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Coexpression cluster:C4425: Difference between revisions

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|full_id=C4425_Fibroblast_Preadipocyte_Ewing_mesodermal_Mesenchymal_Pancreatic_neurofibroma
|full_id=C4425_Fibroblast_Preadipocyte_Ewing_mesodermal_Mesenchymal_Pancreatic_neurofibroma
|id=C4425
|id=C4425
|ontology_enrichment_celltype=CL:0000055!6.23e-28!180;CL:0000057!2.43e-19!75;CL:0002620!7.13e-12!23;CL:0000136!2.02e-08!15
|ontology_enrichment_celltype=CL:0000057!8.24e-19!76;CL:0002620!1.69e-11!23;CL:0000055!1.92e-09!106;CL:0000136!2.91e-08!15
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!8.28e-15!365;UBERON:0000914!4.93e-12!83;UBERON:0002329!4.93e-12!83;UBERON:0003077!4.93e-12!83;UBERON:0003059!4.93e-12!83;UBERON:0007282!4.93e-12!83;UBERON:0009618!4.93e-12!83;UBERON:0007285!4.93e-12!83;UBERON:0002199!8.87e-11!45;UBERON:0002416!8.87e-11!45;UBERON:0001017!1.55e-10!82;UBERON:0004121!4.04e-10!169;UBERON:0002097!7.36e-10!40;UBERON:0002616!1.04e-09!59;UBERON:0000924!1.12e-09!173;UBERON:0006601!1.12e-09!173;UBERON:0000073!1.37e-09!94;UBERON:0001016!1.37e-09!94;UBERON:0000955!2.46e-09!69;UBERON:0006238!2.46e-09!69;UBERON:0005743!2.72e-09!86;UBERON:0001869!4.85e-09!32;UBERON:0001893!1.48e-08!34;UBERON:0000033!1.55e-08!123;UBERON:0004290!1.66e-08!70;UBERON:0003080!2.08e-08!42;UBERON:0003102!2.14e-08!95;UBERON:0002791!2.45e-08!33;UBERON:0002780!3.77e-08!41;UBERON:0001890!3.77e-08!41;UBERON:0006240!3.77e-08!41;UBERON:0002020!3.86e-08!34;UBERON:0003528!3.86e-08!34;UBERON:0000119!4.88e-08!312;UBERON:0001049!6.77e-08!57;UBERON:0005068!6.77e-08!57;UBERON:0006241!6.77e-08!57;UBERON:0007135!6.77e-08!57;UBERON:0000483!1.68e-07!309;UBERON:0000956!1.98e-07!25;UBERON:0000203!1.98e-07!25;UBERON:0000486!2.67e-07!82;UBERON:0000153!2.81e-07!129;UBERON:0007811!2.81e-07!129;UBERON:0000468!3.28e-07!659
|ontology_enrichment_uberon=UBERON:0001016!3.29e-14!89;UBERON:0001017!9.63e-14!81;UBERON:0004121!2.19e-13!171;UBERON:0000924!2.19e-13!171;UBERON:0006601!2.19e-13!171;UBERON:0010314!5.45e-13!132;UBERON:0000955!5.93e-12!68;UBERON:0006238!5.93e-12!68;UBERON:0002199!1.91e-11!46;UBERON:0002416!1.91e-11!46;UBERON:0001049!8.03e-11!56;UBERON:0005068!8.03e-11!56;UBERON:0006241!8.03e-11!56;UBERON:0007135!8.03e-11!56;UBERON:0001869!1.02e-10!32;UBERON:0002780!1.24e-10!41;UBERON:0001890!1.24e-10!41;UBERON:0003080!1.24e-10!41;UBERON:0006240!1.24e-10!41;UBERON:0001893!1.88e-10!34;UBERON:0000073!2.25e-10!53;UBERON:0002616!2.25e-10!53;UBERON:0010371!2.38e-10!104;UBERON:0002097!2.39e-10!41;UBERON:0002791!2.76e-10!32;UBERON:0003528!5.67e-10!34;UBERON:0002020!5.67e-10!34;UBERON:0003075!2.68e-09!82;UBERON:0007284!2.68e-09!82;UBERON:0007524!6.61e-09!73;UBERON:0000119!6.73e-09!309;UBERON:0003102!1.13e-08!99;UBERON:0002346!1.15e-08!86;UBERON:0003077!1.52e-08!72;UBERON:0007285!1.52e-08!72;UBERON:0000956!1.75e-08!25;UBERON:0000203!1.75e-08!25;UBERON:0000468!1.76e-08!656;UBERON:0000483!2.39e-08!306;UBERON:0003056!2.52e-08!61;UBERON:0002329!3.36e-08!71;UBERON:0003059!3.36e-08!71;UBERON:0007282!3.36e-08!71;UBERON:0004290!3.36e-08!71;UBERON:0009618!3.36e-08!71;UBERON:0000486!3.79e-07!83;UBERON:0002619!4.35e-07!22
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190763756034038!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323735061901113!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321935860338303!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464229840657658!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168084742120442!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157352949217862!MYC#4609;3:5.2222818716094:0.00702084375574015:0.029558185230207!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270470220234273!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00472757762622706!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173470909129808!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00884631795295394!RDBP#7936;3:153.638403990025:2.75057764221434e-07:1.40404486009396e-05!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277825237862868!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00631137698635395!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190936838500206!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330689105192465!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140705276967404!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00390174977039504!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109838856858514
