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Coexpression cluster:C1712: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;3:14.6146810753822:0.000649823731412567:0.00532289730862723
|tf_chipseq_enrich=BATF#10538;3:14.6146810753822:0.000649823731412567:0.00532289730862723
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98207,0.126545,0.0918749,0.0686325,0.0569043,0.0639461,0.387306,0.267408,0.312064,0.080156,0.274185,0.53753,0.0545112,0.510703,0.33844,0.0649137,0.0974216,0.595767,0.195675,0.00102387,0.176557,0.396547,0.0472148,0.735114,0.229138,0.0639045,0.141461,0.0900204,0.228387,0.385962,0.334921,0.296227,0.0234946,0.566117,0.0757402,0.430936,0.123626,0.270619,0.132705,0.285556,0.493429,0.233835,0.224471,0.262929,0.223204,0.143824,0.460679,0.11021,0.0775891,0.153079,0.257945,0.211515,0.00825397,0.175283,0.204954,0.209341,0.576888,0.629422,0.084895,0.160115,0.0819954,0.10091,0.122658,0.151161,0.228398,0.056055,0.120552,0.41771,0.893893,0.830533,0.335207,0.434016,0.190688,0.299739,0.278645,0.733648,0.0940982,0.0780533,0.564811,0.0993772,0.274769,0.448923,0.11602,0.344528,0.436413,0.0585992,0.20045,0.274438,0.76735,0.83616,0.0576826,0.336512,0.173868,0.109708,0.0162151,0.0809806,0.154589,0.318794,0.122767,0.0749261,0.176858,0.114361,0.347759,0.242462,0.0620267,0.211111,0.0738743,0.0882327,0.183058,0.150073,0.270522,0.16872,0.341388,0.00450945,0.359135,0.123404,0.430769,0.240825,0.3033,0.336623,0.163542,0.483244,0.27134,0.500871,0.239667,0.00541645,0.29809,0.0301117,0.689826,0.0330886,0.116923,0.148426,0.0983658,0.228743,0.238223,0.156976,0.0327573,0.267391,0.301441,0.21807,0.350528,0.382904,0.0199219,0.190404,0.135865,0.488841,0.18137,0.180609,0.291283,0.273972,0.153023,0.400137,0.37958,0.22307,0.160699,0.391307,0.166736,0.181253,0.0422294,0.263877,0.146486,0.769574,0.262486,0.294204,0.131936,0.288826,0.246621,0.463617,0.335656,0.0965376,0.377203,0.279263,0.336564,0.35463,0.581771,0.800557,0.0594155,0.587524,0.208795,0.0713793,0.212621,0.594469,0.53612,0.629713,0.21728,0.0722318,0.145569,0.0739871,0.537088,0.236988,0.629445,0.306963,0.569605,0.526495,0.215897,0.0473662,0.424482,0.820986,0.0700912,0.359678,0.561689,0.306829,0.00125038,0.255366,0.127834,0.67506,0.855024,0.349068,0.70429,0.476117,0.557035,0.427789,0.689998,0.386595,0.886619,0.433702,0.258394,0.277222,0.432123,0.759415,0.661773,0.494975,0.651196,0.392155,0.626931,0.371758,0.457109,0.562417,0.64845,0.85279,0.254547,0.408817,0.821811,0.1082,0.500384,0.541378,0.47213,0.29416,0.922144,0.666904,0.914902,0.315485,0.311289,0.318577,0.4488,0.389888,0.603509,0.511254,0.193221,0.246387,0.224252,0.587237,0.155054,0.466978,0.00665694,0.257848,0.0717012,0.0197899,0.427276,0.747776,0.466967,0.283682,0.424668,0.247468,0.474058,0.583101,0.341421,0.138015,0.530902,0.498956,0.792095,0.55798,0.708394,0.751439,0.723248,0.34194,0.226858,0.592314,0.27725,0.89036,0.763919,0.317485,0.633504,0.220564,0.845182,0.262394,0.307462,0.135076,0.133253,0.298027,0.274593,0.490712,0.541363,0.128394,0.218812,0.531474,0.364391,0.562305,0.528646,0.361524,0.31558,0.412744,0.54408,0.62698,0.513592,0.415367,0.503942,0.124718,0.36864,0.538745,0.456862,0.122994,0.680686,0.557093,0.693441,0.382214,0.553161,0.639572,0.326875,0.0655077,0.117434,0.306231,0.298354,0.278436,0.453817,0.457741,0.641611,0.426239,0.162155,0.656093,0.209347,0.412586,0.534679,0.41502,0.0487429,0.0962475,0.523749,0.0331565,0.307426,0.206772,0.196912,0.490527,0.714189,0.119992,0.813041,0.318338,0.276338,0.126433,0.102654,0.000661155,0.0555558,0.295666,0.393022,0.293641,0.116969,0.401231,0.255983,0.297663,0.256708,0.338258,0.322052,0.145568,0.153833,0.261242,0.38389,0.00878877,0.388459,0.321362,0.627637,0.280757,0.301366,0.340343,0.343265,0.501812,0.462092,0.336254,0.308589,0.291523,0.19697,0.309816,0.0537285,0.15063,0.198077,0.0439565,0.348739,0.419895,0.138495,0.208834,0.32256,0.377566,0.0667472,0.109684,0.322704,0.403482,0.181288,0.230841,0.352328,0.0357989,0.0707105,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.406458,0.0550411,0.512825,0.244656,0.0197801,0.158985,0.174153,0.0972854,0.333309,0.249919,0.339517,0.303699,0.198326,0.394084,0.458518,0.282501,0.252005,0.390891,0.238377,0.063694,0.197875,0.287909,0.289389,0.117618,0.392533,0.396962,0.316002,0.330317,0.321404,0.225079,0.300542,0.379651,0.185715,0.345505,0.0814929,0.271405,0.311201,0.221943,0.306427,0.367733,0.246925,0.208775,0.390438,0.343014,0.270094,0.276922,0.156279,0.313647,0.461742,0.422872,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.0919467,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.0203447,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.00268881,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.430541,0.508546,0.224871,0.398887,0.389061,0.310732,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.319519,0.309489,0.430805,0.0753413,0.140472,0.185476,0.336314,0.344469,0.184651,0.303359,0.297596,0.42392,0.107309,0.380826,0.259046,0.345068,0.151046,0.483953,0.347171,0.321735,0.15463,0.13907,0.0267252,0.269432,0.250466,0.0986342,0.115686,0.408975,0.162633,0.342661,0.27567,0.0337021,0.33299,0.384731,0.319112,0.526476
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.859849,0.106358,0.621241,0.778743,0.752887,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.501863,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.700122,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.195238,0.413782,0.654459,0.388123,0.301779,1.06799,0.580638,0.821929,0.451846,0.218848,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,1.30959,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.0719601,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.606298,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.285668,1.45429,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.953361,0.526389,0.126633,1.15522,0.840171,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.923751,0.731946,0.0938701
}}
}}

