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Coexpression cluster:C1626: Difference between revisions

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|full_id=C1626_pons_thalamus_amygdala_carcinosarcoma_diencephalon_Neural_medulla
|full_id=C1626_pons_thalamus_amygdala_carcinosarcoma_diencephalon_Neural_medulla
|id=C1626
|id=C1626
|ontology_enrichment_celltype=CL:0000047!2.63e-14!8;CL:0000540!4.17e-10!6;CL:0000031!4.17e-10!6;CL:0000404!4.17e-10!6;CL:0002319!5.75e-07!25
|ontology_enrichment_celltype=CL:0000242!2.33e-08!2;CL:0000047!4.15e-08!8
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.18e-86!82;UBERON:0005743!3.91e-85!86;UBERON:0001049!1.25e-80!57;UBERON:0005068!1.25e-80!57;UBERON:0006241!1.25e-80!57;UBERON:0007135!1.25e-80!57;UBERON:0000073!9.65e-76!94;UBERON:0001016!9.65e-76!94;UBERON:0002616!7.43e-67!59;UBERON:0002780!6.03e-64!41;UBERON:0001890!6.03e-64!41;UBERON:0006240!6.03e-64!41;UBERON:0000955!2.74e-63!69;UBERON:0006238!2.74e-63!69;UBERON:0003080!3.28e-62!42;UBERON:0003075!9.88e-57!86;UBERON:0007284!9.88e-57!86;UBERON:0002346!1.28e-53!90;UBERON:0002619!9.97e-53!22;UBERON:0002020!3.68e-49!34;UBERON:0003528!3.68e-49!34;UBERON:0001950!1.07e-48!20;UBERON:0001893!1.29e-48!34;UBERON:0001869!2.85e-48!32;UBERON:0002791!1.78e-46!33;UBERON:0000956!7.94e-46!25;UBERON:0000203!7.94e-46!25;UBERON:0003056!1.83e-42!61;UBERON:0004121!4.52e-42!169;UBERON:0000924!9.71e-41!173;UBERON:0006601!9.71e-41!173;UBERON:0007023!7.19e-34!115;UBERON:0000033!1.61e-33!123;UBERON:0000153!2.29e-31!129;UBERON:0007811!2.29e-31!129;UBERON:0001871!1.88e-19!7;UBERON:0003076!1.24e-18!15;UBERON:0003057!1.24e-18!15;UBERON:0001894!5.75e-17!7;UBERON:0006222!5.75e-17!7;UBERON:0000025!6.74e-15!194;UBERON:0000200!7.50e-15!6;UBERON:0002021!6.95e-13!5;UBERON:0001872!7.67e-13!5;UBERON:0004733!7.75e-13!12;UBERON:0002028!7.75e-13!12;UBERON:0007277!7.75e-13!12;UBERON:0000349!2.18e-12!5;UBERON:0002298!4.34e-12!8;UBERON:0004732!1.01e-11!13;UBERON:0004111!2.26e-10!241;UBERON:0003296!4.44e-10!4;UBERON:0010133!4.44e-10!4;UBERON:0000483!2.00e-09!309;UBERON:0000119!3.26e-09!312;UBERON:0000988!4.11e-09!3;UBERON:0001896!5.06e-09!3;UBERON:0005290!5.06e-09!3;UBERON:0010096!5.06e-09!3;UBERON:0002771!2.75e-08!3;UBERON:0002240!5.06e-08!3;UBERON:0000477!1.50e-07!286;UBERON:0000475!1.63e-07!365;UBERON:0002680!6.83e-07!9;UBERON:0001895!6.83e-07!9;UBERON:0010092!6.83e-07!9
|ontology_enrichment_uberon=UBERON:0001049!5.79e-78!56;UBERON:0005068!5.79e-78!56;UBERON:0006241!5.79e-78!56;UBERON:0007135!5.79e-78!56;UBERON:0001017!3.29e-75!81;UBERON:0000073!2.29e-73!53;UBERON:0002616!2.29e-73!53;UBERON:0001016!6.67e-67!89;UBERON:0001950!1.88e-66!20;UBERON:0002619!2.45e-66!22;UBERON:0002780!4.21e-63!41;UBERON:0001890!4.21e-63!41;UBERON:0003080!4.21e-63!41;UBERON:0006240!4.21e-63!41;UBERON:0000955!3.49e-58!68;UBERON:0006238!3.49e-58!68;UBERON:0000956!4.62e-58!25;UBERON:0000203!4.62e-58!25;UBERON:0003528!1.42e-55!34;UBERON:0002020!1.42e-55!34;UBERON:0001893!6.88e-55!34;UBERON:0003075!5.69e-54!82;UBERON:0007284!5.69e-54!82;UBERON:0001869!1.04e-53!32;UBERON:0002346!4.43e-51!86;UBERON:0002791!5.53e-49!32;UBERON:0010371!6.22e-46!104;UBERON:0003056!1.12e-43!61;UBERON:0007023!2.13e-36!114;UBERON:0004121!2.86e-36!171;UBERON:0000924!2.86e-36!171;UBERON:0006601!2.86e-36!171;UBERON:0010314!3.38e-