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Coexpression cluster:C449: Difference between revisions

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|ontology_enrichment_disease=DOID:305!3.31e-09!106;DOID:1749!3.13e-07!14;DOID:0050687!9.33e-07!143
|ontology_enrichment_disease=DOID:305!3.31e-09!106;DOID:1749!3.13e-07!14;DOID:0050687!9.33e-07!143
|ontology_enrichment_uberon=UBERON:0001049!4.86e-26!57;UBERON:0005068!4.86e-26!57;UBERON:0006241!4.86e-26!57;UBERON:0007135!4.86e-26!57;UBERON:0001017!5.86e-26!82;UBERON:0007023!2.05e-24!115;UBERON:0005743!2.92e-24!86;UBERON:0000073!4.96e-23!94;UBERON:0001016!4.96e-23!94;UBERON:0003080!9.23e-23!42;UBERON:0002780!1.66e-22!41;UBERON:0001890!1.66e-22!41;UBERON:0006240!1.66e-22!41;UBERON:0000955!2.02e-21!69;UBERON:0006238!2.02e-21!69;UBERON:0002616!2.37e-20!59;UBERON:0004121!4.35e-20!169;UBERON:0000924!2.28e-19!173;UBERON:0006601!2.28e-19!173;UBERON:0002020!2.59e-19!34;UBERON:0003528!2.59e-19!34;UBERON:0001893!8.37e-19!34;UBERON:0003075!1.67e-18!86;UBERON:0007284!1.67e-18!86;UBERON:0001869!3.41e-18!32;UBERON:0002791!4.73e-18!33;UBERON:0002346!2.38e-17!90;UBERON:0000153!1.05e-16!129;UBERON:0007811!1.05e-16!129;UBERON:0002619!1.12e-16!22;UBERON:0000033!1.42e-16!123;UBERON:0001950!3.67e-15!20;UBERON:0003056!2.16e-14!61;UBERON:0000956!2.22e-13!25;UBERON:0000203!2.22e-13!25;UBERON:0000064!1.01e-12!219;UBERON:0000062!2.78e-12!511;UBERON:0004119!1.45e-11!169;UBERON:0000925!1.45e-11!169;UBERON:0006595!1.45e-11!169;UBERON:0000481!5.95e-10!347;UBERON:0000922!7.91e-10!612;UBERON:0004111!8.00e-10!241;UBERON:0001007!8.47e-10!155;UBERON:0001555!8.47e-10!155;UBERON:0007026!8.47e-10!155;UBERON:0000467!1.54e-09!625;UBERON:0000923!1.57e-09!604;UBERON:0005291!1.57e-09!604;UBERON:0006598!1.57e-09!604;UBERON:0002532!1.57e-09!604;UBERON:0000480!2.14e-09!626;UBERON:0002050!2.18e-09!605;UBERON:0005423!2.18e-09!605;UBERON:0000475!2.70e-09!365;UBERON:0005911!8.96e-09!82;UBERON:0004921!1.03e-08!129;UBERON:0004185!1.03e-08!129;UBERON:0001004!1.29e-08!72;UBERON:0000483!2.07e-08!309;UBERON:0000468!5.08e-08!659;UBERON:0000119!5.82e-08!312;UBERON:0000025!6.73e-08!194;UBERON:0000477!8.21e-08!286;UBERON:0002308!1.55e-07!9;UBERON:0000125!1.55e-07!9;UBERON:0002420!1.67e-07!9;UBERON:0007245!1.67e-07!9;UBERON:0010009!1.67e-07!9;UBERON:0010011!1.67e-07!9;UBERON:0000454!1.67e-07!9;UBERON:0000065!4.09e-07!53;UBERON:0001871!9.07e-07!7
|ontology_enrichment_uberon=UBERON:0001049!4.86e-26!57;UBERON:0005068!4.86e-26!57;UBERON:0006241!4.86e-26!57;UBERON:0007135!4.86e-26!57;UBERON:0001017!5.86e-26!82;UBERON:0007023!2.05e-24!115;UBERON:0005743!2.92e-24!86;UBERON:0000073!4.96e-23!94;UBERON:0001016!4.96e-23!94;UBERON:0003080!9.23e-23!42;UBERON:0002780!1.66e-22!41;UBERON:0001890!1.66e-22!41;UBERON:0006240!1.66e-22!41;UBERON:0000955!2.02e-21!69;UBERON:0006238!2.02e-21!69;UBERON:0002616!2.37e-20!59;UBERON:0004121!4.35e-20!169;UBERON:0000924!2.28e-19!173;UBERON:0006601!2.28e-19!173;UBERON:0002020!2.59e-19!34;UBERON:0003528!2.59e-19!34;UBERON:0001893!8.37e-19!34;UBERON:0003075!1.67e-18!86;UBERON:0007284!1.67e-18!86;UBERON:0001869!3.41e-18!32;UBERON:0002791!4.73e-18!33;UBERON:0002346!2.38e-17!90;UBERON:0000