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Coexpression cluster:C2800: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.55e-33!82;UBERON:0007023!1.93e-32!115;UBERON:0005743!1.46e-31!86;UBERON:0000073!9.25e-31!94;UBERON:0001016!9.25e-31!94;UBERON:0001049!6.18e-30!57;UBERON:0005068!6.18e-30!57;UBERON:0006241!6.18e-30!57;UBERON:0007135!6.18e-30!57;UBERON:0000955!1.09e-26!69;UBERON:0006238!1.09e-26!69;UBERON:0002616!1.75e-26!59;UBERON:0002346!7.73e-24!90;UBERON:0000924!9.30e-24!173;UBERON:0006601!9.30e-24!173;UBERON:0003075!6.92e-23!86;UBERON:0007284!6.92e-23!86;UBERON:0004121!9.17e-23!169;UBERON:0003080!1.41e-22!42;UBERON:0002780!3.92e-22!41;UBERON:0001890!3.92e-22!41;UBERON:0006240!3.92e-22!41;UBERON:0000033!2.07e-19!123;UBERON:0000153!2.61e-19!129;UBERON:0007811!2.61e-19!129;UBERON:0002020!5.35e-19!34;UBERON:0003528!5.35e-19!34;UBERON:0001893!7.99e-19!34;UBERON:0002791!2.27e-18!33;UBERON:0001869!1.48e-17!32;UBERON:0004111!3.10e-17!241;UBERON:0003056!2.77e-16!61;UBERON:0000025!4.88e-16!194;UBERON:0000119!2.86e-14!312;UBERON:0000483!3.34e-14!309;UBERON:0000956!5.90e-14!25;UBERON:0000203!5.90e-14!25;UBERON:0000477!1.37e-13!286;UBERON:0002619!6.78e-13!22;UBERON:0000481!2.93e-12!347;UBERON:0000475!4.41e-12!365;UBERON:0000468!6.81e-12!659;UBERON:0001950!8.00e-12!20;UBERON:0000922!1.82e-11!612;UBERON:0000480!1.94e-09!626;UBERON:0000064!2.26e-09!219;UBERON:0000467!2.77e-09!625;UBERON:0000062!3.23e-09!511;UBERON:0002050!4.06e-09!605;UBERON:0005423!4.06e-09!605;UBERON:0000923!7.57e-09!604;UBERON:0005291!7.57e-09!604;UBERON:0006598!7.57e-09!604;UBERON:0002532!7.57e-09!604;UBERON:0003076!1.82e-08!15;UBERON:0003057!1.82e-08!15;UBERON:0004732!2.72e-07!13
|ontology_enrichment_uberon=UBERON:0001017!1.55e-33!82;UBERON:0007023!1.93e-32!115;UBERON:0005743!1.46e-31!86;UBERON:0000073!9.25e-31!94;UBERON:0001016!9.25e-31!94;UBERON:0001049!6.18e-30!57;UBERON:0005068!6.18e-30!57;UBERON:0006241!6.18e-30!57;UBERON:0007135!6.18e-30!57;UBERON:0000955!1.09e-26!69;UBERON:0006238!1.09e-26!69;UBERON:0002616!1.75e-26!59;UBERON:0002346!7.73e-24!90;UBERON:0000924!9.30e-24!173;UBERON:0006601!9.30e-24!173;UBERON:0003075!6.92e-23!86;UBERON:0007284!6.92e-23!86;UBERON:0004121!9.17e-23!169;UBERON:0003080!1.41e-22!42;UBERON:0002780!3.92e-22!41;UBERON:0001890!3.92e-22!41;UBERON:0006240!3.92e-22!41;UBERON:0000033!2.07e-19!123;UBERON:0000153!2.61e-19!129;UBERON:0007811!2.61e-19!129;UBERON:0002020!5.35e-19!34;UBERON:0003528!5.35e-19!34;UBERON:0001893!7.99e-19!34;UBERON:0002791!2.27e-18!33;UBERON:0001869!1.48e-17!32;UBERON:0004111!3.10e-17!241;UBERON:0003056!2.77e-16!61;UBERON:0000025!4.88e-16!194;UBERON:0000119!2.86e-14!312;UBERON:0000483!3.34e-14!309;UBERON:0000956!5.90e-14!25;UBERON:0000203!5.90e-14!25;UBERON:0000477!1.37e-13!286;UBERON:0002619!6.78e-13!22;UBERON:0000481!2.93e-12!347;UBERON:0000475!4.41e-12!365;UBERON:0000468!6.81e-12!659;UBERON:0001950!8.00e-12!20;UBERON:0000922!1.82e-11!612;UBERON:0000480!1.94e-09!626;UBERON:0000064!2.26e-09!219;UBERON:0000467!2.77e-09!625;UBERON:0000062!3.23e-09!511;UBERON:0002050!4.06e-09!605;UBERON:0005423!4.06e-09!605;UBERON:0000923!7.57e-09!604;UBERON:0005291!7.57e-09!604;UBERON:0006598!7.57e-09!604;UBERON:0002532!7.57e-09!604;UBERON:0003076!1.82e-08!15;UBERON:0003057!1.82e-08!15;UBERON:0004732!2.72e-07!13
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99,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.357807,0.254051,0.178782,0.019419,0.0866228,0.0408454,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.0372041,0.159873,0.142462,0.143935,0.332403,0.0379537,0.000812168,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.000207818,0.170848,0.144756,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.0180783,0.216557,0.182956,0.116818,0.0883765,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.787798,0.189107,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