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Coexpression cluster:C4515: Difference between revisions

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|full_id=C4515_mesodermal_astrocytoma_Mesenchymal_Lens_Multipotent_osteoclastoma_bone
|full_id=C4515_mesodermal_astrocytoma_Mesenchymal_Lens_Multipotent_osteoclastoma_bone
|id=C4515
|id=C4515
|ontology_enrichment_celltype=CL:0000055!2.08e-21!180;CL:0000057!5.50e-13!75;CL:0002620!3.39e-11!23
|ontology_enrichment_celltype=CL:0000057!6.20e-13!76;CL:0002620!1.40e-11!23
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!1.19e-26!86;UBERON:0001049!3.97e-26!57;UBERON:0005068!3.97e-26!57;UBERON:0006241!3.97e-26!57;UBERON:0007135!3.97e-26!57;UBERON:0001017!7.81e-26!82;UBERON:0003075!9.84e-25!86;UBERON:0007284!9.84e-25!86;UBERON:0000073!1.01e-23!94;UBERON:0001016!1.01e-23!94;UBERON:0002346!2.85e-22!90;UBERON:0000955!3.48e-22!69;UBERON:0006238!3.48e-22!69;UBERON:0002616!5.75e-22!59;UBERON:0003080!2.38e-20!42;UBERON:0002780!6.28e-20!41;UBERON:0001890!6.28e-20!41;UBERON:0006240!6.28e-20!41;UBERON:0000033!1.61e-19!123;UBERON:0000153!1.99e-18!129;UBERON:0007811!1.99e-18!129;UBERON:0004121!3.81e-18!169;UBERON:0003056!3.93e-18!61;UBERON:0002020!9.24e-18!34;UBERON:0003528!9.24e-18!34;UBERON:0001893!1.37e-17!34;UBERON:0002791!3.59e-17!33;UBERON:0000475!4.81e-17!365;UBERON:0000924!7.67e-17!173;UBERON:0006601!7.67e-17!173;UBERON:0001869!3.20e-16!32;UBERON:0007023!2.35e-14!115;UBERON:0000956!2.66e-12!25;UBERON:0000203!2.66e-12!25;UBERON:0000481!2.97e-10!347;UBERON:0002619!4.33e-10!22;UBERON:0001950!7.38e-09!20;UBERON:0000483!1.49e-08!309;UBERON:0000477!1.62e-08!286;UBERON:0000025!1.75e-08!194;UBERON:0000468!2.70e-08!659;UBERON:0000119!4.24e-08!312;UBERON:0002097!7.96e-08!40;UBERON:0002199!1.92e-07!45;UBERON:0002416!1.92e-07!45;UBERON:0002420!4.31e-07!9;UBERON:0007245!4.31e-07!9;UBERON:0010009!4.31e-07!9;UBERON:0010011!4.31e-07!9;UBERON:0000454!4.31e-07!9;UBERON:0002308!4.57e-07!9;UBERON:0000125!4.57e-07!9;UBERON:0003076!5.49e-07!15;UBERON:0003057!5.49e-07!15
|ontology_enrichment_uberon=UBERON:0001017!8.98e-27!81;UBERON:0001049!4.09e-26!56;UBERON:0005068!4.09e-26!56;UBERON:0006241!4.09e-26!56;UBERON:0007135!4.09e-26!56;UBERON:0001016!7.73e-24!89;UBERON:0000073!1.11e-23!53;UBERON:0002616!1.11e-23!53;UBERON:0000955!5.63e-23!68;UBERON:0006238!5.63e-23!68;UBERON:0003075!6.13e-22!82;UBERON:0007284!6.13e-22!82;UBERON:0002780!1.71e-20!41;UBERON:0001890!1.71e-20!41;UBERON:0003080!1.71e-20!41;UBERON:0006240!1.71e-20!41;UBERON:0002346!5.37e-20!86;UBERON:0010314!1.57e-19!132;UBERON:0003528!1.40e-18!34;UBERON:0002020!1.40e-18!34;UBERON:0001893!1.66e-18!34;UBERON:0010371!2.20e-17!104;UBERON:0002791!4.12e-17!32;UBERON:0001869!6.99e-17!32;UBERON:0004121!3.31e-16!171;UBERON:0000924!3.31e-16!171;UBERON:0006601!3.31e-16!171;UBERON:0003056!3.54e-16!61;UBERON:0000956!1.24e-13!25;UBERON:0000203!1.24e-13!25;UBERON:0007023!1.04e-12!114;UBERON:0002619!6.36e-11!22;UBERON:0011216!5.38e-10!223;UBERON:0001950!2.37e-09!20;UBERON:0002097!8.76e-08!41;UBERON:0002199!5.30e-07!46;UBERON:0002416!5.30e-07!46;UBERON:0003076!7.29e-07!15;UBERON:0003057!7.29e-07!15;UBERON:0002420!8.42e-07!9;UBERON:0007245!8.42e-07!9;UBERON:0010009!8.42e-07!9;UBERON:0010011!8.42e-07!9;UBERON:0000454!8.42e-07!9
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115650730237425
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115650730237425
|tfbs_overrepresentation=0.147255,0.0586687,0.134243,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.000145865,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.0180778,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.0125303,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.000161406,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.21992,0.000682869,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.0400492,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.00606558,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.0281563,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.000307105,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.0413967,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.0381183,0.163502,0.0249262,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.000169443,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.713218,0.198118,0.635872,0.563047,0.0319444,0.807281,0.0083957,0.629514,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.53472,0.248224,0.0408801,0.292154,0.00202409,0.39729,0.581713,0.230901,0.187251,0.0756284,0.181715,0.10624,0.109988,0.00802393,0.218329,0.427027,0.376924,0.463191,0.647576,0.528324,0.520763,0.0792797,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.155672,0.236436,0.283727,0.314747,0.21363,0.0474194,0.448095,0.576651,0.416816,0.292835,0.476744,0.439556,0.373868,0.57762,0.608919,0.18237,0.126021,0.821217,0.747852,0.275351,0.236471,0.185661,0.346319,0.0427964,0.0405716,0.258117,0.0340542,0.513852,0.00691094,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.0138549,0.762864,0.581837,0.412837,0.305671,0.188159,0.191921,0.0225539,0.218623,0.312808,0.032738,0.0451077,0.0747529,0.229003,0.650179,0.589326,0.50215,0.294698,0.34331,0.138202,0.289204,0.327108,0.683186,0.278044,0.490301,0.428671,0.00238478,0.0642385,0.19763,0.15631,0.567452,0.421464,0.48267,0.104399,0.516462,0.858756,0.335105,0.144809,0.145539,0.385517,0.0818086,0.447325,0.127215,0.252232,0.152681,0.0465712,0.137098,0.0369524,0.134788,0.0985856,0.00133722,0.293698,0.284593,0.343734,0.306556,0.00617767,0.06617,0.503082,0.522888,0.284629,0.262537,0.00115172,0.226257,0.405955,0.0175765,0.363685,0.464871,0.40841,0.0228979,0.525396,0.284166,0.437176,0.269226,0.339277,0.552319,0.281425,0.141758,0.124432,0.0385377,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.257493,0.347298,0.539392,0.00966846,0.475069,0.404569,0.0847452,0.262389,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.00220026,0.000222233,0.275244,0.00481323,0.173708,0.141119,0.0241568,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0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}}
}}

