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Coexpression cluster:C3751: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000483!9.65e-23!309;UBERON:0000119!1.54e-22!312;UBERON:0000477!5.98e-18!286;UBERON:0000481!2.54e-17!347;UBERON:0000025!5.28e-16!194;UBERON:0004111!5.24e-15!241;UBERON:0002049!2.75e-14!79;UBERON:0007798!2.75e-14!79;UBERON:0000475!9.53e-14!365;UBERON:0003914!3.48e-13!118;UBERON:0000064!1.34e-12!219;UBERON:0004872!2.96e-12!84;UBERON:0000055!1.10e-11!69;UBERON:0001009!2.06e-11!113;UBERON:0001134!5.09e-11!61;UBERON:0002036!5.09e-11!61;UBERON:0003082!5.09e-11!61;UBERON:0004290!6.43e-11!70;UBERON:0000486!7.43e-11!82;UBERON:0004121!7.77e-11!169;UBERON:0000924!7.99e-11!173;UBERON:0006601!7.99e-11!173;UBERON:0005256!9.08e-11!143;UBERON:0001981!1.31e-10!60;UBERON:0007500!1.31e-10!60;UBERON:0004537!1.31e-10!60;UBERON:0006965!1.31e-10!60;UBERON:0000914!1.71e-10!83;UBERON:0002329!1.71e-10!83;UBERON:0003077!1.71e-10!83;UBERON:0003059!1.71e-10!83;UBERON:0007282!1.71e-10!83;UBERON:0009618!1.71e-10!83;UBERON:0007285!1.71e-10!83;UBERON:0004535!1.98e-10!110;UBERON:0003075!2.36e-10!86;UBERON:0007284!2.36e-10!86;UBERON:0003056!2.64e-10!61;UBERON:0002385!2.72e-10!63;UBERON:0001015!2.72e-10!63;UBERON:0000383!2.72e-10!63;UBERON:0002346!3.36e-10!90;UBERON:0005743!5.51e-10!86;UBERON:0000073!6.46e-10!94;UBERON:0001016!6.46e-10!94;UBERON:0000490!1.88e-09!138;UBERON:0000468!3.26e-09!659;UBERON:0001637!6.12e-09!42;UBERON:0003509!6.12e-09!42;UBERON:0004572!6.12e-09!42;UBERON:0001017!7.43e-09!82;UBERON:0003103!7.92e-09!69;UBERON:0000033!3.46e-08!123;UBERON:0000970!1.63e-07!20;UBERON:0000019!1.94e-07!19;UBERON:0000047!1.94e-07!19;UBERON:0004088!1.94e-07!19;UBERON:0003072!1.94e-07!19;UBERON:0003071!1.94e-07!19;UBERON:0004128!1.94e-07!19;UBERON:0000153!2.82e-07!129;UBERON:0007811!2.82e-07!129;UBERON:0000922!3.25e-07!612;UBERON:0001456!3.29e-07!21;UBERON:0000020!4.48e-07!23;UBERON:0002100!6.81e-07!216;UBERON:0002104!8.37e-07!21
|ontology_enrichment_uberon=UBERON:0000483!9.65e-23!309;UBERON:0000119!1.54e-22!312;UBERON:0000477!5.98e-18!286;UBERON:0000481!2.54e-17!347;UBERON:0000025!5.28e-16!194;UBERON:0004111!5.24e-15!241;UBERON:0002049!2.75e-14!79;UBERON:0007798!2.75e-14!79;UBERON:0000475!9.53e-14!365;UBERON:0003914!3.48e-13!118;UBERON:0000064!1.34e-12!219;UBERON:0004872!2.96e-12!84;UBERON:0000055!1.10e-11!69;UBERON:0001009!2.06e-11!113;UBERON:0001134!5.09e-11!61;UBERON:0002036!5.09e-11!61;UBERON:0003082!5.09e-11!61;UBERON:0004290!6.43e-11!70;UBERON:0000486!7.43e-11!82;UBERON:0004121!7.77e-11!169;UBERON:0000924!7.99e-11!173;UBERON:0006601!7.99e-11!173;UBERON:0005256!9.08e-11!143;UBERON:0001981!1.31e-10!60;UBERON:0007500!1.31e-10!60;UBERON:0004537!1.31e-10!60;UBERON:0006965!1.31e-10!60;UBERON:0000914!1.71e-10!83;UBERON:0002329!1.71e-10!83;UBERON:0003077!1.71e-10!83;UBERON:0003059!1.71e-10!83;UBERON:0007282!1.71e-10!83;UBERON:0009618!1.71e-10!83;UBERON:0007285!1.71e-10!83;UBERON:0004535!1.98e-10!110;UBERON:0003075!2.36e-10!86;UBERON:0007284!2.36e-10!86;UBERON:0003056!2.64e-10!61;UBERON:0002385!2.72e-10!63;UBERON:0001015!2.72e-10!63;UBERON:0000383!2.72e-10!63;UBERON:0002346!3.36e-10!90;UBERON:0005743!5.51e-10!86;UBERON:0000073!6.46e-10!94;UBERON:0001016!6.46e-10!94;UBERON:0000490!1.88e-09!138;UBERON:0000468!3.26e-09!659;UBERON:0001637!6.12e-09!42;UBERON:0003509!6.12e-09!42;UBERON:0004572!6.12e-09!42;UBERON:0001017!7.43e-09!82;UBERON:0003103!7.92e-09!69;UBERON:0000033!3.46e-08!123;UBERON:0000970!1.63e-07!20;UBERON:0000019!1.94e-07!19;UBERON:0000047!1.94e-07!19;UBERON:0004088!1.94e-07!19;UBERON:0003072!1.94e-07!19;UBERON:0003071!1.94e-07!19;UBERON:0004128!1.94e-07!19;UBERON:0000153!2.82e-07!129;UBERON:0007811!2.82e-07!129;UBERON:0000922!3.25e-07!612;UBERON:0001456!3.29e-07!21;UBERON:0000020!4.48e-07!23;UBERON:0002100!6.81e-07!216;UBERON:0002104!8.37e-07!21
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}}
}}