153!1.05e-16!129;UBERON:0007811!1.05e-16!129;UBERON:0002619!1.12e-16!22;UBERON:0000033!1.42e-16!123;UBERON:0001950!3.67e-15!20;UBERON:0003056!2.16e-14!61;UBERON:0000956!2.22e-13!25;UBERON:0000203!2.22e-13!25;UBERON:0000064!1.01e-12!219;UBERON:0000062!2.78e-12!511;UBERON:0004119!1.45e-11!169;UBERON:0000925!1.45e-11!169;UBERON:0006595!1.45e-11!169;UBERON:0000481!5.95e-10!347;UBERON:0000922!7.91e-10!612;UBERON:0004111!8.00e-10!241;UBERON:0001007!8.47e-10!155;UBERON:0001555!8.47e-10!155;UBERON:0007026!8.47e-10!155;UBERON:0000467!1.54e-09!625;UBERON:0000923!1.57e-09!604;UBERON:0005291!1.57e-09!604;UBERON:0006598!1.57e-09!604;UBERON:0002532!1.57e-09!604;UBERON:0000480!2.14e-09!626;UBERON:0002050!2.18e-09!605;UBERON:0005423!2.18e-09!605;UBERON:0000475!2.70e-09!365;UBERON:0005911!8.96e-09!82;UBERON:0004921!1.03e-08!129;UBERON:0004185!1.03e-08!129;UBERON:0001004!1.29e-08!72;UBERON:0000483!2.07e-08!309;UBERON:0000468!5.08e-08!659;UBERON:0000119!5.82e-08!312;UBERON:0000025!6.73e-08!194;UBERON:0000477!8.21e-08!286;UBERON:0002308!1.55e-07!9;UBERON:0000125!1.55e-07!9;UBERON:0002420!1.67e-07!9;UBERON:0007245!1.67e-07!9;UBERON:0010009!1.67e-07!9;UBERON:0010011!1.67e-07!9;UBERON:0000454!1.67e-07!9;UBERON:0000065!4.09e-07!53;UBERON:0001871!9.07e-07!7
|tfbs_overrepresentation=0.689061,0.358133,0.999904,0.301302,0.804895,0.917009,0.27557,0.980283,0.216481,0.173845,0.667499,0.846289,0.784365,0.627466,0.330284,0.374118,0.671892,0.5314,0.328469,0.567681,0.784099,0.647608,0.465937,0.518665,0.267565,0.531123,0.821469,0.502135,0.679558,0.162372,0.813985,0.58852,0.124917,0.819555,0.396396,0.476491,0.999806,0.275353,0.609517,0.397244,0.524798,0.167018,0.66924,0.77493,0.611355,0.23716,0.247404,0.769805,0.579015,0.612276,0.706833,0.335343,0.413445,0.511193,0.803142,0.249693,0.565537,0.826889,0.450152,0.55877,0.196727,0.694797,0.569613,0.439675,0.337348,0.316087,0.958614,0.364804,0.483163,0.738267,0.863353,0.401841,0.495329,0.606354,0.0535436,0.118929,0.524852,0.279376,0.242991,0.0519793,0.521506,0.562637,0.272749,0.591238,0.717858,0.88088,0.385961,0.820872,0.998976,0.378249,0.481853,0.311314,0.52055,0.299461,0.480321,0.591852,0.9882,0.705714,0.510207,0.680397,0.352194,0.90658,0.674381,0.241936,0.836914,0.26395,0.39859,0.8047,0.680845,0.899852,0.77204,0.224036,0.695152,0.122654,0.542784,0.222594,0.139883,0.347995,0.66636,0.473831,0.386371,0.830087,0.669479,0.481961,0.547046,0.76015,0.501999,0.103534,0.476021,0.654565,0.362663,0.434705,0.350835,0.155517,0.626887,0.567835,0.388476,0.34128,0.218379,0.0286445,0.155453,0.632526,0.812211,0.711694,0.961679,0.40951,0.533761,0.475463,0.252695,0.611083,0.806469,0.679366,0.768153,0.179278,0.273911,0.600304,0.434367,0.296632,0.322451,0.222432,0.294925,0.520163,0.597281,0.690485,0.903952,0.589328,0.258891,0.263913,0.260712,0.516945,0.766021,0.66266,0.942439,0.335116,0.457152,0.499551,0.670073,0.770436,0.763415,0.233626,0.718749,0.616374,0.184361,0.593696,0.429712,0.604594,0.772922,0.259702,0.469733,0.752898,0.564428,0.781475,0.617851,0.851232,0.583813,0.297838,0.449841,0.366176,0.401707,0.573392,0.496408,0.36673,0.205196,0.367746,0.658987,0.645982,0.904051,0.701141,0.816282,0.422116,0.291293,