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Coexpression cluster:C4274: Difference between revisions

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|full_id=C4274_neuroectodermal_neuroepithelioma_neuroblastoma_Astrocyte_peripheral_Neural_parietal
|full_id=C4274_neuroectodermal_neuroepithelioma_neuroblastoma_Astrocyte_peripheral_Neural_parietal
|id=C4274
|id=C4274
|ontology_enrichment_celltype=CL:0000047!3.43e-09!8;CL:0002319!2.78e-07!25;CL:0000540!3.28e-07!6;CL:0000031!3.28e-07!6;CL:0000404!3.28e-07!6;CL:0000133!7.12e-07!59
|ontology_enrichment_celltype=CL:0000047!1.90e-11!8;CL:0002319!3.61e-09!25;CL:0000540!7.52e-09!6;CL:0000031!7.52e-09!6;CL:0000404!7.52e-09!6;CL:0000133!1.23e-07!59;CL:0002322!1.65e-07!5
|ontology_enrichment_disease=DOID:3095!4.13e-09!22;DOID:2994!4.13e-09!22;DOID:171!6.32e-08!10
|ontology_enrichment_disease=DOID:3095!4.13e-11!22;DOID:2994!4.13e-11!22;DOID:171!4.30e-10!10
|ontology_enrichment_uberon=UBERON:0001017!4.63e-38!82;UBERON:0000073!6.97e-38!94;UBERON:0001016!6.97e-38!94;UBERON:0005743!1.39e-36!86;UBERON:0007023!3.55e-35!115;UBERON:0001049!7.26e-35!57;UBERON:0005068!7.26e-35!57;UBERON:0006241!7.26e-35!57;UBERON:0007135!7.26e-35!57;UBERON:0002780!1.84e-30!41;UBERON:0001890!1.84e-30!41;UBERON:0006240!1.84e-30!41;UBERON:0003080!2.39e-29!42;UBERON:0001893!8.28e-29!34;UBERON:0002616!2.19e-28!59;UBERON:0002020!2.85e-28!34;UBERON:0003528!2.85e-28!34;UBERON:0002791!6.11e-28!33;UBERON:0002346!9.78e-28!90;UBERON:0001869!1.18e-27!32;UBERON:0000955!1.62e-27!69;UBERON:0006238!1.62e-27!69;UBERON:0000924!2.12e-26!173;UBERON:0006601!2.12e-26!173;UBERON:0003075!8.92e-25!86;UBERON:0007284!8.92e-25!86;UBERON:0004121!6.74e-24!169;UBERON:0000956!2.12e-22!25;UBERON:0000203!2.12e-22!25;UBERON:0002619!1.19e-19!22;UBERON:0003056!5.18e-19!61;UBERON:0001950!2.36e-18!20;UBERON:0000153!2.86e-18!129;UBERON:0007811!2.86e-18!129;UBERON:0000033!3.59e-17!123;UBERON:0000922!6.85e-11!612;UBERON:0000468!1.01e-08!659;UBERON:0000025!3.47e-08!194;UBERON:0002050!4.26e-08!605;UBERON:0005423!4.26e-08!605;UBERON:0004111!6.20e-08!241;UBERON:0001871!8.11e-08!7;UBERON:0002420!8.60e-08!9;UBERON:0007245!8.60e-08!9;UBERON:0010009!8.60e-08!9;UBERON:0010011!8.60e-08!9;UBERON:0000454!8.60e-08!9;UBERON:0000923!9.95e-08!604;UBERON:0005291!9.95e-08!604;UBERON:0006598!9.95e-08!604;UBERON:0002532!9.95e-08!604;UBERON:0000481!1.11e-07!347;UBERON:0002308!2.44e-07!9;UBERON:0000125!2.44e-07!9;UBERON:0000477!2.89e-07!286;UBERON:0003076!5.39e-07!15;UBERON:0003057!5.39e-07!15;UBERON:0000064!5.81e-07!219;UBERON:0000483!6.57e-07!309
|ontology_enrichment_uberon=UBERON:0001016!1.10e-43!89;UBERON:0001017!2.30e-41!81;UBERON:0001893!2.60e-36!34;UBERON:0003528!1.39e-35!34;UBERON:0002020!1.39e-35!34;UBERON:0001869!1.26e-34!32;UBERON:0001049!2.96e-34!56;UBERON:0005068!2.96e-34!56;UBERON:0006241!2.96e-34!56;UBERON:0007135!2.96e-34!56;UBERON:0002791!4.16e-34!32;UBERON:0000073!3.91e-33!53;UBERON:0002616!3.91e-33!53;UBERON:0002780!2.72e-32!41;UBERON:0001890!2.72e-32!41;UBERON:0003080!2.72e-32!41;UBERON:0006240!2.72e-32!41;UBERON:0007023!8.14e-30!114;UBERON:0000955!1.86e-29!68;UBERON:0006238!1.86e-29!68;UBERON:0004121!5.09e-28!171;UBERON:0000924!5.09e-28!171;UBERON:0006601!5.09e-28!171;UBERON:0000956!2.04e-27!25;UBERON:0000203!2.04e-27!25;UBERON:0002346!8.50e-27!86;UBERON:0001950!1.79e-24!20;UBERON:0002619!7.06e-24!22;UBERON:0003075!2.99e-23!82;UBERON:0007284!2.99e-23!82;UBERON:0011216!6.36e-23!223;UBERON:0003056!3.48e-20!61;UBERON:0010371!1.36e-19!104;UBERON:0010314!2.49e-16!132;UBERON:0000477!7.19e-13!373;UBERON:0000922!1.20e-12!592;UBERON:0002420!3.77e-10!9;UBERON:0007245!3.77e-10!9;UBERON:0010009!3.77e-10!9;UBERON:0010011!3.77e-10!9;UBERON:0000454!3.77e-10!9;UBERON:0000468!8.00e-10!656;UBERON:0005423!1.39e-09!581;UBERON:0000125!1.54e-09!9;UBERON:0002308!1.54e-09!9;UBERON:0001871!4.12e-09!6;UBERON:0002050!4.54e-09!564;UBERON:0000923!7.31e-09!560;UBERON:0010316!7.31e-09!560;UBERON:0005291!7.31e-09!560;UBERON:0006598!7.31e-09!560;UBERON:0010317!7.31e-09!560;UBERON:0002532!7.31e-09!560;UBERON:0000025!2.94e-08!192;UBERON:0009663!4.08e-08!7;UBERON:0000200!1.05e-07!6;UBERON:0002021!2.79e-07!5;UBERON:0000013!4.33e-07!5;UBERON:0002410!4.33e-07!5;UBERON:0001872!4.56e-07!5
