Coexpression cluster:C282: Difference between revisions

Revision as of 18:38, 8 August 2012

Full id: C282_acute_B_tonsil_CD19_submaxillary_lymph_throat

Phase1 CAGE Peaks

Hg19::chr11:69440459..69440517,-	p@chr11:69440459..69440517 -
Hg19::chr11:69452606..69452638,-	p@chr11:69452606..69452638 -
Hg19::chr13:80975502..80975505,+	p@chr13:80975502..80975505 +
Hg19::chr13:80975508..80975547,+	p@chr13:80975508..80975547 +
Hg19::chr14:106240433..106240439,-	p@chr14:106240433..106240439 -
Hg19::chr14:106240442..106240463,-	p@chr14:106240442..106240463 -
Hg19::chr14:106241955..106241965,-	p@chr14:106241955..106241965 -
Hg19::chr14:106241968..106241975,-	p@chr14:106241968..106241975 -
Hg19::chr14:106318085..106318118,-	p@chr14:106318085..106318118 -
Hg19::chr14:106320365..106320378,-	p7@IGHM
Hg19::chr14:106330248..106330263,-	p@chr14:106330248..106330263 -
Hg19::chr14:106330406..106330426,-	p1@uc001yrs.2 p1@uc001yrx.1 p1@uc001yrz.1 p1@uc001yse.2 p1@uc001ysm.1
Hg19::chr14:106330458..106330479,-	p1@IGHJ4
Hg19::chr14:106573756..106573760,-	p1@IGHV3-11
Hg19::chr14:96178718..96178752,-	p3@TCL1A
Hg19::chr16:33647774..33647776,-	p1@IGHV3OR16-8
Hg19::chr17:22021942..22021966,+	p@chr17:22021942..22021966 +
Hg19::chr1:105475811..105475815,+	p@chr1:105475811..105475815 +
Hg19::chr1:206290083..206290090,-	p@chr1:206290083..206290090 -
Hg19::chr1:206290105..206290116,-	p@chr1:206290105..206290116 -
Hg19::chr1:206290131..206290135,-	p@chr1:206290131..206290135 -
Hg19::chr1:206290138..206290146,-	p@chr1:206290138..206290146 -
Hg19::chr21:43896378..43896387,-	p@chr21:43896378..43896387 -
Hg19::chr21:43896807..43896814,-	p@chr21:43896807..43896814 -
Hg19::chr21:43896815..43896826,-	p@chr21:43896815..43896826 -
Hg19::chr21:43896828..43896833,-	p@chr21:43896828..43896833 -
Hg19::chr21:43896856..43896865,-	p@chr21:43896856..43896865 -
Hg19::chr21:43896927..43896934,-	p@chr21:43896927..43896934 -
Hg19::chr21:43896964..43896973,-	p@chr21:43896964..43896973 -
Hg19::chr22:22380255..22380263,-	p@chr22:22380255..22380263 -
Hg19::chr22:22380413..22380443,+	p1@uc002zvv.2
Hg19::chr22:22550153..22550172,+	p1@IGLV6-57
Hg19::chr22:22550534..22550548,-	p@chr22:22550534..22550548 -
Hg19::chr22:23246848..23246854,+	p@chr22:23246848..23246854 +
Hg19::chr22:23247044..23247061,+	p1@IGLJ3
Hg19::chr22:23247146..23247167,+	p1@AL713800
Hg19::chr2:111806761..111806769,+	p@chr2:111806761..111806769 +
Hg19::chr2:111806795..111806824,+	p@chr2:111806795..111806824 +
Hg19::chr2:212793161..212793168,-	p@chr2:212793161..212793168 -
Hg19::chr2:239016429..239016447,+	p4@ESPNL
Hg19::chr3:169650168..169650205,+	p1@ENST00000493762
Hg19::chr3:3150439..3150454,-	p1@X61177
Hg19::chr4:144312629..144312638,+	p30@GAB1
Hg19::chr5:114607144..114607156,-	p9@CCDC112
Hg19::chr7:115799916..115799932,-	p6@TFEC
Hg19::chr7:115799942..115799955,-	p5@TFEC

Enriched pathways on this co-expression clusterSummary: 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. Analyst: Emmanuel Dimont link to source dataset data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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. Analyst: Erik Arner link to source dataset data