0.0486133,0.612123,0.5846,0.935981,0.742849,0.731625,0.541744,0.379454,0.549343,0.674538,0.967184,0.711851,0.724056,0.430323,0.629443,0.665879,0.482751,0.367002,0.364245,0.985191,0.97163,0.269067,0.442137,0.522637,0.511981,0.298671,0.654779,0.729971,0.830237,0.77178,0.95705,0.532151,0.470675,0.596079,0.660105,0.463943,0.215893,0.967319,0.598567,0.719257,0.777235,0.778392,0.530741,0.530974,0.720777,0.564774,0.492159,0.410747,0.987744,0.374223,0.756252,0.729674,0.634037,0.227071,0.462045,0.462458,0.507506,0.602056,0.437754,0.908577,0.380895,0.884269,0.986977,0.485308,0.247571,0.640385,0.319657,0.994518,0.4449,0.861122,0.997692,0.815533,0.999925,0.950035,0.994301,0.651123,0.629105,0.856662,0.933662,0.871805,0.947373,0.975166,0.946715,0.918239,0.970674,0.902468,0.719583,0.894053,0.975596,0.987615,0.794489,0.448993,0.420729,0.770227,0.768438,0.574495,0.792737,0.835749,0.983161,0.45673,0.833294,0.999523,0.644152,0.995457,0.852859,0.903913,0.862984,0.882894,0.907153,0.928235,0.708879,0.529268,0.553343,0.885919,0.905932,0.913455,0.764069,0.875225,0.920283,0.93144,0.986634,0.980832,0.921208,0.991346,0.985681,0.967724,0.986827,0.91203,0.771572,0.978543,0.999693,0.997456,0.683155,0.861733,0.778229,0.95574,0.333657,0.673224,0.999262,0.752492,0.89768,0.995548,0.61944,0.911531,0.990803,0.729361,0.398881,0.426856,0.776491,0.898588,0.979641,0.880631,0.979852,0.569258,0.687908,0.698729,0.931399,0.836201,0.936138,0.992155,0.287149,0.434338,0.568291,0.996069,0.998536,0.963264,0.922717,0.954224,0.950562,0.918192,0.945265,0.999782,0.689187,0.997849,0.915827,0.850217,0.578213,0.479801,0.712476,0.98469,0.981925,0.992039,0.908611,0.778109,0.999931,0.949859,0.682461,0.684443,0.971876,0.859897,0.930867,0.828406,0.881343,0.703282,0.295122,0.660855,0.889256,0.654142,0.532861,0.928204,0.722788,0.703545,0.95444,0.748535,0.747024,0.903982,0.963684,0.995602,0.23313,0.892825,0.961861,0.560859,0.894242,0.980893,0.643599,0.943019,0.99961,0.816152,0.909457,0.652642,0.922969,0.669171,0.806614,0.997243,0.696654,0.674059,0.821437,0.995438,0.720638,0.864518,0.854835,0.85603,0.201486,0.495743,0.362586,0.464073,0.993872,0.956223,0.977292,0.957478,0.99114,0.8928,0.868551,0.976329,0.527465,0.411606,0.343055,0.791613,0.448727,0.352607,0.681133,0.843391,0.811748,0.927493,0.986085,0.790157,0.581262,0.918306,0.278514,0.929394,0.629028,0.654328,0.563516,0.903804,0.378469,0.97046,0.124126,0.929842,0.693067,0.877191,0.294642,0.395296,0.0616185,0.555091,0.152765,0.485747,0.137649,0.564305,0.280312,0.0281818,0.252267,0.637288,0.82308,0.211134,0.817832,0.313375,0.469843,0.397202,0.771192,0.578996,0.837366,0.948576,0.797309,0.646484,0.784215,0.303795,0.805265,0.978071,0.632996,0.414266,0.44068,0.743249,0.48964,0.0383949,0.0796581,0.841966,0.0518711,0.905651,0.0347636,0.753219,0.672275,0.825084,0.200598,0.644539,0.283946,0.32592,0.820595,0.344355,0.456534,0.528417,0.721933,0.619736,0.501839,0.343679,0.912469,0.995241,0.661529,0.102243,0.392459,0.82533,0.839122,0.458088,0.43897,0.725918,0.79288,0.339065,0.448611,0.345603,0.268637,0.227239,0.252306,0.884156,0.745672,0.807153,0.307623,0.755863,0.966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}}
}}

