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Coexpression cluster:C1419: Difference between revisions

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|ontology_enrichment_disease=DOID:162!1.46e-13!235;DOID:14566!2.16e-13!239;DOID:2531!2.95e-08!51;DOID:0060083!2.95e-08!51;DOID:0050687!3.43e-07!143;DOID:0050686!6.77e-07!137
|ontology_enrichment_disease=DOID:162!1.46e-13!235;DOID:14566!2.16e-13!239;DOID:2531!2.95e-08!51;DOID:0060083!2.95e-08!51;DOID:0050687!3.43e-07!143;DOID:0050686!6.77e-07!137
|ontology_enrichment_uberon=UBERON:0003104!1.59e-13!238;UBERON:0009142!1.59e-13!238;UBERON:0003914!2.05e-11!118;UBERON:0000119!2.71e-11!312;UBERON:0000481!5.96e-11!347;UBERON:0000483!7.31e-11!309;UBERON:0002100!8.53e-11!216;UBERON:0000490!2.12e-10!138;UBERON:0009569!4.31e-09!113;UBERON:0005256!4.43e-09!143;UBERON:0004290!2.07e-08!70;UBERON:0000486!3.13e-08!82;UBERON:0005177!7.17e-08!107;UBERON:0000475!1.48e-07!365;UBERON:0004211!3.03e-07!16;UBERON:0001285!3.03e-07!16;UBERON:0007684!3.03e-07!16;UBERON:0003220!3.03e-07!16;UBERON:0004208!3.03e-07!16;UBERON:0001048!6.23e-07!168;UBERON:0000914!7.68e-07!83;UBERON:0002329!7.68e-07!83;UBERON:0003077!7.68e-07!83;UBERON:0003059!7.68e-07!83;UBERON:0007282!7.68e-07!83;UBERON:0009618!7.68e-07!83;UBERON:0007285!7.68e-07!83
|ontology_enrichment_uberon=UBERON:0003104!1.59e-13!238;UBERON:0009142!1.59e-13!238;UBERON:0003914!2.05e-11!118;UBERON:0000119!2.71e-11!312;UBERON:0000481!5.96e-11!347;UBERON:0000483!7.31e-11!309;UBERON:0002100!8.53e-11!216;UBERON:0000490!2.12e-10!138;UBERON:0009569!4.31e-09!113;UBERON:0005256!4.43e-09!143;UBERON:0004290!2.07e-08!70;UBERON:0000486!3.13e-08!82;UBERON:0005177!7.17e-08!107;UBERON:0000475!1.48e-07!365;UBERON:0004211!3.03e-07!16;UBERON:0001285!3.03e-07!16;UBERON:0007684!3.03e-07!16;UBERON:0003220!3.03e-07!16;UBERON:0004208!3.03e-07!16;UBERON:0001048!6.23e-07!168;UBERON:0000914!7.68e-07!83;UBERON:0002329!7.68e-07!83;UBERON:0003077!7.68e-07!83;UBERON:0003059!7.68e-07!83;UBERON:0007282!7.68e-07!83;UBERON:0009618!7.68e-07!83;UBERON:0007285!7.68e-07!83
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}}
}}

Revision as of 13:33, 5 September 2012


Full id: C1419_Mesenchymal_Alveolar_Renal_Bronchial_Keratocytes_Trabecular_Pericytes



Phase1 CAGE Peaks

Hg19::chr16:2255447..2255492,+p1@MLST8
Hg19::chr16:28857613..28857627,-p3@TUFM
Hg19::chr16:28857630..28857675,-p1@TUFM
Hg19::chr16:28857677..28857690,-p2@TUFM
Hg19::chr19:19249255..19249307,-p1@TMEM161A
Hg19::chr9:138392519..138392558,+p1@MRPS2


