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Coexpression cluster:C3469: Difference between revisions

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|full_id=C3469_pons_iPS_non_H9_diencephalon_teratocarcinoma_HES3GFP
|full_id=C3469_pons_iPS_non_H9_diencephalon_teratocarcinoma_HES3GFP
|id=C3469
|id=C3469
|ontology_enrichment_celltype=CL:0002322!3.32e-12!5;CL:0000128!8.16e-10!7;CL:0000126!8.16e-10!7;CL:0000127!8.16e-10!7;CL:0002453!8.16e-10!7
|ontology_enrichment_celltype=CL:0002322!9.26e-18!5;CL:0002605!1.13e-09!3;CL:0000128!3.68e-07!7;CL:0000126!3.68e-07!7;CL:0000127!3.68e-07!7;CL:0002453!3.68e-07!7
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!8.42e-78!57;UBERON:0005068!8.42e-78!57;UBERON:0006241!8.42e-78!57;UBERON:0007135!8.42e-78!57;UBERON:0002616!7.92e-68!59;UBERON:0005743!7.69e-66!86;UBERON:0001017!1.99e-64!82;UBERON:0000073!1.10e-60!94;UBERON:0001016!1.10e-60!94;UBERON:0000955!1.20e-57!69;UBERON:0006238!1.20e-57!69;UBERON:0002780!3.75e-54!41;UBERON:0001890!3.75e-54!41;UBERON:0006240!3.75e-54!41;UBERON:0003075!1.10e-53!86;UBERON:0007284!1.10e-53!86;UBERON:0003080!1.26e-52!42;UBERON:0002020!6.59e-52!34;UBERON:0003528!6.59e-52!34;UBERON:0001893!8.37e-52!34;UBERON:0002346!1.28e-50!90;UBERON:0002791!8.08e-50!33;UBERON:0001869!1.04e-48!32;UBERON:0003056!1.77e-37!61;UBERON:0007023!2.56e-37!115;UBERON:0000956!2.02e-35!25;UBERON:0000203!2.02e-35!25;UBERON:0000033!4.73e-32!123;UBERON:0002619!1.55e-30!22;UBERON:0000153!7.03e-30!129;UBERON:0007811!7.03e-30!129;UBERON:0004121!7.20e-28!169;UBERON:0001950!4.25e-27!20;UBERON:0000924!7.50e-27!173;UBERON:0006601!7.50e-27!173;UBERON:0003076!1.66e-25!15;UBERON:0003057!1.66e-25!15;UBERON:0004733!1.05e-23!12;UBERON:0002028!1.05e-23!12;UBERON:0007277!1.05e-23!12;UBERON:0004732!1.25e-21!13;UBERON:0002308!6.32e-18!9;UBERON:0000125!6.32e-18!9;UBERON:0002680!7.44e-18!9;UBERON:0001895!7.44e-18!9;UBERON:0010092!7.44e-18!9;UBERON:0002420!1.42e-17!9;UBERON:0007245!1.42e-17!9;UBERON:0010009!1.42e-17!9;UBERON:0010011!1.42e-17!9;UBERON:0000454!1.42e-17!9;UBERON:0000025!3.38e-16!194;UBERON:0009663!2.83e-14!7;UBERON:0002298!1.12e-12!8;UBERON:0000200!4.07e-12!6;UBERON:0003135!4.13e-12!11;UBERON:0002037!4.68e-12!6;UBERON:0006215!4.68e-12!6;UBERON:0004111!1.18e-11!241;UBERON:0001871!2.55e-11!7;UBERON:0000473!1.57e-10!8;UBERON:0000349!1.94e-10!5;UBERON:0000369!2.28e-09!4;UBERON:0002435!2.28e-09!4;UBERON:0000204!2.28e-09!4;UBERON:0010082!2.28e-09!4;UBERON:0000477!3.12e-09!286;UBERON:0000064!3.22e-09!219;UBERON:0000483!1.07e-07!309;UBERON:0001896!1.59e-07!3;UBERON:0005290!1.59e-07!3;UBERON:0010096!1.59e-07!3;UBERON:0000119!1.71e-07!312;UBERON:0000988!1.73e-07!3;UBERON:0005383!2.29e-07!3;UBERON:0005382!2.29e-07!3;UBERON:0000991!3.50e-07!21;UBERON:0009196!3.50e-07!21;UBERON:0009117!3.50e-07!21;UBERON:0005564!3.50e-07!21;UBERON:0002021!5.91e-07!5;UBERON:0004176!9.11e-07!22;UBERON:0001872!9.93e-07!5
|ontology_enrichment_uberon=UBERON:0001049!2.18e-67!56;UBERON:0005068!2.18e-67!56;UBERON:0006241!2.18e-67!56;UBERON:0007135!2.18e-67!56;UBERON:0000073!2.05e-63!53;UBERON:0002616!2.05e-63!53;UBERON:0001017!4.32e-58!81;UBERON:0001016!2.62e-54!89;UBERON:0000955!1.07e-49!68;UBERON:0006238!1.07e-49!68;UBERON:0003075!1.54e-48!82;UBERON:0007284!1.54e-48!82;UBERON:0002780!1.60e-47!41;UBERON:0001890!1.60e-47!41;UBERON:0003080!1.60e-47!41;UBERON:0006240!1.60e-47!41;UBERON:0002346!7.63e-46!86;UBERON:0003528!3.15e-45!34;UBERON:0002020!3.15e-45!34;UBERON:0001893!4.23e-45!34;UBERON:0001869!4.29e-44!32;UBERON:0002791!5.73e-40!32;UBERON:0010371!2.90e-36!104;UBERON:0003056!6.61e-35!61;UBERON:0000956!5.35e-30!25;UBERON:0000203!5.35e-30!25;UBERON:0010314!1.55e-26!132;UBERON:0004121!1.84e-26!171;UBERON:0000924!1.84e-26!171;UBERON:0006601!1.84e-26!171;UBERON:0007023!4.31e-25!114;UBERON:0002619!4.28e-23!22;UBERON:0001950!6.63e-22!20;UBERON:0003076!3.26e-20!15;UBERON:0003057!3.26e-20!15;UBERON:0002298!1.04e-19!6;UBERON:0011216!9.02e-18!223;UBERON:0000125!6.65e-17!9;UBERON:0002308!6.65e-17!9;UBERON:0004733!1.51e-16!12;UBERON:0002028!1.51e-16!12;UBERON:0007277!1.51e-16!12;UBERON:0004732!3.66e-15!13;UBERON:0000025!3.03e-14!192;UBERON:0002420!1.29e-12!9;UBERON:0007245!1.29e-12!9;UBERON:0010009!1.29e-12!9;UBERON:0010011!1.29e-12!9;UBERON:0000454!1.29e-12!9;UBERON:0000200!1.41e-12!6;UBERON:0009663!1.87e-11!7;UBERON:0000988!6.55e-11!3;UBERON:0001896!1.58e-10!3;UBERON:0005290!1.58e-10!3;UBERON:0010096!1.58e-10!3;UBERON:0004111!1.30e-09!240;UBERON:0002680!3.84e-09!9;UBERON:0001895!3.84e-09!9;UBERON:0010092!3.84e-09!9;UBERON:0000064!3.73e-08!218;UBERON:0000369!7.96e-08!4;UBERON:0002435!7.96e-08!4;UBERON:0000204!7.96e-08!4;UBERON:0010082!7.96e-08!4;UBERON:0000477!1.12e-07!373;UBERON:0001897!1.33e-07!2;UBERON:0010225!1.33e-07!2;UBERON:0002148!1.42e-07!2;UBERON:0006331!1.42e-07!2;UBERON:0009662!1.42e-07!2;UBERON:0001875!1.46e-07!2;UBERON:0006514!1.46e-07!2;UBERON:0000483!1.96e-07!306;UBERON:0001871!2.53e-07!6;UBERON:0000119!2.83e-07!309;UBERON:0002771!7.17e-07!2