Revision as of 20:04, 8 August 2012


Full id: C449_epidermoid_anaplastic_occipital_oral_middle_Wilms_parietal



Phase1 CAGE Peaks

Hg19::chr11:69988499..69988503,-p@chr11:69988499..69988503
-
Hg19::chr17:39678090..39678101,-p4@KRT15
Hg19::chr19:51512580..51512608,-p@chr19:51512580..51512608
-
Hg19::chr2:72258505..72258535,+p@chr2:72258505..72258535
+
Hg19::chr3:193809263..193809278,+p1@ENST00000457815
Hg19::chr4:23975557..23975561,-p@chr4:23975557..23975561
-
Hg19::chr4:23981805..23981809,-p@chr4:23981805..23981809
-
Hg19::chr4:24010751..24010757,-p@chr4:24010751..24010757
-
Hg19::chr4:24053554..24053559,-p@chr4:24053554..24053559
-
Hg19::chr4:24055928..24055932,-p@chr4:24055928..24055932
-
Hg19::chr4:24059076..24059080,-p@chr4:24059076..24059080
-
Hg19::chr4:24105215..24105219,-p@chr4:24105215..24105219
-
Hg19::chr4:24125531..24125534,-p@chr4:24125531..24125534
-
Hg19::chr4:24188430..24188435,-p@chr4:24188430..24188435
-
Hg19::chr4:24202276..24202277,-p@chr4:24202276..24202277
-
Hg19::chr4:24208460..24208464,-p@chr4:24208460..24208464
-
Hg19::chr4:24232569..24232574,-p@chr4:24232569..24232574
-
Hg19::chr5:84943573..84943591,-p@chr5:84943573..84943591
-
Hg19::chr6:43706592..43706595,-p@chr6:43706592..43706595
-
Hg19::chr6:43706642..43706655,-p@chr6:43706642..43706655
-
Hg19::chr7:55088621..55088630,+p@chr7:55088621..55088630
+
Hg19::chr9:135687993..135687996,+p@chr9:135687993..135687996
+