|tf_chipseq_enrich=CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000130053232610631!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280368482054883!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00172103914059853!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323342640421527!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666192542361053!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140592363466734
|tf_chipseq_enrich=CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000130053232610631!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280368482054883!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00172103914059853!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323342640421527!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666192542361053!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140592363466734
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119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.00796449,0.0906475,0.0558058,0.28262,0.166024,0.137332,0.0145999,0.0656973,0.211746,0.026334,0.0801488,0.0757897,3.51254e-05,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.00340073,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.000251928,0.122476,0.108872,0.11002,0.00370214,0.0286025,2.02725e-05,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.0637246,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.0458479,0.0473033,0.094881,0.000364928,0.132886,0.0774373,0.109194,0.128564,0.131452,0.000207829,3.73213e-05,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.00049486,0.000122353,0.21727,0.289306,0.119215,0.192475,0.00108376,0.188967,0.057571,0.047591,0.0899568,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.0121461,6.33791e-09,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.0298844,0.0759837,0.286863,0.000665506,7.74968e-05,6.14922e-06,0.101607,6.57264e-16,0.172982,0.00886538,0.151597,0.0626744,0.191335,0.148574,9.07794e-06,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.0126914,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.0125264,0.166967,0.188651,0.00340589,0.00122372,1.02464e-06,0.0546539,0.0062542,0.0590944,0.0334734,0.00109188,2.50547e-07,0.231073,0.0161946,0.00318326,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.103051,0.0785808,0.449036,0.0162067,0.231447,0.0455669,0.43956,0.37006,0.42622,0.120472,0.197484,0.396996,0.0750251,0.406019,0.381071,0.00201312,0.643768,0.432035,1.22387e-09,0.390366,0.48809,0.50058,0.443185,0.522904,0.000322406,0.336835,0.227104,0.518585,7.82361e-08,0.38649,0.284625,0.00583062,0.192225,1.43632e-07,0.00513616,0.164197,0.462688,0.287881,0.0556235,0.478174,0.336276,0.468444,0.0366482,0.119142,0.243383,0.000171205,0.390974,1.07621e-05,0.00650842,0.161598,1.54935e-05,0.644754,0.150692,7.35021e-06,0.37357,0.000199981,0.477353,0.0201095,9.39021e-05,0.000153842,0.20342,0.200493,0.20558,0.300504,0.25656,0.00254768,0.00960524,0.383291,0.156104,0.141318,0.0168417,0.0961477,4.6719e-05,0.354789,0.163828,0.230581,0.120226,0.28424,2.54652e-05,0.00677385,0.181415,0.282286,0.0192486,0.24884,0.408413,0.00654592,0.322213,0.00480191,0.33942,0.61031,0.387276,0.169614,0.0816402,0.0433137,0.222037,0.0175112,0.416292,0.462712,0.0115406,0.579431,0.204817,0.452428,0.138871,0.673493,0.166905,0.19783,0.0833851,0.056391,0.48065,0.175199,0.0628556,0.373557,0.170369,0.408861,0.000111345,0.534741,0.0140668,0.363192,0.236011,0.203486,0.0413386,0.375787,0.119167,0.351067,0.275347,0.637444,0.305885,0.241132,0.371414,0.0527347,0.303709,2.08454e-10,0.386538,0.035296,0.250964,0.383276,0.0243456,0.504711,0.220231,0.0355483,0.196976,0.191517,0.129584,5.00877e-05,0.307334,0.459728,0.283463,0.201728,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.138622,0.359231,0.339729,0.197805,0.00278185,0.387069,0.00817676,0.173874,0.299887,1.17784e-07,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.00221755,0.341681,0.310674,0.21801,0.198614,0.186804,0.000344402,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.00899848,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,5.0641e-05,0.0521984,0.0455518,0.268741,0.201602,0.0701861,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.00361981,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.000284685,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.000220289,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.000128551,0.0367455,0.13497,0.204393,0.295769,0.286691,0.0687209,0.141729,0.263159,0.00345643,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.000785583,0.206239,0.19924,0.28689,0.236464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}}
}}