Revision as of 15:03, 26 November 2012


Full id: C1712_CD14_Peripheral_Basophils_Mast_CD14CD16_CD34_Natural



Phase1 CAGE Peaks

Hg19::chr13:99934429..99934435,+p@chr13:99934429..99934435
+
Hg19::chr15:67413848..67413862,+p@chr15:67413848..67413862
+
Hg19::chr17:72776166..72776178,-p@chr17:72776166..72776178
-
Hg19::chr19:2495374..2495386,-p@chr19:2495374..2495386
-
Hg19::chr8:48540648..48540655,+p@chr8:48540648..48540655
+


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 monocyte4.82e-6042
CD14-positive, CD16-negative classical monocyte4.82e-6042
myeloid leukocyte9.03e-5472
defensive cell6.71e-5248
phagocyte6.71e-5248
intermediate monocyte1.02e-469
CD14-positive, CD16-positive monocyte1.02e-469
myeloid lineage restricted progenitor cell1.83e-4666
granulocyte monocyte progenitor cell1.07e-4567
monopoietic cell2.20e-4459
monocyte2.20e-4459
monoblast2.20e-4459
promonocyte2.20e-4459
macrophage dendritic cell progenitor8.81e-4361
leukocyte1.84e-42136
nongranular leukocyte1.36e-36115
myeloid cell5.46e-34108
common myeloid progenitor5.46e-34108
hematopoietic stem cell3.92e-33168
angioblastic mesenchymal cell3.92e-33168
hematopoietic lineage restricted progenitor cell4.28e-32120
hematopoietic cell4.12e-31177
hematopoietic oligopotent progenitor cell2.80e-28161
hematopoietic multipotent progenitor cell2.80e-28161
stuff accumulating cell2.47e-2687
basophil4.73e-173
single nucleate cell8.05e-173
mononuclear cell8.05e-173
non-classical monocyte8.02e-163
CD14-low, CD16-positive monocyte8.02e-163
natural killer cell8.44e-163
pro-NK cell8.44e-163
mesenchymal cell4.15e-13354
connective tissue cell1.02e-12361
motile cell2.47e-11386
stem cell5.49e-10441
multi fate stem cell1.22e-09427
somatic stem cell2.09e-09433
circulating cell1.21e-086
Uber Anatomy
Ontology termp-valuen
bone marrow5.78e-4376
hematopoietic system7.91e-4198
blood island7.91e-4198
bone element1.94e-3982
hemolymphoid system1.65e-36108
skeletal element1.85e-3590
immune system3.85e-3493
skeletal system2.27e-31100
lateral plate mesoderm1.43e-16203
musculoskeletal system1.57e-16167
connective tissue3.51e-12371
mesoderm1.84e-08315
mesoderm-derived structure1.84e-08315
presumptive mesoderm1.84e-08315


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
BATF#10538314.61468107538220.0006498237314125670.00532289730862723



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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