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278938324838428!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00662998951040605
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160149,0.123526,0.0906475,0.0558058,0.28262,0.000112257,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.0117175,0.0330727,0.00956472,0.02609,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.0376172,0.0286025,0.0470027,0.0109933,0.038848,0.0874516,0.0550279,0.144067,0.0353101,0.217069,0.190048,0.131088,0.394069,0.0306378,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.0637246,0.147698,0.141463,0.167267,0.140622,0.0889592,0.00643528,0.28711,0.0473033,0.094881,0.118532,0.132886,0.0774373,0.109194,0.128564,0.131452,0.00128046,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.0425274,0.739716,0.0926491,0.21727,0.289306,0.119215,0.192475,0.177967,0.0088427,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.0271723,0.291114,0.0355833,0.125606,0.175094,0.000919297,1.28372e-06,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.000415994,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.000479913,0.0282663,0.251466,0.0461822,0.11903,0.0838874,0.00806892,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.0597157,0.0147868,0.0190329,0.00340589,0.184948,0.156261,0.311847,0.0062542,0.0590944,0.247324,0.178389,0.218229,0.231073,0.0161946,0.0743925,0.0360851,0.0998546,0.131093,0.0434602,0.00935312,0.418146,0.36927,0.449036,0.000211816,0.231447,0.00131394,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.00202987,0.000142346,0.580441,0.0863135,0.432035,0.722159,0.390366,0.0049331,0.50058,0.443185,0.00696618,0.3468,0.151996,0.227104,0.518585,0.250246,0.38649,0.284625,0.0344717,0.55194,0.729153,0.0465139,0.164197,0.0252589,0.287881,0.0556235,0.478174,0.336276,0.468444,0.258219,0.119142,0.243383,0.442897,0.00170027,0.73485,0.029557,0.161598,0.405056,0.0868402,0.150692,0.21803,0.0013757,0.454657,0.0282154,0.0201095,0.746954,0.0175763,0.0222555,0.200493,0.20558,0.300504,0.0361545,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,4.6719e-05,0.0101316,0.000835245,0.230581,0.120226,0.0448825,0.0513026,0.314429,0.181415,0.00475227,0.446891,0.0727621,0.408413,0.516511,0.322213,0.28903,0.33942,0.0156581,0.387276,0.522605,4.99296e-05,0.180745,0.222037,0.416621,0.416292,0.462712,0.382478,0.215157,0.0225745,0.452428,0.138871,0.00583733,0.166905,0.19783,0.0833851,0.056391,0.48065,0.175199,0.332919,0.373557,0.0393909,0.0164118,0.0111982,0.534741,0.39088,0.363192,0.236011,0.203486,0.0413386,0.375787,0.4466,0.351067,0.275347,0.0830022,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.035296,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.127092,0.283463,0.00164832,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.138622,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.0664606,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.00455899,0.0855609,0.131118,0.20837,0.247588,6.79935e-06,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,9.99207e-07,0.201602,0.350452,0.154941,1.01156e-05,0.0986735,0.00610703,0.0595618,0.0251995,0.158479,0.220319,0.195218,0.124213,0.0370716,0.30793,0.0173907,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.0367308,0.261744,0.203781,0.00193951,0.207559,0.141867,0.0199603,0.249101,0.115972,0.224568,0.246105,0.0159159,0.200432,0.139785,0.197112,1.85911e-08,0.156465,1.45157e-05,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,6.31569e-08,0.218161,0.0822373,0.202065,0.00591081,0.0536053,0.0537737,0.0120432,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.00908908,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.0440463,0.283218,0.0342254,0.00084829,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.00259055,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.0228361,0.361435
}}
}}

