!1.42e-07!2;UBERON:0001456!3.02e-07!22;UBERON:0010371!4.38e-07!104
|ontology_enrichment_uberon=UBERON:0006876!4.26e-17!11;UBERON:0002203!8.32e-13!6;UBERON:0001768!8.32e-13!6;UBERON:0002200!8.32e-13!6;UBERON:0000488!1.11e-12!4;UBERON:0001778!7.77e-10!3;UBERON:0001775!7.77e-10!3;UBERON:0000310!9.55e-10!10;UBERON:0001801!1.31e-09!14;UBERON:0007625!2.99e-09!11;UBERON:0003075!3.02e-09!82;UBERON:0007284!3.02e-09!82;UBERON:0010314!4.28e-09!132;UBERON:0001443!8.58e-09!11;UBERON:0002346!1.35e-08!86;UBERON:0000019!4.11e-08!20;UBERON:0000047!4.11e-08!20;UBERON:0010312!4.11e-08!20;UBERON:0004088!4.11e-08!20;UBERON:0010230!4.11e-08!20;UBERON:0003072!4.11e-08!20;UBERON:0004128!4.11e-08!20;UBERON:0003071!4.11e-08!20;UBERON:0000970!1.17e-07!21;UBERON:0002104!1.17e-07!21;UBERON:0005629!1.42e-07!2;UBERON:0005358!1.42e-07!2;UBERON:0001886!1.42e-07!2;UBERON:0004086!1.42e-07!2;UBERON:0005282!1.42e-07!2;UBERON:0005281!1.42e-07!2;UBERON:0001456!3.02e-07!22;UBERON:0010371!4.38e-07!104
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|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,0.581696,0.741427,0.534346,0.739643,0.821651,1.02453,0.392841,0.462021,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.806311,0.682839,1.09415,1.10579,1.63198,0.49475,0.285913,0.491074,0.740899,1.17228,0.371755,0.493145,0.66492,0.183156,0.53106,0.648765,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,3.71684,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,1.49254,1.00941,1.08,0.62601,0.95118,1.02594,1.96757,0.399165,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,2.40752,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,1.40954,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,2.14757,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
}}
}}

Revision as of 15:34, 26 November 2012


Full id: C2549_Fibroblast_Lens_Astrocyte_heart_Ciliary_liposarcoma_Adipocyte



Phase1 CAGE Peaks

Hg19::chr1:201708474..201708479,+p58@NAV1
Hg19::chr1:201708485..201708494,+p55@NAV1
Hg19::chr1:201708502..201708514,+p24@NAV1
Hg19::chr8:24997361..24997368,-p@chr8:24997361..24997368
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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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
vasculature of organ4.26e-1711
vasculature of eye8.32e-136
uvea8.32e-136
vasculature of head8.32e-136
atypical epithelium1.11e-124
ciliary epithelium7.77e-103
ciliary body7.77e-103
breast9.55e-1010
anterior segment of eyeball1.31e-0914
pigment epithelium of eye2.99e-0911
neural plate3.02e-0982
presumptive neural plate3.02e-0982
structure with developmental contribution from neural crest4.28e-09132
chest8.58e-0911
neurectoderm1.35e-0886
camera-type eye4.11e-0820
simple eye4.11e-0820
immature eye4.11e-0820
ocular region4.11e-0820
eyeball of camera-type eye4.11e-0820
optic cup4.11e-0820
optic vesicle4.11e-0820
eye primordium4.11e-0820
eye1.17e-0721
visual system1.17e-0721
vascular plexus1.42e-072
ventricle of nervous system1.42e-072
choroid plexus1.42e-072
brain ventricle1.42e-072
ventricular system of brain1.42e-072
ventricular system of central nervous system1.42e-072
face3.02e-0722
ecto-epithelium4.38e-07104
Disease
Ontology termp-valuen
heart disease9.55e-072


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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