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Coexpression cluster:C2789: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!6.00e-23!659;UBERON:0000064!1.21e-22!219;UBERON:0000481!6.68e-21!347;UBERON:0002346!4.41e-20!90;UBERON:0003075!1.95e-19!86;UBERON:0007284!1.95e-19!86;UBERON:0000924!2.11e-19!173;UBERON:0006601!2.11e-19!173;UBERON:0000922!5.32e-19!612;UBERON:0004121!1.08e-18!169;UBERON:0007023!2.19e-18!115;UBERON:0005743!2.25e-18!86;UBERON:0001049!1.99e-17!57;UBERON:0005068!1.99e-17!57;UBERON:0006241!1.99e-17!57;UBERON:0007135!1.99e-17!57;UBERON:0000475!3.59e-17!365;UBERON:0002050!3.63e-17!605;UBERON:0005423!3.63e-17!605;UBERON:0000467!6.32e-17!625;UBERON:0001017!7.34e-17!82;UBERON:0000923!1.01e-16!604;UBERON:0005291!1.01e-16!604;UBERON:0006598!1.01e-16!604;UBERON:0002532!1.01e-16!604;UBERON:0000480!1.29e-16!626;UBERON:0000033!2.66e-16!123;UBERON:0000073!4.77e-16!94;UBERON:0001016!4.77e-16!94;UBERON:0003056!5.68e-16!61;UBERON:0002020!5.76e-16!34;UBERON:0003528!5.76e-16!34;UBERON:0000483!7.31e-16!309;UBERON:0000955!1.14e-15!69;UBERON:0006238!1.14e-15!69;UBERON:0001893!1.56e-15!34;UBERON:0001869!2.04e-15!32;UBERON:0000153!2.47e-15!129;UBERON:0007811!2.47e-15!129;UBERON:0002616!2.52e-15!59;UBERON:0000477!3.40e-15!286;UBERON:0000119!5.26e-15!312;UBERON:0002791!5.87e-15!33;UBERON:0002780!9.11e-15!41;UBERON:0001890!9.11e-15!41;UBERON:0006240!9.11e-15!41;UBERON:0003080!1.46e-14!42;UBERON:0002619!3.47e-14!22;UBERON:0001950!4.44e-13!20;UBERON:0000062!9.54e-13!511;UBERON:0000956!1.09e-12!25;UBERON:0000203!1.09e-12!25;UBERON:0004111!4.11e-12!241;UBERON:0000025!1.42e-10!194;UBERON:0000063!2.11e-09!97;UBERON:0004119!3.86e-08!169;UBERON:0000925!3.86e-08!169;UBERON:0006595!3.86e-08!169
|ontology_enrichment_uberon=UBERON:0000064!4.14e-20!218;UBERON:0000477!7.95e-20!373;UBERON:0000481!6.97e-19!342;UBERON:0000468!2.98e-18!656;UBERON:0002346!3.93e-18!86;UBERON:0011216!1.07e-17!223;UBERON:0007023!1.45e-17!114;UBERON:0003075!1.47e-17!82;UBERON:0007284!1.47e-17!82;UBERON:0001049!9.29e-17!56;UBERON:0005068!9.29e-17!56;UBERON:0006241!9.29e-17!56;UBERON:0007135!9.29e-17!56;UBERON:0001017!1.79e-16!81;UBERON:0004121!6.47e-16!171;UBERON:0000924!6.47e-16!171;UBERON:0006601!6.47e-16!171;UBERON:0010371!1.12e-15!104;UBERON:0003528!2.31e-15!34;UBERON:0002020!2.31e-15!34;UBERON:0000073!2.77e-15!53;UBERON:0002616!2.77e-15!53;UBERON:0000955!4.32e-15!68;UBERON:0006238!4.32e-15!68;UBERON:0001893!6.81e-15!34;UBERON:0003056!7.78e-15!61;UBERON:0001869!1.24e-14!32;UBERON:0000922!1.36e-14!592;UBERON:0001016!2.53e-14!89;UBERON:0002791!2.70e-14!32;UBERON:0002619!5.71e-14!22;UBERON:0002780!1.27e-13!41;UBERON:0001890!1.27e-13!41;UBERON:0003080!1.27e-13!41;UBERON:0006240!1.27e-13!41;UBERON:0000467!3.71e-13!624;UBERON:0002050!4.80e-13!564;UBERON:0000480!6.39e-13!625;UBERON:0001950!6.74e-13!20;UBERON:0005423!7.85e-13!581;UBERON:0000923!1.50e-12!560;UBERON:0010316!1.50e-12!560;UBERON:0005291!1.50e-12!560;UBERON:0006598!1.50e-12!560;UBERON:0010317!1.50e-12!560;UBERON:0002532!1.50e-12!560;UBERON:0000956!4.50e-12!25;UBERON:0000203!4.50e-12!25;UBERON:0000483!6.70e-12!306;UBERON:0000119!3.71e-11!309;UBERON:0010314!5.08e-11!132;UBERON:0000062!2.39e-10!503;UBERON:0004111!1.61e-09!240;UBERON:0000063!2.84e-09!98;UBERON:0000025!5.79e-09!192;UBERON:0004119!1.36e-07!160;UBERON:0000925!1.36e-07!160;UBERON:0006595!1.36e-07!160
|tf_chipseq_enrich=CTBP2#1488;2:31.3585001696641:0.00149267688204723:0.009542953041389!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249643918134061