Revision as of 12:10, 5 September 2012


Full id: C3751_Mesenchymal_Renal_Reticulocytes_Alveolar_neuroblastoma_nonsmall_Neurons



Phase1 CAGE Peaks

Hg19::chr19:12912626..12912647,-p3@PRDX2
Hg19::chr19:12912657..12912669,-p2@PRDX2
Hg19::chr19:12912688..12912699,-p4@PRDX2


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><br>


Uber Anatomy
Ontology termp-valuen
epithelium9.65e-23309
cell layer1.54e-22312
anatomical cluster5.98e-18286
multi-tissue structure2.54e-17347
tube5.28e-16194
anatomical conduit5.24e-15241
vasculature2.75e-1479
vascular system2.75e-1479
organism subdivision9.53e-14365
epithelial tube3.48e-13118
organ part1.34e-12219
splanchnic layer of lateral plate mesoderm2.96e-1284
vessel1.10e-1169
circulatory system2.06e-11113
skeletal muscle tissue5.09e-1161
striated muscle tissue5.09e-1161
myotome5.09e-1161
dermomyotome6.43e-1170
multilaminar epithelium7.43e-1182
ectoderm-derived structure7.77e-11169
ectoderm7.99e-11173
presumptive ectoderm7.99e-11173
trunk mesenchyme9.08e-11143
blood vessel1.31e-1060
epithelial tube open at both ends1.31e-1060
blood vasculature1.31e-1060
vascular cord1.31e-1060
somite1.71e-1083
paraxial mesoderm1.71e-1083
presomitic mesoderm1.71e-1083
presumptive segmental plate1.71e-1083
trunk paraxial mesoderm1.71e-1083
presumptive paraxial mesoderm1.71e-1083
cardiovascular system1.98e-10110
neural plate2.36e-1086
presumptive neural plate2.36e-1086
pre-chordal neural plate2.64e-1061
muscle tissue2.72e-1063
musculature2.72e-1063
musculature of body2.72e-1063
neurectoderm3.36e-1090
regional part of nervous system6.46e-1094
nervous system6.46e-1094
unilaminar epithelium1.88e-09138
multi-cellular organism3.26e-09659
artery6.12e-0942
arterial blood vessel6.12e-0942
arterial system6.12e-0942
central nervous system7.43e-0982
compound organ7.92e-0969
head3.46e-08123
eye1.63e-0720
camera-type eye1.94e-0719
simple eye1.94e-0719
ocular region1.94e-0719
optic cup1.94e-0719
eye primordium1.94e-0719
optic vesicle1.94e-0719
anterior region of body2.82e-07129
craniocervical region2.82e-07129
embryo3.25e-07612
face3.29e-0721
sense organ4.48e-0723
trunk6.81e-07216
visual system8.37e-0721


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
BRCA1#672320.18423064322380.0001215704860271640.00164167313035828
CCNT2#90536.336201576962630.003930750035764890.0189951694884902
CTCF#1066435.360256373075030.0064925092527670.0279375045877687
E2F6#187635.017155731697390.00791769806886330.0322083223733744
EGR1#195834.988179094810140.008056488137383440.0320513318825304
ELF1#199734.258097958807540.01295179875054610.0462104710886951
EP300#203336.77394172622320.003216880500103790.0167423024144287
FOXA1#3169311.08141974938550.000734755275698670.005811215921143
GTF2F1#2962312.73966087675770.0004835525047438590.00433714703220061
HMGN3#932438.178547723350590.001827766942164210.0108664058560192
JUND#372736.994663941871030.002921845042734990.015671455136514
MAX#414936.452555509007120.003721913834265510.0186424132625224
MXI1#460139.96157162875930.001011470541259020.00720088424393667
MYC#460935.22228187160940.007020843755740150.0294383290912858
NANOG#79923329.24477848101273.99627955670032e-050.00073752861039446
NFKB1#479035.488063424193840.006049381815655430.0269547074297213
PAX5#507936.669565531177830.003370290999677260.017284905800201
POU2F2#545239.106124057742520.001324165192682130.00881923911475856
REST#597839.650028716128020.001112636247114590.00767216539102077
RFX5#5993312.04791082719510.0005717246050312580.00484386679847972
RXRA#6256320.07461713913330.0001235730348432220.00165205378724927
SIN3A#2594235.408884726815140.006318961977991520.027660256926923
SIX5#147912317.0867153554590.0002004060546325010.00239640576365512
SP1#666735.69838137814090.005403962701712170.0246370028201553
TAF7#6879311.43306940492390.0006690181981945830.00542734127708902
TCF12#6938310.63446490218640.0008313523990202070.00629216705567587
TCF7L2#6934310.77017656313730.0008003181298398380.00613508699077678
USF1#739136.361499277207960.00388404057290560.0190184871955407
YY1#752834.911170749853860.008441455341808260.0329244185100315
ZBTB7A#5134137.35190930787590.002516255860282270.014012009906266
ZEB1#6935316.88843201754390.0002075486917327580.002426800024169
ZNF263#1012738.221841637010680.001799043925565870.0109378477437521



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.