Revision as of 16:00, 19 October 2012


Full id: C4515_mesodermal_astrocytoma_Mesenchymal_Lens_Multipotent_osteoclastoma_bone



Phase1 CAGE Peaks

Hg19::chr5:71475449..71475460,+p45@MAP1B
Hg19::chr5:71475473..71475487,+p40@MAP1B
Hg19::chr5:71475488..71475517,+p13@MAP1B


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
fibroblast6.20e-1376
skin fibroblast1.40e-1123
Uber Anatomy
Ontology termp-valuen
central nervous system8.98e-2781
neural tube4.09e-2656
neural rod4.09e-2656
future spinal cord4.09e-2656
neural keel4.09e-2656
nervous system7.73e-2489
regional part of nervous system1.11e-2353
regional part of brain1.11e-2353
brain5.63e-2368
future brain5.63e-2368
neural plate6.13e-2282
presumptive neural plate6.13e-2282
regional part of forebrain1.71e-2041
forebrain1.71e-2041
anterior neural tube1.71e-2041
future forebrain1.71e-2041
neurectoderm5.37e-2086
structure with developmental contribution from neural crest1.57e-19132
brain grey matter1.40e-1834
gray matter1.40e-1834
telencephalon1.66e-1834
ecto-epithelium2.20e-17104
regional part of telencephalon4.12e-1732
cerebral hemisphere6.99e-1732
ectoderm-derived structure3.31e-16171
ectoderm3.31e-16171
presumptive ectoderm3.31e-16171
pre-chordal neural plate3.54e-1661
cerebral cortex1.24e-1325
pallium1.24e-1325
adult organism1.04e-12114
regional part of cerebral cortex6.36e-1122
organ system subdivision5.38e-10223
neocortex2.37e-0920
skin of body8.76e-0841
integument5.30e-0746
integumental system5.30e-0746
posterior neural tube7.29e-0715
chordal neural plate7.29e-0715
basal ganglion8.42e-079
nuclear complex of neuraxis8.42e-079
aggregate regional part of brain8.42e-079
collection of basal ganglia8.42e-079
cerebral subcortex8.42e-079


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
CEBPB#105137.971147625824820.001974187055288560.0115650730237425



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.