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Coexpression cluster:C4665: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.98e-25!57;UBERON:0005068!1.98e-25!57;UBERON:0006241!1.98e-25!57;UBERON:0007135!1.98e-25!57;UBERON:0005743!5.62e-24!86;UBERON:0000073!2.05e-23!94;UBERON:0001016!2.05e-23!94;UBERON:0001017!1.18e-22!82;UBERON:0002616!4.58e-21!59;UBERON:0002346!9.37e-21!90;UBERON:0003075!3.68e-20!86;UBERON:0007284!3.68e-20!86;UBERON:0003080!8.11e-20!42;UBERON:0000955!1.01e-19!69;UBERON:0006238!1.01e-19!69;UBERON:0002780!1.84e-19!41;UBERON:0001890!1.84e-19!41;UBERON:0006240!1.84e-19!41;UBERON:0003056!2.68e-18!61;UBERON:0001893!2.70e-17!34;UBERON:0002020!4.23e-17!34;UBERON:0003528!4.23e-17!34;UBERON:0000025!6.68e-17!194;UBERON:0002791!1.19e-16!33;UBERON:0001869!2.70e-16!32;UBERON:0002050!5.02e-15!605;UBERON:0005423!5.02e-15!605;UBERON:0000923!6.90e-15!604;UBERON:0005291!6.90e-15!604;UBERON:0006598!6.90e-15!604;UBERON:0002532!6.90e-15!604;UBERON:0000922!1.47e-14!612;UBERON:0000468!3.87e-14!659;UBERON:0002619!4.42e-14!22;UBERON:0001950!7.41e-13!20;UBERON:0000467!7.45e-13!625;UBERON:0000480!1.27e-12!626;UBERON:0000956!1.78e-12!25;UBERON:0000203!1.78e-12!25;UBERON:0004111!1.49e-11!241;UBERON:0000924!2.41e-11!173;UBERON:0006601!2.41e-11!173;UBERON:0000119!3.04e-11!312;UBERON:0000483!4.94e-11!309;UBERON:0004121!8.72e-11!169;UBERON:0002371!1.12e-10!80;UBERON:0000033!5.35e-10!123;UBERON:0001474!1.79e-09!86;UBERON:0000477!8.26e-09!286;UBERON:0000153!3.08e-08!129;UBERON:0007811!3.08e-08!129;UBERON:0003081!5.44e-08!216;UBERON:0000062!9.10e-08!511;UBERON:0004765!1.23e-07!101;UBERON:0001434!1.23e-07!101;UBERON:0001986!3.01e-07!18;UBERON:0004638!3.01e-07!18;UBERON:0004852!3.01e-07!18;UBERON:0002405!3.32e-07!115;UBERON:0007023!5.67e-07!115;UBERON:0003076!7.84e-07!15;UBERON:0003057!7.84e-07!15;UBERON:0000064!8.94e-07!219
|ontology_enrichment_uberon=UBERON:0001049!1.98e-25!57;UBERON:0005068!1.98e-25!57;UBERON:0006241!1.98e-25!57;UBERON:0007135!1.98e-25!57;UBERON:0005743!5.62e-24!86;UBERON:0000073!2.05e-23!94;UBERON:0001016!2.05e-23!94;UBERON:0001017!1.18e-22!82;UBERON:0002616!4.58e-21!59;UBERON:0002346!9.37e-21!90;UBERON:0003075!3.68e-20!86;UBERON:0007284!3.68e-20!86;UBERON:0003080!8.11e-20!42;UBERON:0000955!1.01e-19!69;UBERON:0006238!1.01e-19!69;UBERON:0002780!1.84e-19!41;UBERON:0001890!1.84e-19!41;UBERON:0006240!1.84e-19!41;UBERON:0003056!2.68e-18!61;UBERON:0001893!2.70e-17!34;UBERON:0002020!4.23e-17!34;UBERON:0003528!4.23e-17!34;UBERON:0000025!6.68e-17!194;UBERON:0002791!1.19e-16!33;UBERON:0001869!2.70e-16!32;UBERON:0002050!5.02e-15!605;UBERON:0005423!5.02e-15!605;UBERON:0000923!6.90e-15!604;UBERON:0005291!6.90e-15!604;UBERON:0006598!6.90e-15!604;UBERON:0002532!6.90e-15!604;UBERON:0000922!1.47e-14!612;UBERON:0000468!3.87e-14!659;UBERON:0002619!4.42e-14!22;UBERON:0001950!7.41e-13!20;UBERON:0000467!7.45e-13!625;UBERON:0000480!1.27e-12!626;UBERON:0000956!1.78e-12!25;UBERON:0000203!1.78e-12!25;UBERON:0004111!1.49e-11!241;UBERON:0000924!2.41e-11!173;UBERON:0006601!2.41e-11!173;UBERON:0000119!3.04e-11!312;UBERON:0000483!4.94e-11!309;UBERON:0004121!8.72e-11!169;UBERON:0002371!1.12e-10!80;UBERON:0000033!5.35e-10!123;UBERON:0001474!1.79e-09!86;UBERON:0000477!8.26e-09!286;UBERON:0000153!3.08e-08!129;UBERON:0007811!3.08e-08!129;UBERON:0003081!5.44e-08!216;UBERON:0000062!9.10e-08!511;UBERON:0004765!1.23e-07!101;UBERON:0001434!1.23e-07!101;UBERON:0001986!3.01e-07!18;UBERON:0004638!3.01e-07!18;UBERON:0004852!3.01e-07!18;UBERON:0002405!3.32e-07!115;UBERON:0007023!5.67e-07!115;UBERON:0003076!7.84e-07!15;UBERON:0003057!7.84e-07!15;UBERON:0000064!8.94e-07!219
