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Coexpression cluster:C3751: Difference between revisions

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|full_id=C3751_Mesenchymal_Renal_Reticulocytes_Alveolar_neuroblastoma_nonsmall_Neurons
|full_id=C3751_Mesenchymal_Renal_Reticulocytes_Alveolar_neuroblastoma_nonsmall_Neurons
|id=C3751
|id=C3751
|ontology_enrichment_celltype=CL:0000393!4.75e-14!60;CL:0000211!4.75e-14!60;CL:0002321!5.12e-14!248;CL:0000220!2.64e-13!246;CL:0000183!2.92e-13!59;CL:0000222!1.61e-12!119;CL:0000192!1.32e-11!42;CL:0000514!1.32e-11!42;CL:0000187!4.35e-11!54;CL:0000680!1.98e-10!57;CL:0000056!1.98e-10!57;CL:0000355!1.98e-10!57;CL:0000055!3.00e-10!180;CL:0000359!9.76e-10!32;CL:0000221!8.99e-09!71;CL:0000133!4.13e-08!59;CL:0000325!1.41e-07!39
|ontology_enrichment_celltype=CL:0002321!6.06e-14!250;CL:0000055!8.08e-13!106;CL:0000393!1.09e-12!61;CL:0000211!1.09e-12!61;CL:0000183!1.23e-11!59;CL:0000222!1.32e-11!121;CL:0000192!2.08e-10!43;CL:0000514!2.08e-10!43;CL:0000187!7.78e-10!55;CL:0000221!1.35e-09!72;CL:0000680!2.35e-09!58;CL:0000056!2.35e-09!58;CL:0000355!2.35e-09!58;CL:0000359!3.91e-09!32;CL:0000133!1.44e-08!59;CL:1000449!1.74e-07!15;CL:1000497!6.83e-07!17;CL:0002518!6.83e-07!17
|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:0000477!2.36e-26!373;UBERON:0000483!3.86e-23!306;UBERON:0000119!7.58e-23!309;UBERON:0000481!7.32e-20!342;UBERON:0000025!1.42e-16!192;UBERON:0004111!1.04e-15!240;UBERON:0002049!9.63e-14!78;UBERON:0007798!9.63e-14!78;UBERON:0003914!4.87e-13!117;UBERON:0000064!9.21e-13!218;UBERON:0004121!1.69e-12!171;UBERON:0000924!1.69e-12!171;UBERON:0006601!1.69e-12!171;UBERON:0007503!5.24e-12!78;UBERON:0010314!5.53e-12!132;UBERON:0003075!8.06e-12!82;UBERON:0007284!8.06e-12!82;UBERON:0004872!1.21e-11!83;UBERON:0003104!1.75e-11!160;UBERON:0009142!1.75e-11!160;UBERON:0002346!2.69e-11!86;UBERON:0000055!3.25e-11!68;UBERON:0001009!3.81e-11!112;UBERON:0003056!4.71e-11!61;UBERON:0010371!6.09e-11!104;UBERON:0007524!3.48e-10!73;UBERON:0004535!3.78e-10!109;UBERON:0003077!4.64e-10!72;UBERON:0007285!4.64e-10!72;UBERON:0007500!4.94e-10!59;UBERON:0001981!4.94e-10!59;UBERON:0004537!4.94e-10!59;UBERON:0006965!4.94e-10!59;UBERON:0001016!6.78e-10!89;UBERON:0001134!7.05e-10!62;UBERON:0002036!7.05e-10!62;UBERON:0003082!7.05e-10!62;UBERON:0002329!7.75e-10!71;UBERON:0003059!7.75e-10!71;UBERON:0007282!7.75e-10!71;UBERON:0004290!7.75e-10!71;UBERON:0009618!7.75e-10!71;UBERON:0001017!9.26e-10!81;UBERON:0000486!1.27e-09!83;UBERON:0002385!2.87e-09!64;UBERON:0001015!2.87e-09!64;UBERON:0000383!2.87e-09!64;UBERON:0000490!5.60e-09!148;UBERON:0000468!5.67e-09!656;UBERON:0003103!9.34e-09!68;UBERON:0001637!2.58e-08!42;UBERON:0003509!2.58e-08!42;UBERON:0004572!2.58e-08!42;UBERON:0005256!4.00e-08!122;UBERON:0000922!4.15e-08!592;UBERON:0005423!1.18e-07!581;UBERON:0004211!1.74e-07!15;UBERON:0009773!1.74e-07!15;UBERON:0001231!1.74e-07!15;UBERON:0001285!1.74e-07!15;UBERON:0007684!1.74e-07!15;UBERON:0004208!1.74e-07!15;UBERON:0000475!2.38e-07!264;UBERON:0006555!2.52e-07!16;UBERON:0004819!2.52e-07!16;UBERON:0000073!2.76e-07!53;UBERON:0002616!2.76e-07!53;UBERON:0000955!2.89e-07!68;UBERON:0006238!2.89e-07!68;UBERON:0001049!5.34e-07!56;UBERON:0005068!5.34e-07!56;UBERON:0006241!5.34e-07!56;UBERON:0007135!5.34e-07!56;UBERON:0001869!5.47e-07!32;UBERON:0000956!9.53e-07!25;UBERON:0000203!9.53e-07!25
|tf_chipseq_enrich=BRCA1#672;3:20.1842306432238:0.000121570486027164:0.00164167313035828!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189951694884902!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279375045877687!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322083223733744!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320513318825304!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462104710886951!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167423024144287!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.005811215921143!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00433714703220061!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108664058560192!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015671455136514!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186424132625224!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00720088424393667!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294383290912858!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.00073752861039446!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269547074297213!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.017284905800201!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00881923911475856!REST#5978;3:9.65002871612802:0.00111263624711459:0.00767216539102077!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00484386679847972!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165205378724927!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027660256926923!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00239640576365512!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246370028201553!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00542734127708902!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00629216705567587!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613508699077678!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190184871955407!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329244185100315!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.014012009906266!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.002426800024169!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109378477437521
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}}
}}