.833813,0.0150607,0.278645,0.0769795,0.155708,0.248017,0.22995,0.091341,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.0832234,0.0939463,0.286748,0.0114526,0.0471607,0.163865,0.226359,0.0464703,0.709625,0.265324,0.043404,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.0466818,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.0269564,0.137423,0.0448074,0.0754883,0.299492,0.100006,0.0756617,0.197817,0.0345492,0.00462092,0.133127,0.410303,0.223717,0.426452,0.0207859,0.0826805,0.246601,0.0199582,0.608002,4.05918e-06,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.0262879,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.00808241,0.335582,0.317428,0.182843,0.130771,0.00777449,0.135777,0.147842,0.0339286,0.217363,0.119015,0.32805,0.21618,0.0323312,0.107021,0.238657,0.20272,0.392453,0.0724243,0.0780061,0.315336,0.230477,0.279823,0.295555,0.154895,0.0103352,0.0478217,0.158752,0.170854,0.0575231,0.174063,0.0368787,0.0245723,0.54832,0.502211,0.296013,0.282366,0.000152471,0.459994,0.00698686,0.548059,0.25423,0.490559,0.45013,0.00559995,0.0272171,0.111549,0.747471,0.529642,0.244786,0.483077,0.224887,0.603763,0.541914,0.0778742,0.00784768,0.0217959,0.0470729,0.0757071,5.85899e-05,0.0284983,0.360199,0.241059,1.9925e-08,0.00893555,0.365494,0.212703,0.0515679,0.364079,0.680099,0.579886,0.421038,0.0537414,6.0015e-05,0.0458249,0.310552,0.324103,0.142433,0.261345,0.000195845,0.209437,0.0404917,0.000572229,0.598945,0.0221843,0.464001,0.152018,0.0118057,1.00678e-05,0.00283087,0.0500888,0.261575,0.257956,1.75737e-05,0.379063,0.326516,0.16985,0.436016,0.136753,0.0220519,0.183837,0.507324,0.126097,0.0146433,0.0215868,0.212239,0.00548706,0.156999,0.0106153,0.025886,0.39549,0.234254,0.357409,0.599068,0.365184,0.034133,0.0746831,0.404625,0.172147,0.0187136,6.99283e-06,0.139684,0.077723,8.71675e-05,0.274432,0.284496,0.512545,0.162017,0.563206,0.034169,0.110875,0.263302,0.192292,0.180735,0.0182207,0.216102,0.0355932,0.109605,0.0149457,0.582542,0.02784,0.417131,0.0038466,0.0183052,0.156131,0.454761,0.271678,0.00471559,0.122467,0.301581,0.261657,0.346776,0.0260085,0.545655,0.438176,0.349112,0.0124698,0.0134085,0.307816,0.461541,0.000154397,0.382854,0.598787,0.0285097,0.07062,0.0576521,0.0277333,2.35715e-05,0.0690544,0.282281,0.612712,0.2536,0.246827,0.564333,0.00849832,0.387134,0.559969,0.0738474,2.08494e-05,0.574252,0.493455,0.346636,0.457747,0.348802,0.137708,0.0118751,0.022473,0.42505,0.00339873,0.131374,0.0286377,0.416962,0.0806585,0.0125878,0.387805,0.000288393,0.22798,0.102495,6.26089e-06,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.0643357,0.210656,0.246234,0.02408,0.281295,0.00397584,0.118257,0.125087,0.215123,0.321224,0.0265924,0.325254,0.0392149,0.0460393,0.231754,0.249415,0.283107,0.285648,0.0191181,0.391071,0.0433305,0.000250206,0.0316941,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.00521493,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,9.7616e-07,0.338547,0.147872,0.0191872,0.293546,0.210125,0.00536668,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.113839,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.0346487,0.162089,0.0617695,0.0016375,0.233244,0.207281,0.327401,7.88771e-05,0.27845,0.161712,0.237871,0.239139,0.000155126,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,8.01031e-09,0.15156,1.58085e-06,0.313858,0.223773,0.036547,0.00116104,1.40447e-05,0.0528669,4.14804e-06,0.170837,0.327002,0.00492748,0.222656,0.028353,0.127111,0.259989,0.0888526,0.355805,0.0433915,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.0805224,0.0755696,0.0201006,0.00121144,0.00831677,0.325785,0.257476,0.291176,0.376537,0.00739196,0.229571,0.359036,0.335984,0.171704,4.76577e-06,0.0387226,0.256405,0.0109327,0.302133,0.00207843,0.151361,0.279606,0.286696,0.150674,0.00325002,0.246177,0.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}}
}}