GO ID	GO name	FDR corrected p-value
GO:0000187	activation of MAPK activity	0.0023026497156705
GO:0043406	positive regulation of MAP kinase activity	0.0023026497156705
GO:0043405	regulation of MAP kinase activity	0.00304662663369834
GO:0045860	positive regulation of protein kinase activity	0.00304662663369834
GO:0033674	positive regulation of kinase activity	0.00304662663369834
GO:0051347	positive regulation of transferase activity	0.00304662663369834
GO:0000165	MAPKKK cascade	0.00304662663369834
GO:0042571	immunoglobulin complex, circulating	0.00304662663369834
GO:0045859	regulation of protein kinase activity	0.00487417214319682
GO:0043549	regulation of kinase activity	0.00487417214319682
GO:0051338	regulation of transferase activity	0.00487417214319682
GO:0043085	positive regulation of catalytic activity	0.00487417214319682
GO:0045022	early endosome to late endosome transport	0.00487417214319682
GO:0019814	immunoglobulin complex	0.00487417214319682
GO:0019815	B cell receptor complex	0.00487417214319682
GO:0045120	pronucleus	0.00761522141604439
GO:0007243	protein kinase cascade	0.00879561980076875
GO:0030890	positive regulation of B cell proliferation	0.0121822023344553
GO:0030888	regulation of B cell proliferation	0.0128228046362587
GO:0050853	B cell receptor signaling pathway	0.0133992391451083
GO:0050790	regulation of catalytic activity	0.0163912991334839
GO:0001772	immunological synapse	0.0163912991334839
GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	0.0163912991334839
GO:0045807	positive regulation of endocytosis	0.0163912991334839
GO:0050871	positive regulation of B cell activation	0.0163912991334839
GO:0042100	B cell proliferation	0.0163912991334839
GO:0065009	regulation of a molecular function	0.0163912991334839
GO:0005624	membrane fraction	0.0163912991334839
GO:0007257	activation of JNK activity	0.0163912991334839
GO:0042327	positive regulation of phosphorylation	0.0163912991334839
GO:0043507	positive regulation of JNK activity	0.0163912991334839
GO:0008283	cell proliferation	0.0163912991334839
GO:0043506	regulation of JNK activity	0.0163912991334839
GO:0045937	positive regulation of phosphate metabolic process	0.0163912991334839
GO:0050864	regulation of B cell activation	0.0163912991334839
GO:0001934	positive regulation of protein amino acid phosphorylation	0.0163912991334839
GO:0033240	positive regulation of amine metabolic process	0.0163912991334839
GO:0045764	positive regulation of amino acid metabolic process	0.0163912991334839
GO:0050851	antigen receptor-mediated signaling pathway	0.0163912991334839
GO:0050730	regulation of peptidyl-tyrosine phosphorylation	0.0163912991334839
GO:0032946	positive regulation of mononuclear cell proliferation	0.0163912991334839
GO:0002455	humoral immune response mediated by circulating immunoglobulin	0.0163912991334839
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.0163912991334839
GO:0050671	positive regulation of lymphocyte proliferation	0.0163912991334839
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.0163912991334839
GO:0002757	immune response-activating signal transduction	0.0163912991334839
GO:0008286	insulin receptor signaling pathway	0.0163912991334839
GO:0007173	epidermal growth factor receptor signaling pathway	0.0163912991334839
GO:0002764	immune response-regulating signal transduction	0.0163912991334839
GO:0030100	regulation of endocytosis	0.0165495141687404
GO:0000267	cell fraction	0.0165497714336796
GO:0051050	positive regulation of transport	0.0177819698294001
GO:0016197	endosome transport	0.0179265752713593
GO:0005515	protein binding	0.0179265752713593
GO:0018108	peptidyl-tyrosine phosphorylation	0.0179265752713593
GO:0050670	regulation of lymphocyte proliferation	0.0179265752713593
GO:0032944	regulation of mononuclear cell proliferation	0.0179265752713593
GO:0018212	peptidyl-tyrosine modification	0.0183431605664613
