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Coexpression cluster:C2789: Difference between revisions

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|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: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
|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 14:18, 5 September 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
multi-cellular organism6.00e-23659
organ part1.21e-22219
multi-tissue structure6.68e-21347
neurectoderm4.41e-2090
neural plate1.95e-1986
presumptive neural plate1.95e-1986
ectoderm2.11e-19173
presumptive ectoderm2.11e-19173
embryo5.32e-19612
ectoderm-derived structure1.08e-18169
adult organism2.19e-18115
neural tube1.99e-1757
neural rod1.99e-1757
future spinal cord1.99e-1757
neural keel1.99e-1757
organism subdivision3.59e-17365
embryonic structure3.63e-17605
developing anatomical structure3.63e-17605
anatomical system6.32e-17625
central nervous system7.34e-1782
germ layer1.01e-16604
embryonic tissue1.01e-16604
presumptive structure1.01e-16604
epiblast (generic)1.01e-16604
anatomical group1.29e-16626
head2.66e-16123
regional part of nervous system4.77e-1694
nervous system4.77e-1694
pre-chordal neural plate5.68e-1661
gray matter5.76e-1634
brain grey matter5.76e-1634
epithelium7.31e-16309
brain1.14e-1569
future brain1.14e-1569
telencephalon1.56e-1534
cerebral hemisphere2.04e-1532
anterior region of body2.47e-15129
craniocervical region2.47e-15129
regional part of brain2.52e-1559
anatomical cluster3.40e-15286
cell layer5.26e-15312
regional part of telencephalon5.87e-1533
regional part of forebrain9.11e-1541
forebrain9.11e-1541
future forebrain9.11e-1541
anterior neural tube1.46e-1442
regional part of cerebral cortex3.47e-1422
neocortex4.44e-1320
organ9.54e-13511
cerebral cortex1.09e-1225
pallium1.09e-1225
anatomical conduit4.11e-12241
tube1.42e-10194
organ segment2.11e-0997
endoderm-derived structure3.86e-08169
endoderm3.86e-08169
presumptive endoderm3.86e-08169


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.

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