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3187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,1.2533e-05,0.0345419,0.0388736,0.0355977,0.170307,0.201033,0.0488949,0.174921,0.00132287,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.000337112,0.108872,0.11002,0.0376172,0.0286025,0.001389,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.090504,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,6.72149e-05,0.147698,0.141463,0.167267,0.140622,0.0889592,4.27652e-05,0.28711,0.0473033,0.094881,8.21254e-10,0.132886,0.0774373,0.109194,0.128564,0.131452,0.00681584,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.0122266,0.655293,0.21727,0.289306,0.00740669,0.192475,0.177967,1.93633e-06,0.057571,0.047591,0.0143259,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.0370461,3.18684e-05,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.0266106,0.057168,0.234298,0.0759837,0.0457643,0.152372,0.0203723,0.000125914,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.000615006,0.0058211,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.00326415,0.288096,0.11903,0.00362128,0.331451,0.113145,0.112651,0.186638,0.01625,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.000902392,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.000874248,0.0590944,0.247324,0.178389,0.218229,0.0290303,0.407281,0.000500398,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.0177337,0.36927,0.120614,0.407369,0.231447,0.00131394,0.115047,0.37006,0.10748,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.057779,0.276075,0.0198622,0.0100497,0.390366,7.0773e-05,0.50058,0.0217093,0.522904,0.3468,0.0572701,0.227104,0.518585,0.250246,0.38649,0.284625,0.000799065,0.55194,0.0108655,0.28907,0.164197,0.128922,0.287881,0.574635,0.00445792,0.336276,0.468444,0.258219,0.446557,0.243383,0.000933637,0.390974,0.382874,0.000194132,0.161598,0.013901,0.277094,0.496032,4.65435e-05,0.37357,0.00106614,0.477353,0.00492096,0.000558506,0.00415823,0.20342,0.00158025,0.20558,0.300504,0.25656,0.0189087,0.349197,0.0851996,0.156104,0.141318,0.00217346,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.0513026,0.314429,0.181415,0.282286,4.44343e-06,0.0165273,0.408413,0.516511,0.322213,0.656109,0.33942,0.61031,0.0871388,0.00694606,0.00143411,0.0433137,0.222037,0.416621,0.10205,0.462712,0.148994,0.057399,0.204817,0.452428,0.138871,0.103502,0.166905,0.19783,0.0833851,0.316453,0.0289164,0.175199,0.332919,0.373557,0.523625,0.0980968,0.365487,0.178743,0.39088,0.0109626,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,1.13608e-05,0.305885,0.0317395,0.0795725,0.30666,0.303709,0.495883,0.0135408,0.00602464,0.0345164,0.383276,0.457886,0.00582796,0.220231,0.0355483,0.196976,0.191517,0.129584,0.601877,0.307334,0.0246928,0.283463,2.42762e-07,0.0272975,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.24107,0.387069,0.332774,0.0406989,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.119514,0.00111175,0.193601,0.00215229,0.222977,0.00893033,0.310674,0.21801,0.198614,0.186804,0.123324,0.0213665,0.0325925,0.0933115,0.12405,0.00112112,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.0391817,0.113092,0.145701,0.0285999,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.000773769,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.0367308,0.261744,0.203781,0.21382,0.0232077,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,4.66494e-05,0.0215816,0.139785,0.197112,0.000191608,0.156465,0.13108,0.256963,0.222798,0.172134,0.0166394,0.0969345,0.202137,0.310405,0.00467879,0.218161,0.0822373,0.0219487,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.000206969,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.00229305,0.089609,0.0367455,4.73315e-07,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.0597546,0.115817,0.218052,0.223831,0.11528,0.194982,0.00135479,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.0750181
}}
}}