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95801,0.0046858,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.00100412,0.141119,0.00187586,0.0300692,0.00905936,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.00796449,0.0906475,0.0558058,0.28262,1.04001e-06,0.137332,0.0145999,0.0656973,0.211746,0.026334,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.00340073,0.170307,0.201033,0.0488949,0.174921,0.000120455,0.0330727,0.00100273,0.00211059,0.0394698,0.0596469,0.103658,0.122476,0.108872,0.11002,0.00370214,0.0286025,2.02725e-05,1.76131e-08,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,5.99117e-10,0.147698,0.141463,0.167267,0.140622,0.0889592,0.00643528,0.28711,0.0473033,0.094881,2.94436e-06,0.132886,0.0774373,0.00619136,0.128564,0.131452,4.54756e-08,1.52323e-08,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,2.19918e-09,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.00136406,0.057571,0.047591,9.91692e-07,0.0608699,0.175319,0.00583965,0.0713214,0.223874,0.291114,0.0355833,0.000364559,0.175094,1.99579e-12,3.95406e-08,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.000146823,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.00500888,0.152372,0.194941,0.218271,0.101607,0.060512,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,4.25963e-09,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.0126914,0.0154015,0.193653,0.00987736,0.00238639,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.00102368,0.0948451,0.264079,0.249049,0.000516956,0.0997756,0.257598,0.103667,0.00664782,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,9.56941e-05,0.184948,0.156261,0.311847,1.03689e-05,0.0590944,4.44514e-16,0.178389,0.0257622,0.231073,1.3467e-06,2.92681e-12,0.0360851,0.0021796,0.131093,0.0434602,0.133616,0.00233292,0.0785808,0.449036,0.407369,0.231447,0.18653,0.43956,0.37006,0.10748,0.448797,0.197484,0.396996,0.36145,4.87499e-09,0.381071,0.216033,0.643768,0.11074,1.11226e-10,0.390366,0.0305485,0.0334527,0.443185,0.169835,1.06392e-10,9.06946e-16,0.227104,0.000113758,0.00310917,0.0135352,0.284625,0.000799065,0.55194,1.22274e-06,0.28907,0.164197,0.0252589,0.287881,3.12096e-07,0.138768,0.336276,0.468444,0.258219,0.446557,0.243383,8.44761e-10,0.0889613,1.40974e-06,3.45229e-06,0.161598,2.12518e-06,1.42018e-08,0.150692,1.94637e-09,0.0805771,9.90355e-13,5.96264e-05,7.90855e-14,2.7345e-10,4.39284e-14,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.0101317,0.314429,0.181415,0.282286,7.79971e-13,0.0165273,0.408413,0.516511,0.322213,0.656109,0.33942,6.48512e-08,0.387276,0.0391112,1.15611e-06,0.180745,0.222037,0.416621,0.416292,0.462712,1.26158e-12,0.0019893,0.204817,0.452428,0.138871,2.88244e-09,0.166905,0.19783,0.0833851,0.316453,0.000585352,0.175199,0.332919,0.373557,0.170369,0.408861,0.00124345,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,1.26519e-06,0.305885,0.241132,0.371414,0.00623664,0.303709,0.0323359,0.0135408,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.159791,0.196976,0.191517,0.463751,5.00877e-05,0.307334,0.459728,0.283463,0.000222968,0.135386,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.000423937,0.387069,0.332774,0.52832,0.299887,0.266492,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.012591,0.0358457,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.00219731,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.00241368,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.00972162,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.00632223,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0026812,0.258496,0.0377094,0.203781,0.00193951,0.207559,0.010576,0.193031,0.249101,0.115972,0.224568,0.0331281,0.0159159,0.200432,0.139785,0.00149718,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.0219648,0.310405,0.00467879,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.00371523,0.00186843,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.00940743,0.141729,0.263159,0.2559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}}
}}

