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Coexpression cluster:C1734: Difference between revisions

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|tf_chipseq_enrich=FOSL1#8061;2:15.8854318865492:0.00602602150581133:0.0270038470799549!JUN#3725;4:10.0102633538691:0.000190853134780107:0.00230513594810912!JUND#3727;4:5.59573115349682:0.00184959330175546:0.0109326885982251!STAT3#6774;3:6.31167899829254:0.00741117212246054:0.0306116434762767
|tf_chipseq_enrich=FOSL1#8061;2:15.8854318865492:0.00602602150581133:0.0270038470799549!JUN#3725;4:10.0102633538691:0.000190853134780107:0.00230513594810912!JUND#3727;4:5.59573115349682:0.00184959330175546:0.0109326885982251!STAT3#6774;3:6.31167899829254:0.00741117212246054:0.0306116434762767
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0809,0.0898207,0.126545,0.0918749,0.0686325,0.0569043,0.0639461,0.387306,0.267408,0.0547349,0.080156,0.274185,0.53753,0.0545112,0.00618348,0.33844,0.0649137,0.0974216,0.595767,0.195675,0.174786,0.176557,0.396547,0.0472148,0.735114,0.229138,0.0639045,0.141461,0.0900204,0.228387,0.385962,0.00835393,0.296227,0.0234946,0.566117,0.36304,0.430936,0.123626,0.270619,0.132705,0.285556,0.493429,0.233835,0.224471,0.262929,0.223204,0.143824,0.460679,0.431098,0.00309105,0.153079,0.62577,0.211515,0.125701,0.175283,0.0226059,0.209341,0.855975,0.629422,0.00371012,0.160115,0.0819954,0.10091,0.122658,0.151161,0.228398,0.056055,0.00757731,0.41771,0.893893,0.529713,0.0637856,0.434016,0.190688,0.00578502,0.278645,0.733648,0.0940982,0.0780533,0.564811,0.0993772,0.274769,0.448923,0.11602,0.344528,0.436413,0.0585992,0.0215858,0.0416714,0.911136,0.989834,0.319826,0.336512,0.173868,0.109708,0.174594,0.0809806,0.154589,0.318794,0.122767,0.0749261,0.176858,0.114361,0.347759,0.242462,0.0620267,0.0240419,0.0738743,0.0882327,0.183058,0.150073,0.270522,0.16872,0.341388,0.0934526,0.359135,0.00794839,0.430769,0.240825,0.3033,0.336623,0.163542,0.483244,0.27134,0.500871,0.239667,0.10226,0.29809,0.235147,0.689826,0.245965,0.116923,0.148426,0.0983658,0.228743,0.238223,0.156976,0.244789,0.267391,0.301441,0.21807,0.350528,0.382904,0.0199219,0.190404,0.135865,0.488841,0.18137,0.180609,0.291283,0.273972,0.153023,0.400137,0.37958,0.22307,0.160699,0.391307,0.0147448,0.181253,0.0422294,0.263877,0.146486,0.183121,0.262486,0.294204,0.131936,0.288826,0.0332739,0.463617,0.697373,0.0965376,0.377203,0.279263,0.336564,0.0720023,0.581771,0.800557,0.0594155,0.587524,0.208795,0.0713793,0.212621,0.594469,0.53612,0.629713,0.581874,0.355154,0.730614,0.619037,0.180545,0.236988,0.261576,0.306963,0.569605,0.526495,0.580285,0.550495,0.764863,0.248142,0.610475,0.881697,0.0100646,0.672416,0.685628,0.255366,0.349408,0.458608,0.967174,0.349068,0.70429,0.798758,0.557035,0.0191917,0.689998,0.737642,0.886619,0.433702,0.258394,0.644878,0.0198763,0.759415,0.661773,0.494975,0.0224281,0.0895484,0.259088,0.371758,0.91821,0.562417,0.890566,0.85279,0.00339523,0.901563,0.0969507,0.680843,0.746881,0.183869,0.725301,0.660884,0.723387,0.666904,0.914902,0.315485,0.311289,0.318577,0.4488,0.389888,0.603509,0.511254,0.0482305,0.0332078,0.224252,0.587237,0.155054,0.466978,0.518234,0.257848,0.353942,0.192234,0.0191118,0.747776,0.466967,0.044696,0.424668,0.7175,0.215833,0.218352,0.702164,0.0281446,0.530902,0.498956,0.209091,0.55798,0.708394,0.932831,0.723248,0.34194,0.592696,0.0133236,0.644904,0.89036,0.423117,0.317485,0.01922,0.0263405,0.845182,0.262394,0.307462,0.135076,0.469588,0.298027,0.0417211,0.490712,0.541363,0.709432,0.218812,0.531474,0.137231,0.200667,0.528646,0.361524,0.31558,0.412744,0.54408,0.259136,0.513592,0.415367,0.503942,0.124718,0.011528,0.181824,0.456862,0.122994,0.680686,0.557093,0.116707,0.382214,0.048225,0.639572,0.326875,0.0655077,0.332211,0.306231,0.298354,0.646049,0.784543,0.125872,0.0851712,0.426239,0.748909,0.0931042,0.572661,0.412586,0.178696,0.41502,0.55475,0.294859,0.523749,0.499347,0.307426,0.462582,0.557732,0.490527,0.714189,0.0225451,0.813041,0.318338,0.0422834,0.126433,0.417412,0.318174,0.0555558,0.295666,0.393022,0.0480884,0.116969,0.0941346,0.255983,0.297663,0.256708,0.0650385,0.322052,0.145568,0.153833,0.261242,0.38389,0.54721,0.388459,0.321362,0.259785,0.0437263,0.050816,0.340343,0.343265,0.501812,0.462092,0.336254,0.053444,0.291523,0.19697,0.309816,0.0537285,0.15063,0.198077,0.281455,0.348739,0.419895,0.138495,0.0235054,0.00737169,0.377566,0.342366,0.109684,0.322704,0.403482,0.181288,0.230841,0.0709982,0.255358,0.351665,0.265112,0.0633313,0.00602216,0.0854747,0.0747609,0.406458,0.312881,0.512825,0.0327199,0.192188,0.158985,0.174153,0.0972854,0.333309,0.249919,0.339517,0.303699,0.198326,0.394084,0.458518,0.282501,0.252005,0.390891,0.238377,0.334983,0.197875,0.287909,0.0051548,0.117618,0.392533,0.0919602,0.0562195,0.330317,0.321404,0.225079,0.300542,0.379651,0.185715,0.345505,0.0814929,0.271405,0.311201,0.221943,0.306427,0.0114324,0.246925,0.208775,0.390438,0.343014,0.270094,0.276922,0.156279,0.313647,0.128336,0.10563,0.00848325,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.060398,0.292869,0.358198,0.00552168,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.116796,0.430541,0.508546,0.224871,0.398887,0.389061,0.0542381,0.349611,0.11881,0.385709,0.0428885,0.107629,0.0152991,0.0237345,0.253154,0.319519,0.0537766,0.430805,0.00119205,0.480785,0.185476,0.0642384,0.344469,0.184651,0.00601812,0.297596,0.42392,0.425912,0.380826,0.259046,0.067885,0.151046,0.0296322,0.00941969,0.321735,0.15463,0.0101526,0.470121,0.269432,0.250466,0.409882,0.115686,0.0164276,0.162633,0.342661,0.27567,0.248127,0.0628839,0.0858973,0.319112,0.526476
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,1.15291,0.653236,0.733342,0.866061,0.321368,0.106358,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,1.02276,0.287891,0.167776,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.700122,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.0526856,0.413782,0.654459,1.00769,0.301779,0.415749,0.580638,0.414516,0.451846,0.218848,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.880217,0.189341,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.796279,0.934302,0.755403,0.873042,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.96134,0.455791,0.99322,0.28626,1.06255,1.97764,0.211081,1.01093,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,1.23742,1.52665,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,2.12036,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,1.44357,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572
}}
}}