34!132;UBERON:0011216!4.47e-24!223;UBERON:0002298!5.92e-24!6;UBERON:0000200!6.19e-22!6;UBERON:0001871!4.48e-19!6;UBERON:0001872!1.01e-18!5;UBERON:0002021!1.83e-18!5;UBERON:0000025!6.48e-17!192;UBERON:0003076!1.13e-15!15;UBERON:0003057!1.13e-15!15;UBERON:0000988!5.44e-13!3;UBERON:0001896!1.02e-12!3;UBERON:0005290!1.02e-12!3;UBERON:0010096!1.02e-12!3;UBERON:0000349!6.86e-12!5;UBERON:0001870!7.18e-12!3;UBERON:0004111!7.20e-12!240;UBERON:0004733!1.28e-11!12;UBERON:0002028!1.28e-11!12;UBERON:0007277!1.28e-11!12;UBERON:0000477!2.59e-11!373;UBERON:0004732!1.14e-10!13;UBERON:0000483!9.57e-10!306;UBERON:0000119!1.45e-09!309;UBERON:0001894!1.68e-09!7;UBERON:0006222!1.68e-09!7;UBERON:0002148!4.11e-09!2;UBERON:0006331!4.11e-09!2;UBERON:0009662!4.11e-09!2;UBERON:0000007!6.85e-09!2;UBERON:0001876!1.01e-08!2;UBERON:0002702!1.13e-08!2;UBERON:0002771!1.27e-08!2;UBERON:0000064!2.99e-08!218;UBERON:0002360!6.09e-08!2;UBERON:0000094!6.09e-08!2;UBERON:0010743!6.09e-08!2
|tf_chipseq_enrich=HDAC2#3066;4:10.732496189301:0.000145096579747875:0.00188526271364621!REST#5978;4:7.72002297290242:0.000528636377365057:0.00457076369034103!SIN3A#25942;4:4.32710778145211:0.00497705285576288:0.0232353682536775!ZNF143#7702;4:10.8007012417823:0.000141522343086319:0.00184386876117665
|tf_chipseq_enrich=HDAC2#3066;4:10.732496189301:0.000145096579747875:0.00188526271364621!REST#5978;4:7.72002297290242:0.000528636377365057:0.00457076369034103!SIN3A#25942;4:4.32710778145211:0.00497705285576288:0.0232353682536775!ZNF143#7702;4:10.8007012417823:0.000141522343086319:0.00184386876117665
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4,0.7034,0.218241,0.0242146,0.10708,0.327369,0.339826,0.12998,0.123097,0.00340819,0.300809,0.0898207,0.126545,0.0918749,0.0686325,0.0569043,0.0639461,0.387306,0.267408,0.312064,0.080156,0.274185,0.180885,0.0545112,0.510703,0.33844,0.0649137,0.0974216,0.595767,0.195675,0.174786,0.0165942,0.396547,0.0472148,0.735114,0.229138,0.0639045,0.141461,0.0900204,0.228387,0.385962,0.000833826,0.296227,0.00179772,0.566117,0.36304,0.430936,0.123626,0.0404561,0.132705,0.285556,0.493429,0.233835,0.224471,0.262929,0.223204,0.143824,0.127678,0.431098,0.0775891,0.153079,0.62577,0.211515,0.125701,0.175283,0.204954,0.209341,0.855975,0.629422,0.084895,0.160115,0.0819954,0.10091,0.000338668,0.151161,0.228398,0.056055,0.120552,0.0176699,0.655862,0.262721,0.335207,0.434016,2.96291e-06,0.00578502,0.278645,0.733648,0.0940982,0.0780533,0.564811,0.0993772,0.274769,0.448923,0.000285046,0.344528,0.113233,0.0585992,0.20045,0.274438,0.573835,0.989834,0.319826,0.336512,0.0160761,0.109708,0.174594,0.0809806,0.0126171,0.318794,0.122767,0.00287982,0.176858,0.114361,0.347759,0.0321076,0.0620267,0.211111,0.0738743,0.0882327,0.183058,0.150073,0.00413644,0.16872,0.341388,0.00450945,0.359135,2.96011e-07,0.430769,0.240825,0.3033,0.336623,0.163542,0.483244,0.27134,0.500871,0.0313367,0.10226,0.29809,0.235147,0.689826,0.245965,0.116923,2.44259e-05,0.0983658,0.0284215,0.238223,0.156976,0.00299259,0.267391,0.0508431,0.21807,0.350528,0.382904,0.432408,0.190404,0.135865,0.0307173,0.18137,0.180609,0.291283,0.273972,0.153023,0.0018952,0.37958,0.22307,0.160699,0.0891264,0.166736,0.181253,0.0422294,0.263877,0.146486,0.431348,0.0379349,0.294204,0.131936,0.288826,0.246621,0.00383169,0.697373,0.0965376