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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.338474986694436,0.141082552525447,0.0625128387853364,0,0,0,0,0,0.104449645142297,0.191449731291012,0.146465690858417,0.127824212621857,0,0,0,0.110857771591861,0.139210117864267,0,0.0907619220526865,0.260628401312869,0.339112246739202,0.270230845683375,0.247600673195823,0.092187879276543,0.308401558284621,0.360019282223445,0,0.138771381856642,0.189156758681335,0.223799672996739,0.403192519147754,0.21533560773887,0,0,0.0789870938765965,0,0.390329518135136,0,0,0.097343627213097,0,0.319302691559872,0,0,0,0.153055502916071,0.214264287421827,0.0826628337153937,0.126126825037818,0,0,0.195906702716978,0.145455399178477,0.321388154237037,0,0.24072110768047,0,0,0,0,0,0,0,0,0,0.365808586596611,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0523039447392876,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.027549189648299,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0704430934380941,0.728669478596184,0.689418861331763,0.824835589086681,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0781053106522872,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.180895695795133,0.0708131280657094,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.136572456909283,0.0458823664830172,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.103959518714163,0,0.71846931508722,0,0.0302919092799627,0,0,0,0.0929817338882301,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.119873612497281,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0266094859650764,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.106966425460878,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.149361575991736,0,0,0,0,0,0,0,0,0.00458877934581747,0,0,0,0,0,0,0,0,0,0.12315641958565,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0500863030838633,0,0,0,0|full_id=C3991_acute_Mast_leukemia_chronic_Basophils_CD14_hepatoblastoma|gostat_on_coexpression_clusters=GO:0016290!palmitoyl-CoA 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|full_id=C3991_acute_Mast_leukemia_chronic_Basophils_CD14_hepatoblastoma
|gostat_on_coexpression_clusters=GO:0016290!palmitoyl-CoA hydrolase activity!0.0120398951040804!11332$GO:0000062!acyl-CoA binding!0.0120398951040804!11332$GO:0016291!acyl-CoA thioesterase activity!0.0120398951040804!11332$GO:0016289!CoA hydrolase activity!0.0120398951040804!11332$GO:0005504!fatty acid binding!0.0120398951040804!11332
|id=C3991
|ontology_enrichment_celltype=CL:0000037!1.81e-42!172;CL:0000566!1.81e-42!172;CL:0002032!2.97e-39!165;CL:0000837!2.97e-39!165;CL:0000738!3.18e-38!140;CL:0000988!8.34e-38!182;CL:0000763!1.07e-33!112;CL:0000049!1.07e-33!112;CL:0002031!1.52e-33!124;CL:0002087!4.94e-30!119;CL:0000557!5.67e-30!71;CL:0000839!9.16e-30!70;CL:0000766!3.75e-29!76;CL:0002009!3.81e-26!65;CL:0002194!2.07e-25!63;CL:0000576!2.07e-25!63;CL:0000040!2.07e-25!63;CL:0000559!2.07e-25!63;CL:0000860!2.77e-25!45;CL:0002057!3.50e-25!42
|ontology_enrichment_disease=DOID:162!4.67e-09!235;DOID:14566!2.20e-08!239;DOID:0050687!3.88e-07!143
|ontology_enrichment_uberon=UBERON:0002390!2.10e-27!102;UBERON:0003061!2.10e-27!102;UBERON:0002371!2.30e-26!80;UBERON:0001474!1.36e-23!86;UBERON:0002193!5.95e-23!112;UBERON:0002405!1.22e-20!115;UBERON:0004765!4.62e-19!101;UBERON:0001434!4.62e-19!101
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167648594086996!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.0039154095051126
|tfbs_overrepresentation=0.147255,0.0586687,0.039404,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.00599201,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.131316,0.782949,0.268011,0.563047,0.823736,0.807281,0.335423,0.629514,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.53472,0.615744,0.271958,0.292154,0.405773,0.39729,0.581713,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.647576,0.528324,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.577664,0.0474194,0.448095,0.576651,0.416816,0.292835,0.476744,0.439556,0.373868,0.57762,0.608919,0.18237,0.706298,0.248484,0.747852,0.275351,0.236471,0.185661,0.346319,0.179399,0.270984,0.258117,0.503058,0.513852,0.522083,0.248634,0.281576,0.472384,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.421596,0.581837,0.412837,0.671377,0.546839,0.551561,0.448039,0.218623,0.312808,0.333034,0.0451077,0.0747529,0.229003,0.650179,0.223844,0.50215,0.294698,0.34331,0.138202,0.289204,0.327108,0.683186,0.278044,0.490301,0.428671,0.228096,0.336314,0.19763,0.15631,0.567452,0.421464,0.48267,0.420626,0.516462,0.858756,0.335105,0.144809,0.145539,0.08628,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.2348,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.464871,0.753577,0.206222,0.171685,0.284166,0.113671,0.269226,0.339277,0.552319,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.625309,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.630264,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.0434097,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.065697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}}

