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Coexpression cluster:C4455: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!7.91e-36!94;UBERON:0001016!7.91e-36!94;UBERON:0005743!3.03e-35!86;UBERON:0001017!1.95e-34!82;UBERON:0001049!6.97e-29!57;UBERON:0005068!6.97e-29!57;UBERON:0006241!6.97e-29!57;UBERON:0007135!6.97e-29!57;UBERON:0000955!7.12e-29!69;UBERON:0006238!7.12e-29!69;UBERON:0004121!7.58e-29!169;UBERON:0000924!1.63e-28!173;UBERON:0006601!1.63e-28!173;UBERON:0002616!5.77e-28!59;UBERON:0000033!1.04e-27!123;UBERON:0000153!6.18e-27!129;UBERON:0007811!6.18e-27!129;UBERON:0003075!2.21e-26!86;UBERON:0007284!2.21e-26!86;UBERON:0002346!1.38e-25!90;UBERON:0002780!4.50e-22!41;UBERON:0001890!4.50e-22!41;UBERON:0006240!4.50e-22!41;UBERON:0003080!7.77e-22!42;UBERON:0003056!2.05e-21!61;UBERON:0002020!4.60e-19!34;UBERON:0003528!4.60e-19!34;UBERON:0001893!6.42e-19!34;UBERON:0000475!1.10e-18!365;UBERON:0002791!1.67e-18!33;UBERON:0000481!4.09e-18!347;UBERON:0001869!9.68e-18!32;UBERON:0000119!6.61e-17!312;UBERON:0000483!1.42e-16!309;UBERON:0000477!1.49e-15!286;UBERON:0007023!6.94e-15!115;UBERON:0000956!2.62e-14!25;UBERON:0000203!2.62e-14!25;UBERON:0004111!6.77e-14!241;UBERON:0000025!3.66e-13!194;UBERON:0002619!1.22e-12!22;UBERON:0000064!1.06e-11!219;UBERON:0001950!2.23e-11!20;UBERON:0000468!4.09e-11!659;UBERON:0000922!8.15e-11!612;UBERON:0002050!3.29e-09!605;UBERON:0005423!3.29e-09!605;UBERON:0000923!6.39e-09!604;UBERON:0005291!6.39e-09!604;UBERON:0006598!6.39e-09!604;UBERON:0002532!6.39e-09!604;UBERON:0000467!2.86e-08!625;UBERON:0003076!3.57e-08!15;UBERON:0003057!3.57e-08!15;UBERON:0000480!4.63e-08!626;UBERON:0004732!6.32e-07!13
|ontology_enrichment_uberon=UBERON:0001016!2.45e-35!89;UBERON:0001017!7.26e-35!81;UBERON:0000955!6.05e-29!68;UBERON:0006238!6.05e-29!68;UBERON:0001049!1.29e-28!56;UBERON:0005068!1.29e-28!56;UBERON:0006241!1.29e-28!56;UBERON:0007135!1.29e-28!56;UBERON:0000477!7.31e-28!373;UBERON:0004121!8.34e-28!171;UBERON:0000924!8.34e-28!171;UBERON:0006601!8.34e-28!171;UBERON:0000073!1.06e-26!53;UBERON:0002616!1.06e-26!53;UBERON:0003075!1.36e-26!82;UBERON:0007284!1.36e-26!82;UBERON:0002346!1.62e-25!86;UBERON:0011216!2.39e-25!223;UBERON:0010314!3.50e-22!132;UBERON:0002780!5.95e-22!41;UBERON:0001890!5.95e-22!41;UBERON:0003080!5.95e-22!41;UBERON:0006240!5.95e-22!41;UBERON:0003056!2.25e-21!61;UBERON:0000481!1.35e-20!342;UBERON:0010371!3.48e-20!104;UBERON:0003528!3.21e-19!34;UBERON:0002020!3.21e-19!34;UBERON:0001893!7.28e-19!34;UBERON:0002791!5.66e-18!32;UBERON:0001869!9.25e-18!32;UBERON:0000956!2.33e-14!25;UBERON:0000203!2.33e-14!25;UBERON:0000119!3.42e-14!309;UBERON:0000483!5.97e-14!306;UBERON:0007023!1.00e-13!114;UBERON:0002619!1.28e-12!22;UBERON:0004111!4.86e-12!240;UBERON:0000468!1.99e-11!656;UBERON:0001950!2.44e-11!20;UBERON:0000064!6.83e-11!218;UBERON:0000025!9.49e-11!192;UBERON:0000922!2.45e-10!592;UBERON:0005423!2.05e-09!581;UBERON:0000467!4.06e-09!624;UBERON:0000480!6.35e-09!625;UBERON:0003076!7.95e-08!15;UBERON:0003057!7.95e-08!15;UBERON:0002050!4.41e-07!564;UBERON:0000923!6.30e-07!560;UBERON:0010316!6.30e-07!560;UBERON:0005291!6.30e-07!560;UBERON:0006598!6.30e-07!560;UBERON:0010317!6.30e-07!560;UBERON:0002532!6.30e-07!560;UBERON:0000062!7.50e-07!503
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280809696380392!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00309783817986966!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066718502557541!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109883822762837
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280809696380392!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00309783817986966!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066718502557541!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109883822762837
