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Coexpression cluster:C2873: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!7.17e-37!115;UBERON:0003075!1.33e-28!86;UBERON:0007284!1.33e-28!86;UBERON:0002346!2.09e-27!90;UBERON:0001049!5.14e-26!57;UBERON:0005068!5.14e-26!57;UBERON:0006241!5.14e-26!57;UBERON:0007135!5.14e-26!57;UBERON:0005743!6.59e-26!86;UBERON:0002616!4.06e-24!59;UBERON:0001017!5.54e-24!82;UBERON:0000477!6.86e-24!286;UBERON:0000073!1.31e-23!94;UBERON:0001016!1.31e-23!94;UBERON:0004111!2.94e-23!241;UBERON:0000955!1.58e-22!69;UBERON:0006238!1.58e-22!69;UBERON:0000025!6.19e-22!194;UBERON:0003056!9.99e-21!61;UBERON:0003080!2.59e-18!42;UBERON:0002780!6.51e-18!41;UBERON:0001890!6.51e-18!41;UBERON:0006240!6.51e-18!41;UBERON:0000483!7.68e-18!309;UBERON:0000119!9.43e-18!312;UBERON:0000153!2.25e-17!129;UBERON:0007811!2.25e-17!129;UBERON:0000033!4.34e-17!123;UBERON:0004121!3.62e-16!169;UBERON:0000924!7.81e-16!173;UBERON:0006601!7.81e-16!173;UBERON:0001893!7.92e-16!34;UBERON:0002020!1.05e-15!34;UBERON:0003528!1.05e-15!34;UBERON:0002791!2.97e-15!33;UBERON:0001869!4.93e-15!32;UBERON:0000475!2.15e-14!365;UBERON:0002619!1.06e-13!22;UBERON:0000481!9.66e-13!347;UBERON:0001950!1.22e-12!20;UBERON:0000956!1.06e-11!25;UBERON:0000203!1.06e-11!25;UBERON:0000468!1.48e-11!659;UBERON:0000064!3.53e-10!219;UBERON:0000467!3.03e-09!625;UBERON:0000480!4.19e-09!626;UBERON:0003076!6.24e-09!15;UBERON:0003057!6.24e-09!15;UBERON:0000062!8.86e-08!511;UBERON:0004732!1.83e-07!13;UBERON:0007625!3.18e-07!11;UBERON:0004733!3.55e-07!12;UBERON:0002028!3.55e-07!12;UBERON:0007277!3.55e-07!12
|ontology_enrichment_uberon=UBERON:0007023!1.09e-33!114;UBERON:0003075!2.51e-29!82;UBERON:0007284!2.51e-29!82;UBERON:0002346!6.58e-28!86;UBERON:0001049!1.40e-24!56;UBERON:0005068!1.40e-24!56;UBERON:0006241!1.40e-24!56;UBERON:0007135!1.40e-24!56;UBERON:0000477!2.80e-24!373;UBERON:0000073!1.71e-22!53;UBERON:0002616!1.71e-22!53;UBERON:0010371!1.92e-22!104;UBERON:0001017!4.19e-22!81;UBERON:0000955!2.38e-21!68;UBERON:0006238!2.38e-21!68;UBERON:0003056!4.24e-21!61;UBERON:0001016!6.32e-21!89;UBERON:0010314!4.75e-20!132;UBERON:0004111!1.40e-18!240;UBERON:0000025!6.83e-18!192;UBERON:0002780!3.07e-17!41;UBERON:0001890!3.07e-17!41;UBERON:0003080!3.07e-17!41;UBERON:0006240!3.07e-17!41;UBERON:0011216!8.25e-17!223;UBERON:0000483!9.00e-17!306;UBERON:0000119!1.33e-16!309;UBERON:0004121!9.96e-15!171;UBERON:0000924!9.96e-15!171;UBERON:0006601!9.96e-15!171;UBERON:0000481!1.88e-14!342;UBERON:0001893!2.69e-14!34;UBERON:0003528!3.33e-14!34;UBERON:0002020!3.33e-14!34;UBERON:0001869!1.85e-13!32;UBERON:0002791!3.13e-13!32;UBERON:0001950!7.10e-12!20;UBERON:0002619!1.04e-11!22;UBERON:0000956!2.24e-10!25;UBERON:0000203!2.24e-10!25;UBERON:0000468!4.05e-10!656;UBERON:0000064!8.09e-09!218;UBERON:0000467!1.27e-08!624;UBERON:0003076!1.35e-08!15;UBERON:0003057!1.35e-08!15;UBERON:0000480!1.61e-08!625;UBERON:0000062!1.63e-08!503;UBERON:0007625!3.17e-07!11;UBERON:0004732!3.99e-07!13
|tf_chipseq_enrich=CTCFL#140690;3:14.8098557692308:0.000499629176756334:0.00441088517254901!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.0099925442818971!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342609077482901
|tf_chipseq_enrich=CTCFL#140690;3:14.8098557692308:0.000499629176756334:0.00441088517254901!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.0099925442818971!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342609077482901
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91994,0.268299,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.0104244,7.00333e-05,0.178782,0.019419,0.0866228,0.0408454,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.000719925,0.220368,0.0367692,0.064656,0.226143,0.000447146,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.164404,0.013521,0.142462,0.143935,0.0626466,0.0379537,1.93544e-07,0.0012877,0.051459,0.114868,0.0726892,0.18732,0.32305,0.00454179,0.245002,0.170848,0.0303627,0.00598877,0.363016,0.100188,0.223102,0.107653,0.235857,1.7427e-06,0.191914,0.184022,0.216557,0.182956,0.116818,0.000162768,0.0109594,0.0625685,0.124464,0.000168137,0.173134,0.101893,0.142875,0.167635,0.171311,5.44444e-06,0.0465855,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.00979133,7.77569e-09,0.758305,0.278645,0.365775,0.0128057,0.248017,0.028736,1.53275e-05,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.0832234,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,2.93216e-10,4.77058e-15,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.000290291,0.0994829,0.0604041,0.144185,0.0925862,0.00516485,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.00484807,0.0754883,0.299492,0.100006,0.0109294,0.00151424,0.251078,0.279874,0.133127,0.00022115,0.0022412,0.00256165,0.196838,0.0826805,0.246601,0.193021,6.41174e-06,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.0127656,0.110256,0.000238291,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.00777449,0.135777,0.011511,0.0339286,0.217363,0.119015,0.690952,0.00200865,0.243266,0.00594269,0.238657,0.20272,0.0896967,0.0164195,0.0780061,0.315336,0.230477,0.279823,0.295555,0.154895,1.21755e-10,0.0478217,0.158752,0.170854,0.0575231,0.0161134,0.0368787,0.459091,0.54832,0.154964,0.296013,0.649813,0.537932,0.459994,0.0392766,0.548059,0.25423,0.490559,0.45013,0.500698,0.472542,0.685908,0.0510811,0.0410736,0.0943307,0.0046877,0.590496,0.603763,0.184287,0.627201,2.65013e-07,3.58478e-08,0.290703,0.00328655,0.366999,0.139104,0.0744652,0.00278148,0.657141,0.253797,0.0111989,0.212703,0.56318,0.0110532,0.0287777,0.215551,0.104625,0.569409,0.328518,0.187186,0.310552,0.000239931,0.00472069,0.00234287,0.0201581,0.209437,0.11765,1.45606e-05,0.00249952,0.0016718,0.0255132,5.69321e-05,0.579004,3.77804e-08,0.000629358,1.76282e-07,0.261575,0.257956,0.264245,0.0831707,0.326516,0.00100422,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.0912229,0.442469,0.212239,0.294954,0.156999,0.35974,0.0999766,0.39549,0.234254,0.357409,0.0543683,0.365184,0.034133,0.252827,0.0958848,0.759068,0.424691,0.00931622,0.479581,0.000552112,2.97623e-06,0.0207342,0.284496,0.512545,0.512178,0.201413,9.62413e-05,0.000199599,0.263302,0.192292,0.180735,6.46564e-08,0.216102,0.254659,0.109605,0.397869,0.0121932,0.226491,0.0175854,0.463987,0.627953,0.503881,0.454761,0.0840572,0.483658,0.122467,0.301581,0.261657,0.346776,0.466529,0.187223,0.438176,0.349112,0.0485429,0.0862349,0.307816,0.0250382,0.386339,0.382854,0.598787,0.478745,0.611661,0.319747,0.475047,0.557967,0.608127,0.282281,0.0159965,0.2536,0.246827,0.202347,0.000288092,0.0870695,0.559969,0.358813,0.100705,0.210703,0.493455,0.346636,0.457747,0.348802,0.476541,0.215342,0.447581,0.42505,0.254628,0.0382032,0.479347,0.416962,0.632833,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.0445044,0.0453548,0.427316,0.391071,0.0433305,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.0099749,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.0078603,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.0176484,0.253768,0.30702,0.202977,0.170837,0.000748107,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.000477314,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.00104239,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.00304766,0.35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}}
}}

