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Coexpression cluster:C2429: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.02e-23!115;UBERON:0001017!3.77e-14!82;UBERON:0001049!8.41e-14!57;UBERON:0005068!8.41e-14!57;UBERON:0006241!8.41e-14!57;UBERON:0007135!8.41e-14!57;UBERON:0005743!1.21e-13!86;UBERON:0002616!3.14e-12!59;UBERON:0000073!6.65e-12!94;UBERON:0001016!6.65e-12!94;UBERON:0000955!6.98e-12!69;UBERON:0006238!6.98e-12!69;UBERON:0002346!2.37e-10!90;UBERON:0003075!4.53e-10!86;UBERON:0007284!4.53e-10!86;UBERON:0002780!1.23e-09!41;UBERON:0001890!1.23e-09!41;UBERON:0006240!1.23e-09!41;UBERON:0001893!2.00e-09!34;UBERON:0002020!3.22e-09!34;UBERON:0003528!3.22e-09!34;UBERON:0002791!3.64e-09!33;UBERON:0003080!5.09e-09!42;UBERON:0001869!6.08e-09!32;UBERON:0002619!3.68e-08!22;UBERON:0000956!4.53e-08!25;UBERON:0000203!4.53e-08!25;UBERON:0001950!1.70e-07!20
|ontology_enrichment_uberon=UBERON:0007023!1.02e-23!115;UBERON:0001017!3.77e-14!82;UBERON:0001049!8.41e-14!57;UBERON:0005068!8.41e-14!57;UBERON:0006241!8.41e-14!57;UBERON:0007135!8.41e-14!57;UBERON:0005743!1.21e-13!86;UBERON:0002616!3.14e-12!59;UBERON:0000073!6.65e-12!94;UBERON:0001016!6.65e-12!94;UBERON:0000955!6.98e-12!69;UBERON:0006238!6.98e-12!69;UBERON:0002346!2.37e-10!90;UBERON:0003075!4.53e-10!86;UBERON:0007284!4.53e-10!86;UBERON:0002780!1.23e-09!41;UBERON:0001890!1.23e-09!41;UBERON:0006240!1.23e-09!41;UBERON:0001893!2.00e-09!34;UBERON:0002020!3.22e-09!34;UBERON:0003528!3.22e-09!34;UBERON:0002791!3.64e-09!33;UBERON:0003080!5.09e-09!42;UBERON:0001869!6.08e-09!32;UBERON:0002619!3.68e-08!22;UBERON:0000956!4.53e-08!25;UBERON:0000203!4.53e-08!25;UBERON:0001950!1.70e-07!20
|tf_chipseq_enrich=CTBP2#1488;2:31.3585001696641:0.00149267688204723:0.00954061694517323!EP300#2033;3:5.0804562946674:0.0114429840539824:0.0418890224890945!HDAC2#3066;3:10.0617151774697:0.0015637275447474:0.00992429150740603!RXRA#6256;3:15.05596285435:0.000475830799730358:0.00433868455500601!TCF7L2#6934;3:8.07763242235301:0.00297838168583462:0.0158622745990251!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342385393645589
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299,0.198844,0.104946,0.127738,0.00176575,0.161213,0.000308325,0.0737069,0.357807,0.621787,0.178782,0.019419,0.0866228,0.271849,0.00477271,0.105411,0.0997542,0.0237068,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.0439557,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.287316,0.187953,0.051459,0.00686557,0.0726892,0.18732,0.0589328,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.0303023,1.7427e-06,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.00808856,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.0210393,0.00136699,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.00127423,0.0451012,0.0976639,0.351199,0.0360207,0.00342886,0.278645,0.0769795,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.0300882,0.0803251,0.0278785,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.014226,0.226359,7.74729e-06,3.10129e-05,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.00154813,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.0269564,0.137423,0.0448074,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.0988568,0.223717,0.107609,0.196838,0.0826805,5.61987e-07,0.193021,0.608002,0.0219712,0.00463136,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.0475113,0.0578865,0.364334,0.0127656,0.110256,0.415419,0.14794,0.147307,0.240761,0.0277041,0.124417,0.335582,0.0567624,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.00134589,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.00303153,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,6.08835e-05,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.459091,0.189333,0.154964,0.296013,0.649813,0.537932,0.127256,0.170061,0.548059,0.25423,0.146971,0.0229254,0.00559995,0.472542,0.685908,0.747471,0.529642,0.00816509,0.483077,0.061678,0.603763,0.541914,0.627201,3.52173e-05,0.00709718,0.0470729,0.622694,8.21916e-06,0.0284983,0.360199,0.241059,0.000842547,0.0021436,0.0768516,0.212703,0.56318,0.364079,0.680099,0.579886,0.0181617,0.569409,0.328518,0.00865679,0.00059285,0.000239931,0.483764,0.000503744,0.453065,0.209437,1.16585e-08,0.0514874,0.598945,4.40515e-07,0.0255132,0.000283806,0.214786,0.00506481,0.000629358,0.137711,0.261575,0.257956,0.264245,0.0831707,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.0742603,0.0999766,0.39549,0.234254,0.357409,0.00476468,0.0408829,0.50338,0.00320596,0.404625,0.759068,0.00251166,0.715362,0.479581,0.62689,0.635682,0.274432,0.284496,0.16228,0.512178,0.201413,0.00233197,0.684899,0.0381838,0.047857,0.0174164,0.775168,0.216102,0.0355932,0.109605,0.397869,0.217863,0.00233141,0.102502,0.463987,0.627953,0.503881,0.454761,0.639483,0.483658,0.122467,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.741477,0.0862349,0.307816,0.461541,0.386339,0.382854,0.0650585,0.478745,0.24434,0.319747,0.475047,0.197104,0.608127,0.282281,0.0710918,0.2536,0.246827,0.564333,0.00168296,0.387134,0.559969,0.358813,0.303004,0.574252,0.493455,0.346636,0.0243196,0.348802,0.0280449,0.215342,0.447581,0.42505,0.254628,0.355111,0.0286377,0.416962,0.632833,0.0828233,0.152547,0.264038,0.22798,0.102495,0.350933,0.0383658,0.0446972,0.24452,0.329284,0.0029143,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.0597961,0.00394708,0.546295,0.231754,0.249415,0.283107,0.0453548,0.427316,0.391071,0.279553,0.0358792,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.0469743,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.036547,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.00376397,0.373453,0.362662,0.433518,0.184359,0.00831677,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.0433477,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951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}}
}}