GO:0001932	regulation of protein amino acid phosphorylation	0.0183431605664613
GO:0033238	regulation of amine metabolic process	0.0183431605664613
GO:0006521	regulation of amino acid metabolic process	0.0183431605664613
GO:0005070	SH3/SH2 adaptor activity	0.0189530390991739
GO:0009897	external side of plasma membrane	0.0189530390991739
GO:0051251	positive regulation of lymphocyte activation	0.0189530390991739
GO:0016064	immunoglobulin mediated immune response	0.0189530390991739
GO:0019724	B cell mediated immunity	0.0189530390991739
GO:0032943	mononuclear cell proliferation	0.0189530390991739
GO:0046651	lymphocyte proliferation	0.0189530390991739
GO:0060090	molecular adaptor activity	0.02083679111693
GO:0030334	regulation of cell migration	0.02083679111693
GO:0042113	B cell activation	0.0208847812912211
GO:0042325	regulation of phosphorylation	0.0210207957278815
GO:0048471	perinuclear region of cytoplasm	0.0210207957278815
GO:0005938	cell cortex	0.0210207957278815
GO:0007254	JNK cascade	0.021063658652235
GO:0031098	stress-activated protein kinase signaling pathway	0.0212209605631963
GO:0051174	regulation of phosphorus metabolic process	0.0212209605631963
GO:0019220	regulation of phosphate metabolic process	0.0212209605631963
GO:0051270	regulation of cell motility	0.0212209605631963
GO:0002253	activation of immune response	0.0212209605631963
GO:0002449	lymphocyte mediated immunity	0.0212209605631963
GO:0040012	regulation of locomotion	0.0212209605631963
GO:0040011	locomotion	0.0212209605631963
GO:0006959	humoral immune response	0.0212209605631963
GO:0002250	adaptive immune response	0.0212209605631963
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0212209605631963
GO:0051249	regulation of lymphocyte activation	0.0212209605631963
GO:0002443	leukocyte mediated immunity	0.0215300114771818
GO:0050865	regulation of cell activation	0.0218320211279736
GO:0050778	positive regulation of immune response	0.0226816985347564
GO:0051247	positive regulation of protein metabolic process	0.0226816985347564
GO:0002684	positive regulation of immune system process	0.0226980986752123
GO:0030674	protein binding, bridging	0.0237542528318918
GO:0050776	regulation of immune response	0.0253015340852191
GO:0002682	regulation of immune system process	0.0255438676217569
GO:0051240	positive regulation of multicellular organismal process	0.0265358127991985
GO:0003714	transcription corepressor activity	0.0266815515246408
GO:0043235	receptor complex	0.0266815515246408
GO:0002252	immune effector process	0.0266815515246408
GO:0051049	regulation of transport	0.0266815515246408
GO:0006979	response to oxidative stress	0.0287602416636037
GO:0018193	peptidyl-amino acid modification	0.0287602416636037
GO:0050794	regulation of cellular process	0.0332470558260694
GO:0009986	cell surface	0.0344601844956273
GO:0046649	lymphocyte activation	0.0357352879018642
GO:0007242	intracellular signaling cascade	0.0362287889255353
GO:0005792	microsome	0.0366396893322418
GO:0042598	vesicular fraction	0.037857257568268
GO:0050789	regulation of biological process	0.0387558675942245
GO:0003823	antigen binding	0.0389146599002675
GO:0045321	leukocyte activation	0.0391106792141685
GO:0044424	intracellular part	0.0391106792141685
GO:0003713	transcription coactivator activity	0.0400040428996724
GO:0010324	membrane invagination	0.041392071455171
GO:0006897	endocytosis	0.041392071455171
GO:0001775	cell activation	0.0433443669758211
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.0433443669758211
GO:0016564	transcription repressor activity	0.0437879095111814
GO:0065007	biological regulation	0.0460642644108429
GO:0016477	cell migration	0.0464545485533415
GO:0008284	positive regulation of cell proliferation	0.0464545485533415
GO:0007166	cell surface receptor linked signal transduction	0.0473492756125023