Revision as of 15:04, 26 November 2012


Full id: C1734_immature_Basophils_CD14_Mast_Natural_CD34_Eosinophils



Phase1 CAGE Peaks

Hg19::chr14:90379471..90379485,+p@chr14:90379471..90379485
+
Hg19::chr15:50358743..50358748,+p@chr15:50358743..50358748
+
Hg19::chr1:151918514..151918521,+p@chr1:151918514..151918521
+
Hg19::chr1:151964954..151964962,-p@chr1:151964954..151964962
-
Hg19::chr8:27252724..27252729,-p@chr8:27252724..27252729
-


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
classical monocyte2.31e-10242
CD14-positive, CD16-negative classical monocyte2.31e-10242
defensive cell1.28e-8848
phagocyte1.28e-8848
granulocyte monocyte progenitor cell2.13e-8667
myeloid leukocyte1.26e-8472
macrophage dendritic cell progenitor4.33e-8161
myeloid lineage restricted progenitor cell5.73e-7866
monopoietic cell5.93e-7459
monocyte5.93e-7459
monoblast5.93e-7459
promonocyte5.93e-7459
myeloid cell2.05e-60108
common myeloid progenitor2.05e-60108
leukocyte5.39e-57136
hematopoietic lineage restricted progenitor cell2.16e-50120
stuff accumulating cell1.87e-4887
hematopoietic stem cell7.61e-47168
angioblastic mesenchymal cell7.61e-47168
nongranular leukocyte1.83e-44115
hematopoietic cell5.06e-44177
hematopoietic oligopotent progenitor cell2.85e-42161
hematopoietic multipotent progenitor cell2.85e-42161
mesenchymal cell1.31e-18354
connective tissue cell4.54e-18361
motile cell3.61e-16386
basophil1.42e-143
multi fate stem cell7.66e-14427
somatic stem cell1.60e-13433
stem cell4.17e-13441
intermediate monocyte5.44e-129
CD14-positive, CD16-positive monocyte5.44e-129
CD1a-positive Langerhans cell2.74e-102
immature CD1a-positive Langerhans cell2.74e-102
histamine secreting cell1.22e-075
biogenic amine secreting cell1.22e-075
granulocytopoietic cell1.22e-075
mast cell1.22e-075
mast cell progenitor1.22e-075
basophil mast progenitor cell1.22e-075
somatic cell2.18e-07588
immature conventional dendritic cell2.81e-075
common dendritic progenitor2.81e-075
natural killer cell9.47e-073
pro-NK cell9.47e-073
Uber Anatomy
Ontology termp-valuen
bone marrow1.36e-7976
bone element3.15e-7382
hematopoietic system1.02e-6698
blood island1.02e-6698
skeletal element4.81e-6690
immune system1.15e-6393
hemolymphoid system8.43e-60108
skeletal system1.16e-58100
musculoskeletal system7.56e-32167
lateral plate mesoderm7.15e-28203
connective tissue2.47e-17371
mesoderm7.62e-15315
mesoderm-derived structure7.62e-15315
presumptive mesoderm7.62e-15315


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
FOSL1#8061215.88543188654920.006026021505811330.0270038470799549
JUN#3725410.01026335386910.0001908531347801070.00230513594810912
JUND#372745.595731153496820.001849593301755460.0109326885982251
STAT3#677436.311678998292540.007411172122460540.0306116434762767



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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