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81323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.00327141,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.166024,0.000481141,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.000803238,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.000943525,0.0015938,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.000241884,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.0254773,0.019326,0.000416291,0.394069,0.237101,0.286988,0.00297388,0.172491,0.0818785,0.00117737,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.00015325,0.445524,0.132886,0.0774373,0.109194,0.128564,0.00904548,0.687347,0.448776,0.00136743,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.047822,1.60279e-05,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.696435,0.936279,0.206454,0.218192,0.00608582,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.00678942,0.0929549,0.0158019,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.0203723,0.218271,0.101607,0.327067,0.0159074,0.000904138,0.151597,0.0626744,0.0195983,0.000615006,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.0200941,0.137219,0.0282663,0.00326415,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.00020131,0.113069,0.025556,0.16791,0.09066,0.00213659,0.166967,0.0190329,0.0813902,0.0182671,0.156261,0.0065917,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.252227,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.0291288,0.544776,0.43956,1.74936e-09,1.99593e-06,0.448797,0.197484,0.0919774,0.00118142,0.406019,0.381071,0.216033,0.643768,2.24673e-06,0.722159,0.0886602,0.48809,0.153829,0.443185,0.169835,0.3468,0.871256,0.000149461,0.518585,0.0167433,0.38649,0.0450114,0.0344717,0.0091887,0.0108655,0.0465139,0.164197,0.128922,0.0461094,0.574635,0.478174,0.000849258,0.132529,0.258219,3.00528e-06,0.032364,0.777351,0.390974,0.000456298,0.683217,0.161598,0.405056,0.0868402,0.496032,0.21803,0.0805771,0.78509,0.477353,0.199161,0.160298,0.43491,0.20342,0.200493,0.20558,0.300504,0.25656,0.107337,0.0696455,0.383291,0.156104,0.0104921,0.411941,0.0961477,0.00677445,0.354789,0.163828,0.230581,0.120226,0.28424,0.20075,0.314429,0.181415,0.282286,0.78,0.0727621,0.408413,0.00654592,0.000699859,0.656109,2.91166e-07,0.61031,0.0871388,0.522605,0.802166,0.180745,0.222037,1.63765e-06,0.000241329,0.0252635,0.148994,0.0118519,0.00169113,0.122646,0.138871,0.308032,0.166905,0.0210039,0.00357741,0.316453,0.48065,0.175199,0.332919,0.373557,0.170369,0.0980968,0.365487,0.534741,0.0889149,0.363192,0.236011,0.203486,0.273398,0.375787,0.119167,0.351067,0.000346951,0.637444,0.305885,0.241132,0.0118241,0.30666,0.303709,0.000713369,0.0867777,0.508064,0.000230825,0.00154968,0.457886,0.504711,0.0262575,0.509064,0.196976,0.191517,0.463751,0.0145214,0.307334,0.459728,0.0048173,0.563586,0.135386,7.2347e-08,0.273281,0.000116083,0.0418805,0.384593,0.138622,0.359231,0.339729,0.197805,0.608187,0.387069,0.000809836,0.52832,0.299887,0.00375452,0.0227114,0.17639,0.0779009,0.276869,0.205298,0.000574807,6.89206e-05,0.258854,0.00129444,0.0719199,0.0386691,0.00081525,0.00135583,0.0140817,0.219428,0.208013,0.0900729,0.0953646,3.92648e-05,0.0348699,0.00145945,0.0358457,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,6.46033e-05,0.123324,0.199468,0.0325925,0.0933115,0.000350724,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.0267847,1.50104e-10,0.000103317,0.0391817,7.85423e-06,0.145701,0.229428,0.162145,0.000154811,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,4.46698e-06,0.00610703,0.0595618,5.79916e-06,0.158479,0.220319,0.0204324,0.124213,0.259632,0.30793,0.180606,0.000773769,0.0363723,0.0119784,0.00203642,0.123917,0.184317,0.185335,0.0723291,0.0367308,0.261744,0.0223377,0.0246892,0.207559,0.141867,0.193031,0.0339803,0.115972,0.0273485,0.0331281,0.173026,0.200432,0.139785,0.0208458,0.240478,0.00072309,0.00899301,0.256963,0.222798,0.0157468,0.176789,0.00485777,0.202137,0.310405,0.280943,0.0257454,0.0822373,0.202065,0.00591081,0.0536053,0.0537737,0.0120432,0.078016,0.0407233,0.0537355,0.00717361,0.0377035,0.211332,0.187731,0.0297055,6.87647e-05,2.01194e-06,0.0981146,0.064145,0.121913,0.0638699,0.104603,8.74929e-07,0.0762523,0.128736,0.109171,0.04411,0.066952,0.00414049,0.0367455,0.13497,0.204393,0.000476622,0.286691,0.000980315,0.141729,0.0381402,7.20472e-07,0.200105,0.227491,0.000495614,0.0352561,0.0168099,0.0446853,0.264413,1.48336e-05,0.160658,0.206239,0.19924,0.00501043,0.0304659,0.325148,0.115817,0.218052,0.0271615,0.00691586,0.194982,0.190993,0.0440463,0.283218,0.0342254,0.164638,0.0272695,0.0935776,0.000754551,0.00230715,0.0232618,0.0958756,0.0859274,0.056548,0.171683,0.158847,0.0406636,0.00259055,0.270604,0.101021,0.222548,0.0164735,0.157274,0.215705,0.035048,0.205954,7.71155e-06
}}
}}