Revision as of 13:19, 5 September 2012


Full id: C2800_pineal_teratocarcinoma_hepatoblastoma_optic_testicular_spinal_H9



Phase1 CAGE Peaks

Hg19::chr5:115808548..115808552,-p@chr5:115808548..115808552
-
Hg19::chr5:115910459..115910474,-p2@SEMA6A
Hg19::chr5:115910475..115910491,-p3@SEMA6A
Hg19::chr5:115910498..115910536,-p1@SEMA6A


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>

Cell Type
Ontology termp-valuen
melanocyte2.91e-0710
melanoblast2.91e-0710
Uber Anatomy
Ontology termp-valuen
central nervous system1.55e-3382
adult organism1.93e-32115
regional part of nervous system9.25e-3194
nervous system9.25e-3194
neural tube6.18e-3057
neural rod6.18e-3057
future spinal cord6.18e-3057
neural keel6.18e-3057
brain1.09e-2669
future brain1.09e-2669
regional part of brain1.75e-2659
neurectoderm7.73e-2490
ectoderm9.30e-24173
presumptive ectoderm9.30e-24173
neural plate6.92e-2386
presumptive neural plate6.92e-2386
ectoderm-derived structure9.17e-23169
anterior neural tube1.41e-2242
regional part of forebrain3.92e-2241
forebrain3.92e-2241
future forebrain3.92e-2241
head2.07e-19123
anterior region of body2.61e-19129
craniocervical region2.61e-19129
gray matter5.35e-1934
brain grey matter5.35e-1934
telencephalon7.99e-1934
regional part of telencephalon2.27e-1833
cerebral hemisphere1.48e-1732
anatomical conduit3.10e-17241
pre-chordal neural plate2.77e-1661
tube4.88e-16194
cell layer2.86e-14312
epithelium3.34e-14309
cerebral cortex5.90e-1425
pallium5.90e-1425
anatomical cluster1.37e-13286
regional part of cerebral cortex6.78e-1322
multi-tissue structure2.93e-12347
organism subdivision4.41e-12365
multi-cellular organism6.81e-12659
neocortex8.00e-1220
embryo1.82e-11612
anatomical group1.94e-09626
organ part2.26e-09219
anatomical system2.77e-09625
organ3.23e-09511
embryonic structure4.06e-09605
developing anatomical structure4.06e-09605
germ layer7.57e-09604
embryonic tissue7.57e-09604
presumptive structure7.57e-09604
epiblast (generic)7.57e-09604
posterior neural tube1.82e-0815
chordal neural plate1.82e-0815
segmental subdivision of nervous system2.72e-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
BCLAF1#9774316.23948570759140.000380256706766480.00376718176797423
CTBP2#1488347.03775025449611.60047699357395e-050.000370379385623466
EBF1#187936.679850134926750.005184294118278910.0240598335148832
EP300#203335.08045629466740.01144298405398240.041912527586935
IRF4#3662316.43588451505810.0003669431395554610.00365993453844263
JUND#372735.245997956403270.01043432751748420.0387109065965164
NANOG#79923321.93358386075950.0001557535816382770.00196529519303129
PAX5#507935.002174148383370.01196533174786410.0435174565543661
POU2F2#545236.829593043306890.004860473775203740.0227725548700598
RAD21#588537.766275421592250.0033411193858720.0172735591080187
REST#597837.237521537096020.004104697304192610.0195892196011959
RFX5#599339.035933120396320.002144561191324070.0123880434878703
TAF7#687938.574802053692940.00250055433515240.0140383483421481
TCF12#693837.975848676639820.003090920396013070.0162872167123718
TCF7L2#693438.077632422353010.002978381685834620.0158671294065947
TRIM28#10155313.94289378394690.0005972858184258420.00499639035567292
USF1#739134.771124457905970.01370465887188020.0483270036776274
ZEB1#6935312.66632401315790.000793336075912850.00613515190168546
ZNF263#1012736.166381227758010.006539814347975980.0279876934391191



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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