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Coexpression cluster:C1677: Difference between revisions

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|ontology_enrichment_disease=DOID:8692!9.13e-44!31;DOID:1240!1.00e-40!39;DOID:2531!7.87e-33!51;DOID:0060083!7.87e-33!51;DOID:1036!6.69e-13!8;DOID:0050686!4.60e-07!137
|ontology_enrichment_disease=DOID:8692!9.13e-44!31;DOID:1240!1.00e-40!39;DOID:2531!7.87e-33!51;DOID:0060083!7.87e-33!51;DOID:1036!6.69e-13!8;DOID:0050686!4.60e-07!137
|ontology_enrichment_uberon=UBERON:0002390!5.53e-19!102;UBERON:0003061!5.53e-19!102;UBERON:0002193!2.59e-16!112;UBERON:0000178!1.99e-12!15;UBERON:0000179!1.99e-12!15;UBERON:0000463!1.99e-12!15;UBERON:0004177!8.48e-09!7;UBERON:0002405!2.51e-07!115;UBERON:0002371!3.25e-07!80
|ontology_enrichment_uberon=UBERON:0002390!5.53e-19!102;UBERON:0003061!5.53e-19!102;UBERON:0002193!2.59e-16!112;UBERON:0000178!1.99e-12!15;UBERON:0000179!1.99e-12!15;UBERON:0000463!1.99e-12!15;UBERON:0004177!8.48e-09!7;UBERON:0002405!2.51e-07!115;UBERON:0002371!3.25e-07!80
|tf_chipseq_enrich=CCNT2#905;5:6.33620157696263:9.78880505817628e-05:0.001389228171587!ELF1#1997;4:3.40647836704603:0.0123506610529955:0.0447288539327899!EP300#2033;4:5.41915338097856:0.0020938692794389:0.0121133115645776!FOSL1#8061;4:31.7708637730984:1.96715033715934e-06:7.22388235100509e-05!GATA1#2623;4:10.8482465150404:0.000139095691709438:0.00181542301255211!GATA2#2624;4:10.1959453868432:0.000177544777760982:0.00215661770697595!REST#5978;5:9.65002871612802:1.19441074361324e-05:0.000301311747952229!TAL1#6886;4:23.8948933419522:6.10828383356726e-06:0.000181491623127719!USF1#7391;4:5.08919942176637:0.0026686777536004:0.0147148532763989
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0686325,0.0569043,0.0639461,0.0871536,0.267408,0.312064,0.080156,0.274185,0.53753,0.0545112,0.160961,0.33844,0.0649137,0.0974216,0.595767,0.195675,0.174786,0.176557,0.396547,0.0472148,0.735114,0.229138,0.0639045,0.141461,0.0900204,0.228387,0.385962,0.334921,0.296227,0.208788,0.566117,0.36304,0.430936,0.123626,0.270619,0.132705,0.285556,0.493429,0.233835,0.224471,0.262929,0.223204,0.143824,0.460679,0.431098,0.0775891,0.000675218,0.62577,0.211515,0.125701,0.175283,0.204954,0.209341,0.306485,0.0789618,0.084895,0.160115,0.0819954,0.10091,0.122658,0.151161,0.228398,0.056055,0.120552,0.41771,0.388874,0.830533,0.335207,0.434016,0.190688,0.299739,0.278645,0.733648,0.0940982,0.0780533,0.564811,0.0993772,0.274769,0.448923,0.11602,0.344528,0.436413,0.0585992,0.20045,0.274438,0.911136,0.83616,0.319826,0.336512,0.173868,0.109708,0.174594,0.0809806,0.154589,0.318794,0.122767,0.0749261,0.176858,0.114361,0.347759,0.242462,0.0620267,0.211111,0.0738743,0.0882327,0.183058,0.150073,0.270522,0.0151089,0.341388,0.0934526,0.359135,0.123404,0.430769,0.240825,0.3033,0.336623,0.163542,0.483244,0.27134,0.500871,0.239667,0.10226,0.29809,0.235147,0.32673,0.245965,0.116923,0.148426,0.0983658,0.228743,0.238223,0.156976,0.244789,0.267391,0.301441,0.21807,0.350528,0.382904,0.110951,0.190404,0.135865,0.488841,0.18137,0.180609,0.291283,0.273972,0.153023,0.400137,0.37958,0.22307,0.160699,0.391307,0.166736,0.181253