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5,0.271662,0.03989,0.171436,0.05892,0.0691994,0.268299,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.357807,0.621787,0.00109949,0.019419,0.0866228,0.000327905,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.00106467,0.0514927,0.324236,0.220368,0.0367692,0.064656,0.226143,0.0248217,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.000915068,0.159873,0.142462,0.143935,0.332403,0.0379537,0.0922008,0.0188872,0.051459,0.114868,0.0726892,0.0187556,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.0253522,0.00118257,0.116818,0.389792,0.36316,0.0625685,0.124464,0.0454742,0.173134,0.101893,0.142875,0.167635,0.171311,0.20386,0.0465855,0.0685131,0.00888201,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.00493244,0.00979133,0.0360207,4.12233e-09,0.0430331,0.365775,0.155708,0.248017,0.22995,0.000795073,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.0457255,0.0779623,0.0471607,0.163865,0.0278061,0.0464703,0.0792764,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.0466818,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.00484807,0.0754883,0.299492,0.100006,0.362866,0.0210009,0.251078,0.0434358,0.133127,0.00022115,0.223717,0.426452,0.196838,0.0826805,0.0332683,0.193021,0.240896,0.202165,0.0946865,0.00758581,0.079499,0.0188178,0.195618,0.127688,0.0217469,0.220353,0.24948,0.0170013,0.0475113,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.0277041,0.124417,0.335582,0.317428,0.182843,0.00894967,0.327768,0.135777,0.011511,0.0339286,0.217363,0.119015,3.17987e-05,0.21618,0.243266,0.107021,0.0310605,0.20272,0.392453,0.61565,0.0780061,0.0559668,0.230477,0.279823,0.295555,0.502112,0.000385252,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.1267,0.54832,0.000773574,0.296013,0.282366,0.0434876,0.127256,0.0392766,0.548059,0.25423,0.490559,0.45013,0.500698,0.472542,0.322168,0.399934,0.0074346,1.90238e-06,0.14198,0.590496,0.603763,0.00835925,0.259354,0.14959,0.293249,0.290703,0.254935,0.00037277,0.478691,0.360199,0.241059,0.0236144,0.000453758,0.0111989,0.212703,0.201391,0.364079,0.680099,0.0119013,0.104625,0.206595,0.328518,0.00865679,0.0541711,0.00456853,0.142433,2.66735e-06,0.00104728,0.209437,0.000136886,0.0514874,0.0651244,8.0873e-05,0.464001,0.00127982,0.214786,0.150592,0.00283087,0.315519,0.261575,0.257956,0.264245,0.0831707,0.0602936,0.16985,0.00284816,0.475063,0.202522,0.0180408,6.51978e-08,0.126097,0.0912229,0.442469,0.212239,0.294954,0.156999,0.0742603,0.301684,0.00017745,0.234254,0.0011219,0.000254095,0.365184,0.15578,0.620526,0.0958848,0.416164,0.000272349,0.132999,0.479581,0.62689,0.884725,0.00068395,0.284496,0.000881831,0.512178,0.201413,0.034169,0.321001,0.0381838,0.552023,0.180735,0.439629,0.216102,0.00340007,0.109605,0.0924199,0.582542,0.00233141,0.0175854,0.129731,0.0183052,0.0342559,0.454761,0.639483,0.142363,0.452129,0.301581,0.0376831,0.346776,0.00395053,0.545655,0.438176,0.349112,0.155207,0.385425,0.0531591,0.0250382,0.0866806,0.382854,0.000370843,0.478745,6.88674e-06,0.319747,0.0277333,0.0498053,0.241014,0.282281,0.000452027,0.2536,0.246827,0.0519643,0.12664,0.00162371,0.050476,0.358813,0.668972,0.210703,0.493455,0.0685505,0.0243196,0.00956892,0.0280449,0.00199432,0.022473,0.42505,0.254628,0.00910372,0.0286377,0.416962,0.264955,0.0828233,0.0473484,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.0582227,0.00407337,0.00757805,0.266651,0.187728,0.0292096,0.249415,0.283107,0.285648,0.10809,0.0890097,0.279553,0.00344219,0.240967,0.0137102,0.256687,0.0432189,0.122439,0.16188,0.0293669,0.0469743,0.353147,0.112422,0.000953659,0.267687,0.315656,0.284866,0.00406065,0.00400315,0.338547,0.147872,0.0191872,0.00540153,0.210125,0.292967,0.0258076,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.0369803,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.00326229,0.162089,0.330223,0.0874139,0.029604,0.207281,0.327401,0.0205476,0.0429696,0.161712,0.237871,0.0311922,0.00468829,0.328852,0.0627948,0.262022,0.274403,0.266687,0.184534,0.248707,0.0567862,0.15156,0.0460134,0.00673322,0.0271466,0.25788,0.181895,0.000242325,0.0528669,0.0221551,0.170837,0.327002,0.0452813,0.222656,0.00239762,0.127111,0.037179,0.0888526,0.355805,0.279739,0.108118,0.00363197,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.0627853,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.038024,0.373453,0.362662,0.433518,0.0181468,0.00831677,0.0600054,0.257476,0.291176,0.081972,0.322827,0.229571,0.0105454,0.335984,0.171704,0.208256,0.265058,0.00347609,0.0756763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}}
}}