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
epithelial cell5.76e-24254
embryonic cell1.09e-21248
mesodermal cell2.86e-10119
animal cell1.14e-09679
eukaryotic cell1.14e-09679
non-terminally differentiated cell1.34e-08180
contractile cell4.54e-0859
epithelial cell of nephron3.03e-0716
electrically responsive cell5.28e-0760
electrically active cell5.28e-0760
Uber Anatomy
Ontology termp-valuen
mesenchyme1.59e-13238
entire embryonic mesenchyme1.59e-13238
epithelial tube2.05e-11118
cell layer2.71e-11312
multi-tissue structure5.96e-11347
epithelium7.31e-11309
trunk8.53e-11216
unilaminar epithelium2.12e-10138
subdivision of trunk4.31e-09113
trunk mesenchyme4.43e-09143
dermomyotome2.07e-0870
multilaminar epithelium3.13e-0882
trunk region element7.17e-08107
organism subdivision1.48e-07365
nephron epithelium3.03e-0716
nephron3.03e-0716
uriniferous tubule3.03e-0716
metanephric mesenchyme3.03e-0716
nephrogenic mesenchyme3.03e-0716
primordium6.23e-07168
somite7.68e-0783
paraxial mesoderm7.68e-0783
presomitic mesoderm7.68e-0783
presumptive segmental plate7.68e-0783
trunk paraxial mesoderm7.68e-0783
presumptive paraxial mesoderm7.68e-0783
Disease
Ontology termp-valuen
cancer1.46e-13235
disease of cellular proliferation2.16e-13239
hematologic cancer2.95e-0851
immune system cancer2.95e-0851
cell type cancer3.43e-07143
organ system cancer6.77e-07137


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
ATF3#467414.97544968400585.47577390976406e-050.000927329903294712
BCLAF1#9774414.43509840674796.32554335174458e-050.00103240103471301
BRCA1#672310.09211532161190.002171044253359580.0125264731659368
CCNT2#90555.280167980802190.0005100943974832530.00446777497305883
CTCF#1066443.573504248716680.01316635007238510.046603417447632
E2F4#187436.334030157642220.008197175368374340.0323607937364448
EGR1#195854.156815912341780.001617966818864440.0101330556845397
ELF1#199764.258097958807540.0001677224776288830.00205258587310557
ELK4#2005410.8237877723120.0001950599973010460.00234969677717693
EP300#203355.644951438519330.0003688138931814860.00367018143782575
ETS1#211346.485840614801560.001410474068463220.0091701009235701
FOSL2#235538.465100302280850.003598315634615090.0182234742781285
GABPB1#255355.889736530151810.0003000175973670210.00309864891726803
GATA1#262336.780154071900220.006765763983348560.0287520192324601
GTF2F1#296248.493107251171770.0005001017319378380.00441132810657567
HEY1#2346264.040111043105710.0002298968555807510.00253192003585342
HMGN3#932456.815456436125490.0001472107253583660.00189996798636955
IRF1#365956.364303127969920.000205667514205090.00244004424810467
JUND#372744.663109294580680.004917643408260230.0229898728699772
MAX#414944.301703672671410.006644923910676370.0282983692834419
MEF2A#420539.371615454822030.002687399947103910.0148024557288954
MYC#460965.22228187160944.92821127172503e-050.000853986157304946
NFKB1#479054.57338618682820.00102196259371130.00724545185829978
NR3C1#290849.982015554115360.0002673219180401920.00286024319211143
PAX5#507966.669565531177831.13557256338955e-050.000289899933873969
PBX3#5090414.60967512449616.03404227507469e-050.000991175434360689
POLR2A#543062.147453176558070.01019570676818780.0380241900858008
POU2F2#545257.588436714785448.70203885493171e-050.00129058823625421
RAD21#588546.903355930304220.00111085151625360.00771281887421953
RFX5#599348.03194055146340.0006204615428381410.00511044030540005
SIN3A#2594254.507403939012610.001096110061208640.00766037464417618
SIX5#147912514.23892946288253.91539088341565e-060.000127548193534949
SMC3#9126410.02995522995520.0002623881821065520.00281004505240219
SP1#666765.69838137814092.91961319085282e-050.000609599124429184
SP2#6668521.79460874487054.74083619440168e-072.23837337842277e-05
SRF#672249.19811884144520.0003672404582485860.00365800917682633
STAT1#6772310.35329374859960.002016680459920930.0117206505594704
TAF1#687263.343046285745290.0007162474284635620.00573168072801364
TAF7#687947.622046269949280.000759279015141480.00596676757429353
TBP#690863.706770687096390.000385416472907960.00377780488165504
TCF7L2#693447.180117708758230.0009553297120679730.0068752535693679
TFAP2A#702038.259317186522480.003860738477055590.0190445714058761
TFAP2C#702247.206152406573480.0009421413689212550.00681887057718413
THAP1#55145420.91276306856751.46974095435158e-050.000349177150890637
USF1#739144.240999518138640.007005367750829420.0296028162059022
YY1#752854.092642291544880.001743365462849530.0107260881045386
ZBTB7A#5134156.126591089896580.0002476072821414750.00268925300952304
ZEB1#693538.444216008771930.003623843810733590.0183376434783277
ZNF143#7702613.50087655222791.64963374888971e-079.1156666190631e-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.

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