Revision as of 15:48, 19 October 2012


Full id: C4274_neuroectodermal_neuroepithelioma_neuroblastoma_Astrocyte_peripheral_Neural_parietal



Phase1 CAGE Peaks

Hg19::chr3:122746538..122746562,-p2@SEMA5B
Hg19::chr3:122746566..122746623,-p1@SEMA5B
Hg19::chr3:122746628..122746635,-p8@SEMA5B


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
neuronal stem cell1.90e-118
neural cell3.61e-0925
neuron7.52e-096
neuroblast7.52e-096
electrically signaling cell7.52e-096
neurectodermal cell1.23e-0759
embryonic stem cell1.65e-075
Uber Anatomy
Ontology termp-valuen
nervous system1.10e-4389
central nervous system2.30e-4181
telencephalon2.60e-3634
brain grey matter1.39e-3534
gray matter1.39e-3534
cerebral hemisphere1.26e-3432
neural tube2.96e-3456
neural rod2.96e-3456
future spinal cord2.96e-3456
neural keel2.96e-3456
regional part of telencephalon4.16e-3432
regional part of nervous system3.91e-3353
regional part of brain3.91e-3353
regional part of forebrain2.72e-3241
forebrain2.72e-3241
anterior neural tube2.72e-3241
future forebrain2.72e-3241
adult organism8.14e-30114
brain1.86e-2968
future brain1.86e-2968
ectoderm-derived structure5.09e-28171
ectoderm5.09e-28171
presumptive ectoderm5.09e-28171
cerebral cortex2.04e-2725
pallium2.04e-2725
neurectoderm8.50e-2786
neocortex1.79e-2420
regional part of cerebral cortex7.06e-2422
neural plate2.99e-2382
presumptive neural plate2.99e-2382
organ system subdivision6.36e-23223
pre-chordal neural plate3.48e-2061
ecto-epithelium1.36e-19104
structure with developmental contribution from neural crest2.49e-16132
anatomical cluster7.19e-13373
embryo1.20e-12592
basal ganglion3.77e-109
nuclear complex of neuraxis3.77e-109
aggregate regional part of brain3.77e-109
collection of basal ganglia3.77e-109
cerebral subcortex3.77e-109
multi-cellular organism8.00e-10656
developing anatomical structure1.39e-09581
neural nucleus1.54e-099
nucleus of brain1.54e-099
temporal lobe4.12e-096
embryonic structure4.54e-09564
germ layer7.31e-09560
germ layer / neural crest7.31e-09560
embryonic tissue7.31e-09560
presumptive structure7.31e-09560
germ layer / neural crest derived structure7.31e-09560
epiblast (generic)7.31e-09560
tube2.94e-08192
telencephalic nucleus4.08e-087
gyrus1.05e-076
occipital lobe2.79e-075
sympathetic nervous system4.33e-075
autonomic nervous system4.33e-075
parietal lobe4.56e-075
Disease
Ontology termp-valuen
germ cell and embryonal cancer4.13e-1122
germ cell cancer4.13e-1122
neuroectodermal tumor4.30e-1010


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
CTBP2#1488362.71700033932814.049570681927e-060.000130053232610631
CTCF#1066435.360256373075030.0064925092527670.0280368482054883
CTCFL#140690319.74647435897440.0001298372005551160.00172103914059853
E2F6#187635.017155731697390.00791769806886330.0323342640421527
RAD21#5885310.35503389545630.0009004912073565420.00666192542361053
ZBTB7A#5134137.35190930787590.002516255860282270.0140592363466734



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.