,0.377203,0.279263,0.336564,0.35463,0.581771,0.0805078,0.0594155,0.587524,0.208795,0.0713793,0.212621,0.594469,0.53612,0.629713,0.000290897,0.355154,0.377285,0.0739871,0.537088,0.0671798,0.261576,4.07471e-05,0.0538109,0.526495,0.0577201,0.191067,0.764863,0.820986,0.610475,0.0656039,0.561689,0.672416,0.685628,0.0759172,0.708698,0.96913,0.967174,0.349068,0.70429,0.217481,0.557035,0.427789,0.326931,0.386595,0.639789,0.433702,0.00356416,0.644878,0.432123,0.172498,0.661773,0.494975,0.651196,0.0142241,0.626931,0.371758,0.109303,0.562417,0.183098,0.570752,0.254547,0.0859085,0.821811,0.1082,0.133485,0.183869,0.255876,0.660884,0.116,0.401389,0.705225,0.315485,0.311289,0.318577,0.120474,0.0139453,0.603509,0.511254,0.0482305,0.246387,0.224252,0.587237,0.155054,0.466978,0.518234,0.257848,0.353942,0.192234,0.427276,0.0133812,0.466967,0.283682,0.424668,0.0012153,0.797471,0.583101,0.0015715,0.00440505,2.7991e-06,0.498956,0.465544,0.00020535,0.349033,0.932831,0.723248,0.34194,0.592696,0.592314,0.000710533,0.647996,0.177129,0.0567843,0.01922,0.220564,0.286976,1.6901e-05,0.307462,0.135076,0.133253,0.298027,0.274593,0.000667335,0.541363,0.709432,0.583627,0.531474,0.720644,0.0101223,0.528646,0.361524,0.00685623,0.412744,0.185983,0.62698,0.513592,0.101553,0.815658,0.0239664,0.011528,0.538745,0.0241542,0.453004,0.680686,0.196391,0.693441,0.382214,0.553161,0.00398326,0.0313098,0.339393,0.0073807,0.306231,0.298354,0.278436,0.784543,0.457741,0.0206327,0.00255556,0.748909,0.0931042,0.0549063,0.412586,0.178696,0.0172799,0.55475,0.000135665,0.00702347,0.499347,0.307426,5.79879e-06,0.049727,0.490527,0.714189,0.44799,0.813041,0.0571105,0.276338,0.126433,0.417412,0.318174,0.0555558,0.295666,0.393022,0.293641,0.116969,0.401231,0.255983,0.297663,0.0361982,0.338258,0.322052,0.145568,0.153833,0.261242,0.0854897,0.54721,0.0137717,0.321362,0.259785,0.280757,0.301366,0.0659025,0.343265,0.501812,0.462092,0.000849,0.308589,0.291523,0.19697,0.309816,0.0537285,0.15063,0.198077,0.281455,0.348739,0.419895,0.138495,0.208834,0.00737169,0.377566,0.342366,0.109684,0.322704,0.0952935,0.181288,0.230841,0.0709982,0.255358,0.351665,0.265112,7.24561e-07,0.10772,8.34265e-12,7.37741e-05,0.000208987,0.312881,0.512825,0.244656,0.192188,0.158985,0.174153,0.0972854,0.00822058,0.249919,0.339517,0.303699,0.198326,0.0905116,0.458518,0.282501,0.000235041,0.0140681,0.238377,0.334983,0.197875,0.0461189,0.289389,0.117618,0.392533,0.396962,0.316002,0.330317,0.0582923,0.225079,0.300542,0.379651,0.185715,0.345505,0.375521,0.00418052,0.311201,0.221943,0.306427,0.367733,0.246925,0.208775,0.390438,0.343014,0.000318673,0.276922,0.156279,0.313647,0.128336,0.422872,0.336468,0.13327,0.0552906,0.17149,0.0877361,0.0880065,0.0311458,0.126615,0.0669467,0.0879453,0.0275302,0.0148259,0.060398,0.292869,0.358198,0.29552,0.00909114,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.109896,0.508546,0.224871,0.398887,0.0138446,0.00651415,0.349611,0.445995,0.0134421,0.0428885,0.107629,0.400591,0.00182588,0.253154,0.0575641,0.309489,0.430805,0.0753413,0.00457903,0.0183753,0.0642384,0.00917639,0.184651,0.303359,0.297596,0.018596,0.425912,0.380826,0.259046,0.345068,0.151046,0.483953,0.347171,0.321735,0.15463,1.85896e-05,4.75608e-06,0.269432,0.250466,0.00212259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}}
}}