Revision as of 15:56, 19 October 2012


Full id: C4425_Fibroblast_Preadipocyte_Ewing_mesodermal_Mesenchymal_Pancreatic_neurofibroma



Phase1 CAGE Peaks

Hg19::chr4:77870896..77870914,+p1@SEPT11
Hg19::chr4:77870934..77870956,+p3@SEPT11
Hg19::chr4:77870960..77871020,+p2@SEPT11


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>

Cell Type
Ontology termp-valuen
fibroblast8.24e-1976
skin fibroblast1.69e-1123
non-terminally differentiated cell1.92e-09106
fat cell2.91e-0815
Uber Anatomy
Ontology termp-valuen
nervous system3.29e-1489
central nervous system9.63e-1481
ectoderm-derived structure2.19e-13171
ectoderm2.19e-13171
presumptive ectoderm2.19e-13171
structure with developmental contribution from neural crest5.45e-13132
brain5.93e-1268
future brain5.93e-1268
integument1.91e-1146
integumental system1.91e-1146
neural tube8.03e-1156
neural rod8.03e-1156
future spinal cord8.03e-1156
neural keel8.03e-1156
cerebral hemisphere1.02e-1032
regional part of forebrain1.24e-1041
forebrain1.24e-1041
anterior neural tube1.24e-1041
future forebrain1.24e-1041
telencephalon1.88e-1034
regional part of nervous system2.25e-1053
regional part of brain2.25e-1053
ecto-epithelium2.38e-10104
skin of body2.39e-1041
regional part of telencephalon2.76e-1032
brain grey matter5.67e-1034
gray matter5.67e-1034
neural plate2.68e-0982
presumptive neural plate2.68e-0982
dense mesenchyme tissue6.61e-0973
cell layer6.73e-09309
surface structure1.13e-0899
neurectoderm1.15e-0886
paraxial mesoderm1.52e-0872
presumptive paraxial mesoderm1.52e-0872
cerebral cortex1.75e-0825
pallium1.75e-0825
multi-cellular organism1.76e-08656
epithelium2.39e-08306
pre-chordal neural plate2.52e-0861
somite3.36e-0871
presomitic mesoderm3.36e-0871
presumptive segmental plate3.36e-0871
dermomyotome3.36e-0871
trunk paraxial mesoderm3.36e-0871
multilaminar epithelium3.79e-0783
regional part of cerebral cortex4.35e-0722


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
CCNT2#90536.336201576962630.003930750035764890.0190763756034038
E2F6#187635.017155731697390.00791769806886330.0323735061901113
EGR1#195834.988179094810140.008056488137383440.0321935860338303
ELF1#199734.258097958807540.01295179875054610.0464229840657658
EP300#203336.77394172622320.003216880500103790.0168084742120442
JUND#372736.994663941871030.002921845042734990.0157352949217862
MYC#460935.22228187160940.007020843755740150.029558185230207
NFKB1#479035.488063424193840.006049381815655430.0270470220234273
NRF1#4899312.21027944771090.0005492172401020010.00472757762622706
PAX5#507936.669565531177830.003370290999677260.0173470909129808
POU2F2#545239.106124057742520.001324165192682130.00884631795295394
RDBP#79363153.6384039900252.75057764221434e-071.40404486009396e-05
SIN3A#2594235.408884726815140.006318961977991520.0277825237862868
TCF12#6938310.63446490218640.0008313523990202070.00631137698635395
USF1#739136.361499277207960.00388404057290560.0190936838500206
YY1#752834.911170749853860.008441455341808260.0330689105192465
ZBTB7A#5134137.35190930787590.002516255860282270.0140705276967404
ZNF143#7702313.50087655222790.0004062804962997170.00390174977039504
ZNF263#1012738.221841637010680.001799043925565870.0109838856858514



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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