Latest revision as of 12:37, 17 September 2013


Full id: C3991_acute_Mast_leukemia_chronic_Basophils_CD14_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr1:6355208..6355215,-p25@ACOT7
Hg19::chr20:36322424..36322516,+p1@CTNNBL1
Hg19::chr2:219152622..219152637,-p@chr2:219152622..219152637
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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:0016290palmitoyl-CoA hydrolase activity0.0120398951040804
GO:0000062acyl-CoA binding0.0120398951040804
GO:0016291acyl-CoA thioesterase activity0.0120398951040804
GO:0016289CoA hydrolase activity0.0120398951040804
GO:0005504fatty acid binding0.0120398951040804



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
classical monocyte2.45e-6642
CD14-positive, CD16-negative classical monocyte2.45e-6642
myeloid lineage restricted progenitor cell1.06e-5866
defensive cell4.33e-5748
phagocyte4.33e-5748
myeloid leukocyte1.03e-5672
granulocyte monocyte progenitor cell5.65e-5167
myeloid cell1.13e-49108
common myeloid progenitor1.13e-49108
monopoietic cell3.80e-4459
monocyte3.80e-4459
monoblast3.80e-4459
promonocyte3.80e-4459
macrophage dendritic cell progenitor1.78e-4261
hematopoietic stem cell2.92e-39168
angioblastic mesenchymal cell2.92e-39168
hematopoietic cell9.87e-37177
hematopoietic oligopotent progenitor cell1.54e-35161
hematopoietic multipotent progenitor cell1.54e-35161
leukocyte2.84e-35136
hematopoietic lineage restricted progenitor cell1.68e-34120
intermediate monocyte2.24e-319
CD14-positive, CD16-positive monocyte2.24e-319
stuff accumulating cell2.56e-3087
nongranular leukocyte7.45e-28115
mesenchymal cell8.12e-15354
connective tissue cell2.57e-14361
motile cell1.49e-12386
histamine secreting cell1.56e-125
biogenic amine secreting cell1.56e-125
granulocytopoietic cell1.56e-125
mast cell1.56e-125
mast cell progenitor1.56e-125
basophil mast progenitor cell1.56e-125
non-classical monocyte6.87e-123
CD14-low, CD16-positive monocyte6.87e-123
basophil1.96e-113
stem cell1.67e-10441
multi fate stem cell2.13e-10427
somatic stem cell4.21e-10433
erythroid lineage cell8.77e-082
erythroblast8.77e-082
megakaryocyte-erythroid progenitor cell8.77e-082
erythroid progenitor cell8.77e-082
reticulocyte8.77e-082
proerythroblast8.77e-082
basophilic erythroblast8.77e-082
polychromatophilic erythroblast8.77e-082
orthochromatic erythroblast8.77e-082
endocrine cell5.92e-079
Uber Anatomy
Ontology termp-valuen
bone marrow6.01e-4776
bone element6.32e-4382
hematopoietic system2.59e-3998
blood island2.59e-3998
skeletal element2.17e-3890
immune system6.90e-3793
hemolymphoid system7.06e-35108
skeletal system9.88e-34100
musculoskeletal system6.93e-17167
lateral plate mesoderm1.02e-16203
connective tissue1.71e-14371
mesoderm5.69e-09315
mesoderm-derived structure5.69e-09315
presumptive mesoderm5.69e-09315


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)
MA0003.10.0471418
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.12.29491
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.21.34467
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.481578
MA0102.21.88331
MA0258.11.29138
MA0259.11.40979
MA0442.10



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
EP300#203336.77394172622320.003216880500103790.0167648594086996
HDAC2#3066313.41562023662630.0004140761399857210.0039154095051126



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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