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Coexpression cluster:C4779: Difference between revisions

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|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168599278642214!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187521327095786!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278505262499771
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168599278642214!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187521327095786!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278505262499771
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,1.18351,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,1.40888,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,2.72118,0.534793,0.439574,1.46099,0.427404,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,2.04167,0.63803,0.151453,0.726632,0.939121,0.808003,1.98239,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,2.64968,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,2.02451,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,2.35823,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,3.17979,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,3.03565,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
}}
}}

Revision as of 16:57, 26 November 2012


Full id: C4779_cerebellum_occipital_Hair_Fibroblast_heart_caudate_neuroectodermal



Phase1 CAGE Peaks

Hg19::chr8:93074803..93074845,-p1@RUNX1T1
Hg19::chr8:93074848..93074871,-p3@RUNX1T1
Hg19::chr8:93074872..93074884,-p10@RUNX1T1


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
fibroblast2.85e-2776
skin fibroblast4.88e-1523
Uber Anatomy
Ontology termp-valuen
nervous system3.11e-2189
structure with developmental contribution from neural crest1.66e-19132
central nervous system1.73e-1981
neural tube2.12e-1756
neural rod2.12e-1756
future spinal cord2.12e-1756
neural keel2.12e-1756
brain4.19e-1768
future brain4.19e-1768
regional part of nervous system6.79e-1753
regional part of brain6.79e-1753
cerebral hemisphere1.12e-1632
telencephalon1.43e-1634
brain grey matter2.37e-1634
gray matter2.37e-1634
ectoderm-derived structure4.25e-16171
ectoderm4.25e-16171
presumptive ectoderm4.25e-16171
regional part of telencephalon4.59e-1632
adult organism5.45e-16114
regional part of forebrain9.23e-1641
forebrain9.23e-1641
anterior neural tube9.23e-1641
future forebrain9.23e-1641
neurectoderm5.82e-1486
neural plate1.02e-1382
presumptive neural plate1.02e-1382
regional part of cerebral cortex1.47e-1322
integument3.69e-1346
integumental system3.69e-1346
neocortex7.65e-1320
cerebral cortex2.08e-1225
pallium2.08e-1225
skin of body1.36e-1141
ecto-epithelium2.41e-11104
pre-chordal neural plate7.13e-1161
surface structure2.91e-0999
tissue2.33e-08773
organ system subdivision4.34e-08223
multi-cellular organism5.89e-08656
dermis2.82e-079
dermatome2.82e-079
future dermis2.82e-079
multi-tissue structure5.52e-07342


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
EP300#203336.77394172622320.003216880500103790.0168599278642214
MAX#414936.452555509007120.003721913834265510.0187521327095786
SIN3A#2594235.408884726815140.006318961977991520.0278505262499771



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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