Revision as of 15:58, 19 October 2012


Full id: C4455_parietal_temporal_occipital_duodenum_Neurons_extraskeletal_Neural



Phase1 CAGE Peaks

Hg19::chr5:124081979..124082021,-p7@ZNF608
Hg19::chr5:124082279..124082319,-p3@ZNF608
Hg19::chr5:124082322..124082364,-p1@ZNF608


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
nervous system2.45e-3589
central nervous system7.26e-3581
brain6.05e-2968
future brain6.05e-2968
neural tube1.29e-2856
neural rod1.29e-2856
future spinal cord1.29e-2856
neural keel1.29e-2856
anatomical cluster7.31e-28373
ectoderm-derived structure8.34e-28171
ectoderm8.34e-28171
presumptive ectoderm8.34e-28171
regional part of nervous system1.06e-2653
regional part of brain1.06e-2653
neural plate1.36e-2682
presumptive neural plate1.36e-2682
neurectoderm1.62e-2586
organ system subdivision2.39e-25223
structure with developmental contribution from neural crest3.50e-22132
regional part of forebrain5.95e-2241
forebrain5.95e-2241
anterior neural tube5.95e-2241
future forebrain5.95e-2241
pre-chordal neural plate2.25e-2161
multi-tissue structure1.35e-20342
ecto-epithelium3.48e-20104
brain grey matter3.21e-1934
gray matter3.21e-1934
telencephalon7.28e-1934
regional part of telencephalon5.66e-1832
cerebral hemisphere9.25e-1832
cerebral cortex2.33e-1425
pallium2.33e-1425
cell layer3.42e-14309
epithelium5.97e-14306
adult organism1.00e-13114
regional part of cerebral cortex1.28e-1222
anatomical conduit4.86e-12240
multi-cellular organism1.99e-11656
neocortex2.44e-1120
organ part6.83e-11218
tube9.49e-11192
embryo2.45e-10592
developing anatomical structure2.05e-09581
anatomical system4.06e-09624
anatomical group6.35e-09625
posterior neural tube7.95e-0815
chordal neural plate7.95e-0815
embryonic structure4.41e-07564
germ layer6.30e-07560
germ layer / neural crest6.30e-07560
embryonic tissue6.30e-07560
presumptive structure6.30e-07560
germ layer / neural crest derived structure6.30e-07560
epiblast (generic)6.30e-07560
organ7.50e-07503


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#1066435.360256373075030.0064925092527670.0280809696380392
NR3C1#2908314.9730233311730.0002978331194675480.00309783817986966
RAD21#5885310.35503389545630.0009004912073565420.0066718502557541
ZNF263#1012738.221841637010680.001799043925565870.0109883822762837



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.