,0.0422294,0.263877,0.146486,0.431348,0.262486,0.294204,0.131936,0.288826,0.246621,0.463617,0.697373,0.0965376,0.377203,0.279263,0.0643411,0.35463,0.581771,0.47901,0.0594155,0.587524,0.208795,0.0713793,0.212621,0.594469,0.53612,0.629713,0.581874,0.355154,0.377285,0.619037,0.537088,0.603804,0.261576,0.306963,0.206759,0.526495,0.580285,0.550495,0.764863,0.820986,0.610475,0.881697,0.561689,0.672416,0.685628,0.623136,0.708698,0.67506,0.445257,0.349068,0.70429,0.798758,0.557035,0.427789,0.326931,0.737642,0.886619,0.433702,0.258394,0.644878,0.00272845,0.759415,0.661773,0.494975,0.28382,0.392155,0.259088,0.371758,0.243193,0.562417,0.890566,0.300573,0.254547,0.408817,0.821811,0.680843,0.500384,0.541378,0.47213,0.660884,0.469682,0.198685,0.446908,0.315485,0.311289,0.318577,0.4488,0.389888,0.603509,0.511254,0.553178,0.246387,0.224252,0.587237,0.155054,0.466978,0.518234,0.257848,0.0717012,0.192234,0.427276,0.747776,0.466967,0.283682,0.424668,0.7175,0.797471,0.583101,0.702164,0.477016,0.831202,0.498956,0.792095,0.197115,0.708394,0.932831,0.723248,0.34194,0.226858,0.592314,0.644904,0.647996,0.763919,0.317485,0.633504,0.220564,0.286976,0.262394,0.307462,0.135076,0.469588,0.664443,0.274593,0.490712,0.183857,0.709432,0.583627,0.531474,0.720644,0.562305,0.528646,0.361524,0.31558,0.412744,0.54408,0.62698,0.163034,0.415367,0.815658,0.45585,0.36864,0.538745,0.456862,0.453004,0.316163,0.557093,0.693441,0.382214,0.553161,0.639572,0.68995,0.339393,0.694478,0.306231,0.298354,0.646049,0.199987,0.457741,0.641611,0.426239,0.401917,0.656093,0.572661,0.412586,0.534679,0.41502,0.55475,0.294859,0.523749,0.499347,0.307426,0.790204,0.557732,0.490527,0.714189,0.44799,0.499536,0.318338,0.276338,0.126433,0.417412,0.318174,0.0555558,0.295666,0.393022,0.293641,0.116969,0.401231,0.255983,0.297663,0.256708,0.338258,0.322052,0.145568,0.153833,0.261242,0.38389,0.54721,0.388459,0.321362,0.627637,0.280757,0.301366,0.340343,0.343265,0.501812,0.462092,0.336254,0.308589,0.291523,0.19697,0.309816,0.0537285,0.15063,0.198077,0.281455,0.348739,0.419895,0.138495,0.208834,0.32256,0.377566,0.342366,0.109684,0.322704,0.403482,0.181288,0.230841,0.352328,0.255358,0.351665,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.406458,0.312881,0.512825,0.244656,0.192188,0.158985,0.174153,0.0972854,0.333309,0.249919,0.339517,0.303699,0.198326,0.394084,0.458518,0.282501,0.252005,0.390891,0.238377,0.334983,0.197875,0.287909,0.289389,0.117618,0.392533,0.396962,0.316002,0.330317,0.321404,0.225079,0.300542,0.379651,0.185715,0.345505,0.375521,0.271405,0.0544127,0.221943,0.306427,0.367733,0.246925,0.208775,0.390438,0.343014,0.270094,0.276922,0.156279,0.313647,0.461742,0.422872,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.430541,0.508546,0.224871,0.398887,0.389061,0.310732,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.319519,0.309489,0.430805,0.362154,0.480785,0.185476,0.336314,0.344469,0.184651,0.303359,0.297596,0.42392,0.425912,0.380826,0.259046,0.345068,0.151046,0.483953,0.347171,0.321735,0.15463,0.13907,0.470121,0.269432,0.250466,0.409882,0.115686,0.408975,0.162633,0.342661,0.27567,0.248127,0.33299,0.384731,0.319112,0.526476
}}
}}

