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Coexpression cluster:C2571: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106554131246602!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434992788365071
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106554131246602!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434992788365071
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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,1.44778,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,2.14358,0.0842336,2.13139,0.740899,1.17228,2.59922,0.493145,0.66492,0.539378,0.53106,3.53051,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,2.7761,1.32819,0.893276,2.35456,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,2.34631,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,2.60183,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,2.21427,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,7.52185,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,1.23342,9.69978,1.24902,2.65458,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,11.6895
}}
}}

Revision as of 15:35, 26 November 2012


Full id: C2571_Mesothelial_merkel_Pericytes_mesenchymal_cervical_Meningeal_ovary



Phase1 CAGE Peaks

Hg19::chr1:22469330..22469371,+p@chr1:22469330..22469371
+
Hg19::chr1:22469532..22469541,-p4@WNT4
Hg19::chr1:22469582..22469595,-p1@WNT4
Hg19::chr1:22469609..22469630,-p2@WNT4


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 organism5.86e-14114
endoderm-derived structure3.20e-11160
endoderm3.20e-11160
presumptive endoderm3.20e-11160
organ system subdivision4.79e-11223
digestive system6.72e-10145
digestive tract6.72e-10145
primitive gut6.72e-10145
organ part1.38e-08218
immaterial anatomical entity2.51e-08117
neural tube2.64e-0856
neural rod2.64e-0856
future spinal cord2.64e-0856
neural keel2.64e-0856
subdivision of trunk4.06e-08112
subdivision of digestive tract8.53e-08118
regional part of nervous system1.01e-0753
regional part of brain1.01e-0753
regional part of forebrain1.81e-0741
forebrain1.81e-0741
anterior neural tube1.81e-0741
future forebrain1.81e-0741
organ4.13e-07503
endo-epithelium6.82e-0782
organism subdivision8.24e-07264


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
E2F1#186944.907389214879320.001724022357361790.0106554131246602
PAX5#507935.002174148383370.01196533174786410.0434992788365071



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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