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Coexpression cluster:C1461: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;4:16.2385345282024:3.98325915717398e-05:0.00074247296647527!CEBPB#1051;6:7.97114762582482:3.89609159898068e-06:0.000126998723628571!EP300#2033;6:6.7739417262232:1.03454107484288e-05:0.000269711521007278!ESR1#2099;6:30.7686032961545:1.17571957705476e-09:1.07616982390905e-07!FOS#2353;6:8.9979553088944:1.88302066097805e-06:6.94178590935003e-05!GATA2#2624;6:12.744931733554:2.33109997620343e-07:1.22710559684833e-05!GATA3#2625;4:18.1576775714707:2.56597141799789e-05:0.000554839521582363!GTF2F1#2962;6:12.7396608767577:2.33689372527042e-07:1.22891663531479e-05!JUN#3725;6:12.5128291923363:2.60292147666678e-07:1.34577483218615e-05!JUNB#3726;6:30.6106326598211:1.2126128927106e-09:1.10702865298778e-07!JUND#3727;6:6.99466394187103:8.53468650061654e-06:0.000232244430286058!MAFF#23764;6:56.3153564899452:3.12096011318554e-11:3.59768160332213e-09!MAFK#7975;6:27.1007331378299:2.5187992661962e-09:2.12832424403127e-07!MXI1#4601;5:8.30130969063275:5.60234779909565e-05:0.000939472706791507!NFE2#4778;6:77.204260651629:4.69314969603843e-12:6.15763644603716e-10!NFKB1#4790;5:4.5733861868282:0.0010219625937113:0.00724594374233633!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380377730643269!SMARCB1#6598;4:12.1684771874383:0.000123498546319347:0.00166062375164752!SMARCC1#6599;4:29.1089062130876:3.97173589497568e-06:0.000128382582833601!STAT1#6772;6:20.7065874971992:1.2666425711927e-08:9.38870713220686e-07!STAT3#6774;6:10.5194649971542:7.37398960627247e-07:3.26742511875049e-05!TAF1#6872;6:3.34304628574529:0.000716247428463562:0.00573255921383294!TBP#6908;6:3.70677068709639:0.00038541647290796:0.00377815947193866!TFAP2A#7020;6:16.518634373045:4.91595718330683e-08:3.15949324472235e-06!TFAP2C#7022;6:10.8092286098602:6.2644941908553e-07:2.86452499474053e-05!TRIM28#10155;6:18.5905250452625:2.41896703530258e-08:1.69326071179602e-06!ZNF263#10127;6:8.22184163701068:3.23542093046082e-06:0.000108755753639008
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}}
}}

Revision as of 14:54, 26 November 2012


Full id: C1461_medulla_locus_globus_spinal_mesothelioma_kidney_testicular



Phase1 CAGE Peaks

Hg19::chr1:110546475..110546482,+p27@AHCYL1
Hg19::chr1:110546552..110546575,+p7@AHCYL1
Hg19::chr1:110546650..110546663,+p12@AHCYL1
Hg19::chr1:110546674..110546695,+p5@AHCYL1
Hg19::chr1:110546700..110546758,+p2@AHCYL1
Hg19::chr1:110546760..110546769,+p21@AHCYL1


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>

Cell Type
Ontology termp-valuen
germ line cell1.33e-087
germ cell1.33e-087
Uber Anatomy
Ontology termp-valuen
neural tube4.31e-2356
neural rod4.31e-2356
future spinal cord4.31e-2356
neural keel4.31e-2356
adult organism8.78e-23114
regional part of nervous system7.54e-2253
regional part of brain7.54e-2253
regional part of forebrain5.03e-1941
forebrain5.03e-1941
anterior neural tube5.03e-1941
future forebrain5.03e-1941
brain2.17e-1868
future brain2.17e-1868
central nervous system3.52e-1681
organ system subdivision1.92e-15223
brain grey matter1.70e-1434
gray matter1.70e-1434
tube2.57e-14192
telencephalon5.73e-1434
nervous system1.14e-1389
neural plate4.34e-1382
presumptive neural plate4.34e-1382
regional part of telencephalon1.19e-1232
neurectoderm1.58e-1286
cerebral hemisphere3.14e-1232
pre-chordal neural plate3.24e-1161
neural nucleus4.04e-119
nucleus of brain4.04e-119
basal ganglion1.05e-109
nuclear complex of neuraxis1.05e-109
aggregate regional part of brain1.05e-109
collection of basal ganglia1.05e-109
cerebral subcortex1.05e-109
anatomical conduit2.08e-10240
anatomical cluster4.29e-09373
telencephalic nucleus7.06e-097
ecto-epithelium1.32e-08104
regional part of cerebral cortex1.38e-0822
brainstem3.88e-086
multi-tissue structure5.77e-08342
cerebral cortex5.06e-0725
pallium5.06e-0725
neocortex5.15e-0720
diencephalon5.50e-077
future diencephalon5.50e-077
Disease
Ontology termp-valuen
carcinoma1.12e-20106
cell type cancer2.13e-16143
cancer1.68e-10235
disease of cellular proliferation3.74e-10239


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
BATF#10538416.23853452820243.98325915717398e-050.00074247296647527
CEBPB#105167.971147625824823.89609159898068e-060.000126998723628571
EP300#203366.77394172622321.03454107484288e-050.000269711521007278
ESR1#2099630.76860329615451.17571957705476e-091.07616982390905e-07
FOS#235368.99795530889441.88302066097805e-066.94178590935003e-05
GATA2#2624612.7449317335542.33109997620343e-071.22710559684833e-05
GATA3#2625418.15767757147072.56597141799789e-050.000554839521582363
GTF2F1#2962612.73966087675772.33689372527042e-071.22891663531479e-05
JUN#3725612.51282919233632.60292147666678e-071.34577483218615e-05
JUNB#3726630.61063265982111.2126128927106e-091.10702865298778e-07
JUND#372766.994663941871038.53468650061654e-060.000232244430286058
MAFF#23764656.31535648994523.12096011318554e-113.59768160332213e-09
MAFK#7975627.10073313782992.5187992661962e-092.12832424403127e-07
MXI1#460158.301309690632755.60234779909565e-050.000939472706791507
NFE2#4778677.2042606516294.69314969603843e-126.15763644603716e-10
NFKB1#479054.57338618682820.00102196259371130.00724594374233633
POLR2A#543062.147453176558070.01019570676818780.0380377730643269
SMARCB1#6598412.16847718743830.0001234985463193470.00166062375164752
SMARCC1#6599429.10890621308763.97173589497568e-060.000128382582833601
STAT1#6772620.70658749719921.2666425711927e-089.38870713220686e-07
STAT3#6774610.51946499715427.37398960627247e-073.26742511875049e-05
TAF1#687263.343046285745290.0007162474284635620.00573255921383294
TBP#690863.706770687096390.000385416472907960.00377815947193866
TFAP2A#7020616.5186343730454.91595718330683e-083.15949324472235e-06
TFAP2C#7022610.80922860986026.2644941908553e-072.86452499474053e-05
TRIM28#10155618.59052504526252.41896703530258e-081.69326071179602e-06
ZNF263#1012768.221841637010683.23542093046082e-060.000108755753639008



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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