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Coexpression cluster:C4455: Difference between revisions

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|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: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
|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-07,0.200105,0.227491,0.000495614,0.0352561,0.01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}}
}}

Revision as of 13:34, 5 September 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
regional part of nervous system7.91e-3694
nervous system7.91e-3694
central nervous system1.95e-3482
neural tube6.97e-2957
neural rod6.97e-2957
future spinal cord6.97e-2957
neural keel6.97e-2957
brain7.12e-2969
future brain7.12e-2969
ectoderm-derived structure7.58e-29169
ectoderm1.63e-28173
presumptive ectoderm1.63e-28173
regional part of brain5.77e-2859
head1.04e-27123
anterior region of body6.18e-27129
craniocervical region6.18e-27129
neural plate2.21e-2686
presumptive neural plate2.21e-2686
neurectoderm1.38e-2590
regional part of forebrain4.50e-2241
forebrain4.50e-2241
future forebrain4.50e-2241
anterior neural tube7.77e-2242
pre-chordal neural plate2.05e-2161
gray matter4.60e-1934
brain grey matter4.60e-1934
telencephalon6.42e-1934
organism subdivision1.10e-18365
regional part of telencephalon1.67e-1833
multi-tissue structure4.09e-18347
cerebral hemisphere9.68e-1832
cell layer6.61e-17312
epithelium1.42e-16309
anatomical cluster1.49e-15286
adult organism6.94e-15115
cerebral cortex2.62e-1425
pallium2.62e-1425
anatomical conduit6.77e-14241
tube3.66e-13194
regional part of cerebral cortex1.22e-1222
organ part1.06e-11219
neocortex2.23e-1120
multi-cellular organism4.09e-11659
embryo8.15e-11612
embryonic structure3.29e-09605
developing anatomical structure3.29e-09605
germ layer6.39e-09604
embryonic tissue6.39e-09604
presumptive structure6.39e-09604
epiblast (generic)6.39e-09604
anatomical system2.86e-08625
posterior neural tube3.57e-0815
chordal neural plate3.57e-0815
anatomical group4.63e-08626
segmental subdivision of nervous system6.32e-0713


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.

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