Revision as of 14:25, 19 October 2012


Full id: C2789_aorta_Fibroblast_ductus_seminal_pharyngeal_amygdala_occipital



Phase1 CAGE Peaks

Hg19::chr4:30721263..30721290,+p@chr4:30721263..30721290
+
Hg19::chr4:30721292..30721311,+p@chr4:30721292..30721311
+
Hg19::chr4:30721690..30721722,+p2@PCDH7
Hg19::chr4:30721968..30722034,+p1@PCDH7


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
organ part4.14e-20218
anatomical cluster7.95e-20373
multi-tissue structure6.97e-19342
multi-cellular organism2.98e-18656
neurectoderm3.93e-1886
organ system subdivision1.07e-17223
adult organism1.45e-17114
neural plate1.47e-1782
presumptive neural plate1.47e-1782
neural tube9.29e-1756
neural rod9.29e-1756
future spinal cord9.29e-1756
neural keel9.29e-1756
central nervous system1.79e-1681
ectoderm-derived structure6.47e-16171
ectoderm6.47e-16171
presumptive ectoderm6.47e-16171
ecto-epithelium1.12e-15104
brain grey matter2.31e-1534
gray matter2.31e-1534
regional part of nervous system2.77e-1553
regional part of brain2.77e-1553
brain4.32e-1568
future brain4.32e-1568
telencephalon6.81e-1534
pre-chordal neural plate7.78e-1561
cerebral hemisphere1.24e-1432
embryo1.36e-14592
nervous system2.53e-1489
regional part of telencephalon2.70e-1432
regional part of cerebral cortex5.71e-1422
regional part of forebrain1.27e-1341
forebrain1.27e-1341
anterior neural tube1.27e-1341
future forebrain1.27e-1341
anatomical system3.71e-13624
embryonic structure4.80e-13564
anatomical group6.39e-13625
neocortex6.74e-1320
developing anatomical structure7.85e-13581
germ layer1.50e-12560
germ layer / neural crest1.50e-12560
embryonic tissue1.50e-12560
presumptive structure1.50e-12560
germ layer / neural crest derived structure1.50e-12560
epiblast (generic)1.50e-12560
cerebral cortex4.50e-1225
pallium4.50e-1225
epithelium6.70e-12306
cell layer3.71e-11309
structure with developmental contribution from neural crest5.08e-11132
organ2.39e-10503
anatomical conduit1.61e-09240
organ segment2.84e-0998
tube5.79e-09192
endoderm-derived structure1.36e-07160
endoderm1.36e-07160
presumptive endoderm1.36e-07160


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#1488231.35850016966410.001492676882047230.009542953041389
ZNF263#1012748.221841637010680.0002187871180958320.00249643918134061



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.