Revision as of 14:13, 5 September 2012


Full id: C4665_CD14_amygdala_brain_temporal_medial_occipital_hippocampus



Phase1 CAGE Peaks

Hg19::chr7:150783530..150783552,+p2@AGAP3
Hg19::chr7:150783553..150783570,+p1@AGAP3
Hg19::chr7:150783576..150783596,+p3@AGAP3


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>

Uber Anatomy
Ontology termp-valuen
neural tube1.98e-2557
neural rod1.98e-2557
future spinal cord1.98e-2557
neural keel1.98e-2557
regional part of nervous system2.05e-2394
nervous system2.05e-2394
central nervous system1.18e-2282
regional part of brain4.58e-2159
neurectoderm9.37e-2190
neural plate3.68e-2086
presumptive neural plate3.68e-2086
anterior neural tube8.11e-2042
brain1.01e-1969
future brain1.01e-1969
regional part of forebrain1.84e-1941
forebrain1.84e-1941
future forebrain1.84e-1941
pre-chordal neural plate2.68e-1861
telencephalon2.70e-1734
gray matter4.23e-1734
brain grey matter4.23e-1734
tube6.68e-17194
regional part of telencephalon1.19e-1633
cerebral hemisphere2.70e-1632
embryonic structure5.02e-15605
developing anatomical structure5.02e-15605
germ layer6.90e-15604
embryonic tissue6.90e-15604
presumptive structure6.90e-15604
epiblast (generic)6.90e-15604
embryo1.47e-14612
multi-cellular organism3.87e-14659
regional part of cerebral cortex4.42e-1422
neocortex7.41e-1320
anatomical system7.45e-13625
anatomical group1.27e-12626
cerebral cortex1.78e-1225
pallium1.78e-1225
anatomical conduit1.49e-11241
ectoderm2.41e-11173
presumptive ectoderm2.41e-11173
cell layer3.04e-11312
epithelium4.94e-11309
ectoderm-derived structure8.72e-11169
bone marrow1.12e-1080
head5.35e-10123
bone element1.79e-0986
anatomical cluster8.26e-09286
anterior region of body3.08e-08129
craniocervical region3.08e-08129
lateral plate mesoderm5.44e-08216
organ9.10e-08511
skeletal element1.23e-07101
skeletal system1.23e-07101
endothelium3.01e-0718
blood vessel endothelium3.01e-0718
cardiovascular system endothelium3.01e-0718
immune system3.32e-07115
adult organism5.67e-07115
posterior neural tube7.84e-0715
chordal neural plate7.84e-0715
organ part8.94e-07219


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#90536.336201576962630.003930750035764890.0191110098685
E2F4#1874312.66806031528440.0004917987006298980.00438924666681644
E2F6#187635.017155731697390.00791769806886330.0324242821869589
EBF1#187938.9064668465690.00141523283560980.00919074133305884
EGR1#195834.988179094810140.008056488137383440.0322416969222589
ELF1#199734.258097958807540.01295179875054610.0464868001136945
EP300#203336.77394172622320.003216880500103790.0168447120857528
ETS1#211339.728760922202340.001085840092584840.00765106284101118
GABPB1#255337.067683836182170.002832212825417420.0154784654774343
HMGN3#932438.178547723350590.001827766942164210.0109186153218949
IRF1#365937.63716375356390.002244692747297240.0128710588467649
MYC#460935.22228187160940.007020843755740150.029601142505581
PAX5#507936.669565531177830.003370290999677260.0173642060932018
POU2F2#545239.106124057742520.001324165192682130.00885594829396318
REST#597839.650028716128020.001112636247114590.00771188060873378
SIN3A#2594235.408884726815140.006318961977991520.0278235199637192
SMARCB1#6598318.25271578115740.000164397760679890.00203937970396093
YY1#752834.911170749853860.008441455341808260.0331186008430921
ZBTB7A#5134137.35190930787590.002516255860282270.0140901423940818
ZNF263#1012738.221841637010680.001799043925565870.0110109205662315



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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