Revision as of 15:23, 19 October 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
anatomical cluster2.36e-26373
epithelium3.86e-23306
cell layer7.58e-23309
multi-tissue structure7.32e-20342
tube1.42e-16192
anatomical conduit1.04e-15240
vasculature9.63e-1478
vascular system9.63e-1478
epithelial tube4.87e-13117
organ part9.21e-13218
ectoderm-derived structure1.69e-12171
ectoderm1.69e-12171
presumptive ectoderm1.69e-12171
epithelial vesicle5.24e-1278
structure with developmental contribution from neural crest5.53e-12132
neural plate8.06e-1282
presumptive neural plate8.06e-1282
splanchnic layer of lateral plate mesoderm1.21e-1183
mesenchyme1.75e-11160
entire embryonic mesenchyme1.75e-11160
neurectoderm2.69e-1186
vessel3.25e-1168
circulatory system3.81e-11112
pre-chordal neural plate4.71e-1161
ecto-epithelium6.09e-11104
dense mesenchyme tissue3.48e-1073
cardiovascular system3.78e-10109
paraxial mesoderm4.64e-1072
presumptive paraxial mesoderm4.64e-1072
epithelial tube open at both ends4.94e-1059
blood vessel4.94e-1059
blood vasculature4.94e-1059
vascular cord4.94e-1059
nervous system6.78e-1089
skeletal muscle tissue7.05e-1062
striated muscle tissue7.05e-1062
myotome7.05e-1062
somite7.75e-1071
presomitic mesoderm7.75e-1071
presumptive segmental plate7.75e-1071
dermomyotome7.75e-1071
trunk paraxial mesoderm7.75e-1071
central nervous system9.26e-1081
multilaminar epithelium1.27e-0983
muscle tissue2.87e-0964
musculature2.87e-0964
musculature of body2.87e-0964
unilaminar epithelium5.60e-09148
multi-cellular organism5.67e-09656
compound organ9.34e-0968
artery2.58e-0842
arterial blood vessel2.58e-0842
arterial system2.58e-0842
trunk mesenchyme4.00e-08122
embryo4.15e-08592
developing anatomical structure1.18e-07581
nephron epithelium1.74e-0715
renal tubule1.74e-0715
nephron tubule1.74e-0715
nephron1.74e-0715
uriniferous tubule1.74e-0715
nephrogenic mesenchyme1.74e-0715
organism subdivision2.38e-07264
excretory tube2.52e-0716
kidney epithelium2.52e-0716
regional part of nervous system2.76e-0753
regional part of brain2.76e-0753
brain2.89e-0768
future brain2.89e-0768
neural tube5.34e-0756
neural rod5.34e-0756
future spinal cord5.34e-0756
neural keel5.34e-0756
cerebral hemisphere5.47e-0732
cerebral cortex9.53e-0725
pallium9.53e-0725


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.

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