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


GO IDGO nameFDR corrected p-value
GO:0005200structural constituent of cytoskeleton0.0333451077357824
GO:0008544epidermis development0.0333451077357824
GO:0007398ectoderm development0.0333451077357824
GO:0045111intermediate filament cytoskeleton0.0333451077357824
GO:0005882intermediate filament0.0333451077357824
GO:0009888tissue development0.0359119274696809



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>disease_data<br>


Cell Type
Ontology termp-valuen
endo-epithelial cell9.68e-1143
endodermal cell1.05e-1059
respiratory epithelial cell3.45e-0713
Uber Anatomy
Ontology termp-valuen
neural tube4.86e-2657
neural rod4.86e-2657
future spinal cord4.86e-2657
neural keel4.86e-2657
central nervous system5.86e-2682
adult organism2.05e-24115
regional part of nervous system4.96e-2394
nervous system4.96e-2394
anterior neural tube9.23e-2342
regional part of forebrain1.66e-2241
forebrain1.66e-2241
future forebrain1.66e-2241
brain2.02e-2169
future brain2.02e-2169
regional part of brain2.37e-2059
ectoderm-derived structure4.35e-20169
ectoderm2.28e-19173
presumptive ectoderm2.28e-19173
gray matter2.59e-1934
brain grey matter2.59e-1934
telencephalon8.37e-1934
neural plate1.67e-1886
presumptive neural plate1.67e-1886
cerebral hemisphere3.41e-1832
regional part of telencephalon4.73e-1833
neurectoderm2.38e-1790
anterior region of body1.05e-16129
craniocervical region1.05e-16129
regional part of cerebral cortex1.12e-1622
head1.42e-16123
neocortex3.67e-1520
pre-chordal neural plate2.16e-1461
cerebral cortex2.22e-1325
pallium2.22e-1325
organ part1.01e-12219
organ2.78e-12511
endoderm-derived structure1.45e-11169
endoderm1.45e-11169
presumptive endoderm1.45e-11169
multi-tissue structure5.95e-10347
embryo7.91e-10612
anatomical conduit8.00e-10241
digestive system8.47e-10155
digestive tract8.47e-10155
primitive gut8.47e-10155
anatomical system1.54e-09625
germ layer1.57e-09604
embryonic tissue1.57e-09604
presumptive structure1.57e-09604
epiblast (generic)1.57e-09604
anatomical group2.14e-09626
embryonic structure2.18e-09605
developing anatomical structure2.18e-09605
organism subdivision2.70e-09365
endo-epithelium8.96e-0982
subdivision of digestive tract1.03e-08129
endodermal part of digestive tract1.03e-08129
respiratory system1.29e-0872
epithelium2.07e-08309
multi-cellular organism5.08e-08659
cell layer5.82e-08312
tube6.73e-08194
anatomical cluster8.21e-08286
nucleus of brain1.55e-079
neural nucleus1.55e-079
basal ganglion1.67e-079
nuclear complex of neuraxis1.67e-079
aggregate regional part of brain1.67e-079
collection of basal ganglia1.67e-079
cerebral subcortex1.67e-079
respiratory tract4.09e-0753
temporal lobe9.07e-077
Disease
Ontology termp-valuen
carcinoma3.31e-09106
squamous cell carcinoma3.13e-0714
cell type cancer9.33e-07143


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)

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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


No analysis results for this cluster

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.