Revision as of 14:31, 19 October 2012


Full id: C2873_cerebellum_pineal_mesothelioma_Endothelial_Lymphatic_merkel_chronic



Phase1 CAGE Peaks

Hg19::chr7:103629614..103629646,-p5@RELN
Hg19::chr7:103630045..103630056,-p3@RELN
Hg19::chr7:103630073..103630088,-p2@RELN
Hg19::chr7:103630096..103630116,-p1@RELN


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
adult organism1.09e-33114
neural plate2.51e-2982
presumptive neural plate2.51e-2982
neurectoderm6.58e-2886
neural tube1.40e-2456
neural rod1.40e-2456
future spinal cord1.40e-2456
neural keel1.40e-2456
anatomical cluster2.80e-24373
regional part of nervous system1.71e-2253
regional part of brain1.71e-2253
ecto-epithelium1.92e-22104
central nervous system4.19e-2281
brain2.38e-2168
future brain2.38e-2168
pre-chordal neural plate4.24e-2161
nervous system6.32e-2189
structure with developmental contribution from neural crest4.75e-20132
anatomical conduit1.40e-18240
tube6.83e-18192
regional part of forebrain3.07e-1741
forebrain3.07e-1741
anterior neural tube3.07e-1741
future forebrain3.07e-1741
organ system subdivision8.25e-17223
epithelium9.00e-17306
cell layer1.33e-16309
ectoderm-derived structure9.96e-15171
ectoderm9.96e-15171
presumptive ectoderm9.96e-15171
multi-tissue structure1.88e-14342
telencephalon2.69e-1434
brain grey matter3.33e-1434
gray matter3.33e-1434
cerebral hemisphere1.85e-1332
regional part of telencephalon3.13e-1332
neocortex7.10e-1220
regional part of cerebral cortex1.04e-1122
cerebral cortex2.24e-1025
pallium2.24e-1025
multi-cellular organism4.05e-10656
organ part8.09e-09218
anatomical system1.27e-08624
posterior neural tube1.35e-0815
chordal neural plate1.35e-0815
anatomical group1.61e-08625
organ1.63e-08503
pigment epithelium of eye3.17e-0711
segmental subdivision of nervous system3.99e-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
CTCFL#140690314.80985576923080.0004996291767563340.00441088517254901
E2F6#187645.017155731697390.00157802193473060.0099925442818971
ZBTB7A#5134135.513931980906920.009038352821081090.0342609077482901



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.