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Coexpression cluster:C2269: Difference between revisions

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|tf_chipseq_enrich=MAX#4149;4:6.45255550900712:0.000576761319564549:0.00484799802446696!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000229845465881214!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00507240481714295!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248206689407024
|tf_chipseq_enrich=MAX#4149;4:6.45255550900712:0.000576761319564549:0.00484799802446696!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000229845465881214!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00507240481714295!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248206689407024
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|tfbs_overrepresentation_for_novel_motifs=1.44014,0.0888524,0.581696,0.741427,1.32255,0.739643,0.821651,0.395818,0.392841,0.902371,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,1.67497,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.849366,1.72987,0.537869,1.46495,0.682839,1.09415,1.10579,0.344471,0.49475,2.67722,0.491074,0.740899,1.17228,0.371755,1.23481,0.66492,0.183156,3.33079,0.648765,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,2.95051,0.336329,0.859396,0.823598,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,1.03184,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,5.0756,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,1.52945,0.516141,1.44917,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,1.1313,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,2.02143,1.24863,0.68598,1.37788,0.852645,1.52813,0.774456,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,1.53017,2.49031,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
}}
}}

Revision as of 15:23, 26 November 2012


Full id: C2269_merkel_small_Mast_anaplastic_acute_colon_pineal



Phase1 CAGE Peaks

Hg19::chr13:72441074..72441172,-p2@DACH1
Hg19::chr13:72441259..72441268,-p8@DACH1
Hg19::chr13:72441289..72441300,-p13@DACH1
Hg19::chr13:72441315..72441454,-p1@DACH1


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.86e-32114
neural plate2.99e-2182
presumptive neural plate2.99e-2182
neural tube1.31e-2056
neural rod1.31e-2056
future spinal cord1.31e-2056
neural keel1.31e-2056
central nervous system1.55e-2081
regional part of nervous system2.20e-2053
regional part of brain2.20e-2053
nervous system3.08e-2089
neurectoderm7.10e-2086
brain2.19e-1868
future brain2.19e-1868
pre-chordal neural plate1.12e-1661
regional part of forebrain2.31e-1541
forebrain2.31e-1541
anterior neural tube2.31e-1541
future forebrain2.31e-1541
ecto-epithelium9.44e-15104
anatomical cluster1.48e-12373
organ system subdivision1.58e-12223
brain grey matter3.24e-1234
gray matter3.24e-1234
telencephalon1.17e-1134
cerebral hemisphere1.53e-1132
regional part of telencephalon2.68e-1132
ectoderm-derived structure1.23e-10171
ectoderm1.23e-10171
presumptive ectoderm1.23e-10171
structure with developmental contribution from neural crest2.07e-10132
embryo3.51e-10592
developing anatomical structure3.77e-09581
germ layer1.80e-08560
germ layer / neural crest1.80e-08560
embryonic tissue1.80e-08560
presumptive structure1.80e-08560
germ layer / neural crest derived structure1.80e-08560
epiblast (generic)1.80e-08560
embryonic structure2.19e-08564
cerebral cortex3.47e-0825
pallium3.47e-0825
multi-cellular organism3.99e-08656
organ5.67e-08503
tube3.01e-07192
neocortex6.73e-0720
anatomical conduit8.61e-07240
anatomical system8.89e-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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
MAX#414946.452555509007120.0005767613195645490.00484799802446696
TRIM28#10155418.59052504526258.36730015875654e-060.000229845465881214
USF1#739146.361499277207960.0006105011399140830.00507240481714295
ZNF263#1012748.221841637010680.0002187871180958320.00248206689407024



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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