Revision as of 15:07, 19 October 2012


Full id: C3469_pons_iPS_non_H9_diencephalon_teratocarcinoma_HES3GFP



Phase1 CAGE Peaks

Hg19::chr14:96343250..96343261,+p3@ENST00000554321
Hg19::chr14:96343264..96343291,+p2@ENST00000554321
Hg19::chr14:96343299..96343304,+p4@ENST00000554321


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
embryonic stem cell9.26e-185
astrocyte of the cerebral cortex1.13e-093
oligodendrocyte3.68e-077
macroglial cell3.68e-077
astrocyte3.68e-077
oligodendrocyte precursor cell3.68e-077
Uber Anatomy
Ontology termp-valuen
neural tube2.18e-6756
neural rod2.18e-6756
future spinal cord2.18e-6756
neural keel2.18e-6756
regional part of nervous system2.05e-6353
regional part of brain2.05e-6353
central nervous system4.32e-5881
nervous system2.62e-5489
brain1.07e-4968
future brain1.07e-4968
neural plate1.54e-4882
presumptive neural plate1.54e-4882
regional part of forebrain1.60e-4741
forebrain1.60e-4741
anterior neural tube1.60e-4741
future forebrain1.60e-4741
neurectoderm7.63e-4686
brain grey matter3.15e-4534
gray matter3.15e-4534
telencephalon4.23e-4534
cerebral hemisphere4.29e-4432
regional part of telencephalon5.73e-4032
ecto-epithelium2.90e-36104
pre-chordal neural plate6.61e-3561
cerebral cortex5.35e-3025
pallium5.35e-3025
structure with developmental contribution from neural crest1.55e-26132
ectoderm-derived structure1.84e-26171
ectoderm1.84e-26171
presumptive ectoderm1.84e-26171
adult organism4.31e-25114
regional part of cerebral cortex4.28e-2322
neocortex6.63e-2220
posterior neural tube3.26e-2015
chordal neural plate3.26e-2015
brainstem1.04e-196
organ system subdivision9.02e-18223
neural nucleus6.65e-179
nucleus of brain6.65e-179
segmental subdivision of hindbrain1.51e-1612
hindbrain1.51e-1612
presumptive hindbrain1.51e-1612
segmental subdivision of nervous system3.66e-1513
tube3.03e-14192
basal ganglion1.29e-129
nuclear complex of neuraxis1.29e-129
aggregate regional part of brain1.29e-129
collection of basal ganglia1.29e-129
cerebral subcortex1.29e-129
gyrus1.41e-126
telencephalic nucleus1.87e-117
pons6.55e-113
medulla oblongata1.58e-103
myelencephalon1.58e-103
future myelencephalon1.58e-103
anatomical conduit1.30e-09240
regional part of metencephalon3.84e-099
metencephalon3.84e-099
future metencephalon3.84e-099
organ part3.73e-08218
corpus striatum7.96e-084
striatum7.96e-084
ventral part of telencephalon7.96e-084
future corpus striatum7.96e-084
anatomical cluster1.12e-07373
dorsal plus ventral thalamus1.33e-072
thalamic complex1.33e-072
locus ceruleus1.42e-072
brainstem nucleus1.42e-072
hindbrain nucleus1.42e-072
globus pallidus1.46e-072
pallidum1.46e-072
epithelium1.96e-07306
temporal lobe2.53e-076
cell layer2.83e-07309
middle temporal gyrus7.17e-072


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
CTCF#1066435.360256373075030.0064925092527670.0278938324838428
RAD21#5885310.35503389545630.0009004912073565420.00662998951040605



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.