Revision as of 14:17, 5 September 2012


Full id: C1677_acute_CD34_CD133_chronic_Whole_leukemia_myelodysplastic



Phase1 CAGE Peaks

Hg19::chr12:54694979..54694993,+p2@COPZ1
Hg19::chr21:21630930..21630941,-p3@ENST00000436373
Hg19::chr21:21630952..21630969,-p2@ENST00000436373
Hg19::chr21:21630981..21630991,-p4@ENST00000436373
Hg19::chr21:21630994..21631007,-p1@ENST00000436373


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:0006890retrograde vesicle-mediated transport, Golgi to ER0.00610502766984575
GO:0030126COPI vesicle coat0.00610502766984575
GO:0030663COPI coated vesicle membrane0.00610502766984575
GO:0006891intra-Golgi vesicle-mediated transport0.00610502766984575
GO:0030137COPI-coated vesicle0.00610502766984575
GO:0030120vesicle coat0.0130822021496695
GO:0030662coated vesicle membrane0.0130822021496695
GO:0005798Golgi-associated vesicle0.0148777985231535
GO:0048193Golgi vesicle transport0.0148777985231535
GO:0030659cytoplasmic vesicle membrane0.0148777985231535
GO:0044433cytoplasmic vesicle part0.0148777985231535
GO:0012506vesicle membrane0.0148777985231535
GO:0030117membrane coat0.0148777985231535
GO:0048475coated membrane0.0148777985231535
GO:0030135coated vesicle0.0175968444601436
GO:0045045secretory pathway0.0269339456022607
GO:0032940secretion by cell0.0310279053338043
GO:0006461protein complex assembly0.0310279053338043
GO:0016023cytoplasmic membrane-bound vesicle0.0310279053338043
GO:0031988membrane-bound vesicle0.0310279053338043
GO:0000139Golgi membrane0.0310279053338043
GO:0046903secretion0.0310279053338043
GO:0044431Golgi apparatus part0.0310279053338043
GO:0031410cytoplasmic vesicle0.0310279053338043
GO:0031982vesicle0.0310279053338043
GO:0006886intracellular protein transport0.0365334800605023
GO:0016192vesicle-mediated transport0.0403011630493086
GO:0005794Golgi apparatus0.0445692671275504
GO:0065003macromolecular complex assembly0.0468093399432393
GO:0022607cellular component assembly0.0486606617214176
GO:0015031protein transport0.0486923487162438
GO:0005783endoplasmic reticulum0.0486923487162438
GO:0046907intracellular transport0.0486923487162438
GO:0045184establishment of protein localization0.0486923487162438
GO:0008104protein localization0.0493019461405191
GO:0033036macromolecule localization0.049888461403827
GO:0012505endomembrane system0.049888461403827



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
myeloid cell3.20e-36112
common myeloid progenitor3.20e-36112
hematopoietic stem cell2.93e-34172
angioblastic mesenchymal cell2.93e-34172
hematopoietic cell2.34e-31182
hematopoietic oligopotent progenitor cell7.14e-31165
hematopoietic multipotent progenitor cell7.14e-31165
CD14-positive, CD16-negative classical monocyte4.29e-1042
classical monocyte4.03e-0945
myeloid lineage restricted progenitor cell5.83e-0970
leukocyte1.01e-08140
myeloid leukocyte1.15e-0876
hematopoietic lineage restricted progenitor cell5.55e-08124
nongranular leukocyte7.43e-08119
granulocyte monocyte progenitor cell8.11e-0871
monopoietic cell1.56e-0763
monocyte1.56e-0763
monoblast1.56e-0763
promonocyte1.56e-0763
mesenchymal cell1.57e-07358
macrophage dendritic cell progenitor3.72e-0765
connective tissue cell4.26e-07365
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.53e-19102
blood island5.53e-19102
hemolymphoid system2.59e-16112
blood1.99e-1215
haemolymphatic fluid1.99e-1215
organism substance1.99e-1215
hemopoietic organ8.48e-097
immune system2.51e-07115
bone marrow3.25e-0780
Disease
Ontology termp-valuen
myeloid leukemia9.13e-4431
leukemia1.00e-4039
hematologic cancer7.87e-3351
immune system cancer7.87e-3351
chronic leukemia6.69e-138
organ system cancer4.60e-07137


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
CCNT2#90556.336201576962639.78880505817628e-050.001389228171587
ELF1#199743.406478367046030.01235066105299550.0447288539327899
EP300#203345.419153380978560.00209386927943890.0121133115645776
FOSL1#8061431.77086377309841.96715033715934e-067.22388235100509e-05
GATA1#2623410.84824651504040.0001390956917094380.00181542301255211
GATA2#2624410.19594538684320.0001775447777609820.00215661770697595
REST#597859.650028716128021.19441074361324e-050.000301311747952229
TAL1#6886423.89489334195226.10828383356726e-060.000181491623127719
USF1#739145.089199421766370.00266867775360040.0147148532763989



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.