Revision as of 11:31, 19 October 2012


Full id: C1626_pons_thalamus_amygdala_carcinosarcoma_diencephalon_Neural_medulla



Phase1 CAGE Peaks

Hg19::chr11:22359292..22359301,+p9@SLC17A6
Hg19::chr11:22359398..22359428,+p5@SLC17A6
Hg19::chr11:22359432..22359478,+p4@SLC17A6
Hg19::chr11:22359501..22359513,+p7@SLC17A6
Hg19::chr11:22359910..22359937,+p1@SLC17A6


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
Merkel cell2.33e-082
neuronal stem cell4.15e-088
Uber Anatomy
Ontology termp-valuen
neural tube5.79e-7856
neural rod5.79e-7856
future spinal cord5.79e-7856
neural keel5.79e-7856
central nervous system3.29e-7581
regional part of nervous system2.29e-7353
regional part of brain2.29e-7353
nervous system6.67e-6789
neocortex1.88e-6620
regional part of cerebral cortex2.45e-6622
regional part of forebrain4.21e-6341
forebrain4.21e-6341
anterior neural tube4.21e-6341
future forebrain4.21e-6341
brain3.49e-5868
future brain3.49e-5868
cerebral cortex4.62e-5825
pallium4.62e-5825
brain grey matter1.42e-5534
gray matter1.42e-5534
telencephalon6.88e-5534
neural plate5.69e-5482
presumptive neural plate5.69e-5482
cerebral hemisphere1.04e-5332
neurectoderm4.43e-5186
regional part of telencephalon5.53e-4932
ecto-epithelium6.22e-46104
pre-chordal neural plate1.12e-4361
adult organism2.13e-36114
ectoderm-derived structure2.86e-36171
ectoderm2.86e-36171
presumptive ectoderm2.86e-36171
structure with developmental contribution from neural crest3.38e-34132
organ system subdivision4.47e-24223
brainstem5.92e-246
gyrus6.19e-226
temporal lobe4.48e-196
parietal lobe1.01e-185
occipital lobe1.83e-185
tube6.48e-17192
posterior neural tube1.13e-1515
chordal neural plate1.13e-1515
pons5.44e-133
medulla oblongata1.02e-123
myelencephalon1.02e-123
future myelencephalon1.02e-123
limbic system6.86e-125
frontal cortex7.18e-123
anatomical conduit7.20e-12240
segmental subdivision of hindbrain1.28e-1112
hindbrain1.28e-1112
presumptive hindbrain1.28e-1112
anatomical cluster2.59e-11373
segmental subdivision of nervous system1.14e-1013
epithelium9.57e-10306
cell layer1.45e-09309
diencephalon1.68e-097
future diencephalon1.68e-097
locus ceruleus4.11e-092
brainstem nucleus4.11e-092
hindbrain nucleus4.11e-092
pituitary gland6.85e-092
amygdala1.01e-082
middle frontal gyrus1.13e-082
middle temporal gyrus1.27e-082
organ part2.99e-08218
meninx6.09e-082
membrane organ6.09e-082
meningeal cluster6.09e-082


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
HDAC2#3066410.7324961893010.0001450965797478750.00188526271364621
REST#597847.720022972902420.0005286363773650570.00457076369034103
SIN3A#2594244.327107781452110.004977052855762880.0232353682536775
ZNF143#7702410.80070124178230.0001415223430863190.00184386876117665



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.