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Coexpression cluster:C4269: Difference between revisions

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|tf_chipseq_enrich=FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582665954735712!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107456175007658!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015716655048321!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666145354902322!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197525072852855!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330317405186629!ZZZ3#26009;3:239.413212435233:7.25894005043406e-08:4.37964436699759e-06
|tf_chipseq_enrich=FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582665954735712!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107456175007658!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015716655048321!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666145354902322!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197525072852855!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330317405186629!ZZZ3#26009;3:239.413212435233:7.25894005043406e-08:4.37964436699759e-06
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,2.62123,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,1.65118,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,0.439574,0.599922,1.96994,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,3.64044,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.82001,2.64731,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,3.45954,0.450952,1.27663,1.05794,2.54524,2.38768,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.05469,1.86486,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,17.6833,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,2.94727,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,1.3017,0.936473,0.0768232
}}
}}

Revision as of 16:38, 26 November 2012


Full id: C4269_anaplastic_parietal_salivary_small_seminal_pineal_ductus



Phase1 CAGE Peaks

Hg19::chr3:114819047..114819069,-p16@ZBTB20
Hg19::chr3:114819073..114819100,-p10@ZBTB20
Hg19::chr3:114819101..114819121,-p7@ZBTB20


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 organism9.76e-47114
neural tube1.92e-3756
neural rod1.92e-3756
future spinal cord1.92e-3756
neural keel1.92e-3756
central nervous system2.90e-3681
regional part of nervous system3.41e-3553
regional part of brain3.41e-3553
brain7.34e-3368
future brain7.34e-3368
nervous system1.12e-3289
regional part of forebrain8.62e-2941
forebrain8.62e-2941
anterior neural tube8.62e-2941
future forebrain8.62e-2941
neurectoderm2.65e-2886
neural plate2.80e-2782
presumptive neural plate2.80e-2782
telencephalon2.54e-2334
brain grey matter3.83e-2334
gray matter3.83e-2334
cerebral hemisphere4.26e-2232
regional part of telencephalon5.06e-2232
organ system subdivision9.70e-21223
pre-chordal neural plate2.40e-1961
ecto-epithelium1.03e-17104
cerebral cortex2.58e-1725
pallium2.58e-1725
ectoderm-derived structure5.88e-17171
ectoderm5.88e-17171
presumptive ectoderm5.88e-17171
structure with developmental contribution from neural crest8.38e-17132
regional part of cerebral cortex4.47e-1622
neocortex1.08e-1420
anatomical cluster5.47e-14373
posterior neural tube1.11e-0915
chordal neural plate1.11e-0915
tube1.66e-09192
anatomical conduit3.56e-09240
multi-tissue structure4.07e-09342
basal ganglion1.07e-079
nuclear complex of neuraxis1.07e-079
aggregate regional part of brain1.07e-079
collection of basal ganglia1.07e-079
cerebral subcortex1.07e-079
segmental subdivision of hindbrain1.29e-0712
hindbrain1.29e-0712
presumptive hindbrain1.29e-0712
neural nucleus2.83e-079
nucleus of brain2.83e-079
diencephalon6.61e-077
future diencephalon6.61e-077


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
FOXA1#3169311.08141974938550.000734755275698670.00582665954735712
FOXA2#3170324.63046375266526.68983856509345e-050.00107456175007658
JUND#372736.994663941871030.002921845042734990.015716655048321
RAD21#5885310.35503389545630.0009004912073565420.00666145354902322
TRIM28#10155318.59052504526250.0001555969297255280.00197525072852855
YY1#752834.911170749853860.008441455341808260.0330317405186629
ZZZ3#260093239.4132124352337.25894005043406e-084.37964436699759e-06



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.