Revision as of 11:37, 5 September 2012


Full id: C2429_alveolar_synovial_gastric_signet_hepatoblastoma_small_colon



Phase1 CAGE Peaks

Hg19::chr17:63534783..63534784,-p@chr17:63534783..63534784
-
Hg19::chr17:63556428..63556442,-p1@AXIN2
Hg19::chr17:63556446..63556459,-p3@AXIN2
Hg19::chr17:63556476..63556485,-p5@AXIN2


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 organism1.02e-23115
central nervous system3.77e-1482
neural tube8.41e-1457
neural rod8.41e-1457
future spinal cord8.41e-1457
neural keel8.41e-1457
regional part of brain3.14e-1259
regional part of nervous system6.65e-1294
nervous system6.65e-1294
brain6.98e-1269
future brain6.98e-1269
neurectoderm2.37e-1090
neural plate4.53e-1086
presumptive neural plate4.53e-1086
regional part of forebrain1.23e-0941
forebrain1.23e-0941
future forebrain1.23e-0941
telencephalon2.00e-0934
gray matter3.22e-0934
brain grey matter3.22e-0934
regional part of telencephalon3.64e-0933
anterior neural tube5.09e-0942
cerebral hemisphere6.08e-0932
regional part of cerebral cortex3.68e-0822
cerebral cortex4.53e-0825
pallium4.53e-0825
neocortex1.70e-0720


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#1488231.35850016966410.001492676882047230.00954061694517323
EP300#203335.08045629466740.01144298405398240.0418890224890945
HDAC2#3066310.06171517746970.00156372754474740.00992429150740603
RXRA#6256315.055962854350.0004758307997303580.00433868455500601
TCF7L2#693438.077632422353010.002978381685834620.0158622745990251
ZBTB7A#5134135.513931980906920.009038352821081090.0342385393645589



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.