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji links to source dataset cell_data uberon_data

Cell Type
Ontology term	p-value	n
leukocyte	3.93e-25	140
hematopoietic stem cell	4.39e-23	172
angioblastic mesenchymal cell	4.39e-23	172
nongranular leukocyte	7.85e-21	119
hematopoietic oligopotent progenitor cell	1.31e-20	165
hematopoietic multipotent progenitor cell	1.31e-20	165
hematopoietic cell	3.53e-20	182
lymphocyte of B lineage	3.54e-19	24
pro-B cell	3.54e-19	24
hematopoietic lineage restricted progenitor cell	5.35e-19	124
lymphocyte	4.39e-14	53
common lymphoid progenitor	4.39e-14	53
lymphoid lineage restricted progenitor cell	2.00e-13	52
B cell	2.98e-12	14
myeloid leukocyte	2.99e-09	76
myeloid cell	1.89e-08	112
common myeloid progenitor	1.89e-08	112
granulocyte monocyte progenitor cell	1.03e-07	71
myeloid lineage restricted progenitor cell	2.92e-07	70
monopoietic cell	7.05e-07	63
monocyte	7.05e-07	63
monoblast	7.05e-07	63
promonocyte	7.05e-07	63
macrophage dendritic cell progenitor	7.94e-07	65

Uber Anatomy
Ontology term	p-value	n
adult organism	6.38e-32	115
hematopoietic system	5.70e-13	102
blood island	5.70e-13	102
hemolymphoid system	3.78e-11	112
blood	5.20e-08	15
haemolymphatic fluid	5.20e-08	15
organism substance	5.20e-08	15

Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon link to source data Novel motifs data Jaspar motifs data

Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysisSummary: 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. Analyst: Erik Arner link to source dataset data

No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. Analyst:NA link to data source data

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

@@ Line 6: / Line 6: @@
 |ontology_enrichment_disease=
 |ontology_enrichment_uberon=UBERON:0007023!6.38e-32!115;UBERON:0002390!5.70e-13!102;UBERON:0003061!5.70e-13!102;UBERON:0002193!3.78e-11!112;UBERON:0000178!5.20e-08!15;UBERON:0000179!5.20e-08!15;UBERON:0000463!5.20e-08!15
+|tfbs_overrepresentation=0.913058,0.604283,0.651416,0.527476,0.967189,0.965921,0.490358,0.999728,0.399564,0.329216,0.669682,0.980072,0.959555,0.873134,0.706103,0.624608,0.676035,0.795036,0.202967,0.826819,0.959451,0.640736,0.730585,0.783216,0.478511,0.718167,0.874568,0.767358,0.687084,0.777534,0.970304,0.843816,0.243463,0.972133,0.652005,0.741597,1,0.490038,0.860016,0.653027,0.788952,0.317572,0.901066,0.602777,0.861391,0.432221,0.448046,0.953634,0.539825,0.862076,0.923125,0.574335,0.672241,0.441052,0.96657,0.451551,0.825018,0.974449,0.713668,0.819271,0.367475,0.916378,0.828433,0.702141,0.577016,0.548142,0.898644,0.612833,0.748436,0.939355,0.932735,0.658537,0.760658,0.857635,0.10869,0.232598,0.789002,0.49594,0.441259,0.105607,0.785883,0.0479957,0.486199,0.55783,0.897049,0.936283,0.639308,0.972557,0.999933,0.62977,0.160437,0.0445687,0.784988,0.52487,0.745535,0.846448,0.980529,0.92251,0.775175,0.544031,0.230372,0.958092,0.210081,0.439628,0.891923,0.473116,0.654645,0.951131,0.908185,0.952716,0.95457,0.411605,0.916581,0.239367,0.805309,0.409316,0.270265,0.591101,0.668032,0.738845,0.93897,0.884353,0.901216,0.747211,0.809085,0.798642,0.767226,0.204295,0.741113,0.891665,0.610099,0.69659,0.594817,0.297724,0.610351,0.826948,0.642389,0.582246,0.402601,0.058958,0.297612,0.87671,0.969709,0.925766,0.998083,0.667626,0.79719,0.154349,0.45613,0.587084,0.96774,0.907293,0.809096,0.338406,0.487914,0.853022,0.696211,0.981229,0.556889,0.409059,0.363786,0.784624,0.850688,0.913889,0.720481,0.844456,0.465515,0.61756,0.468257,0.925171,0.585069,0.896906,0.961268,0.574031,0.365147,0.764826,0.901586,0.81205,0.950902,0.426707,0.742559,0.865107,0.346945,0.847895,0.69096,0.856301,0.954937,0.466738,0.734574,0.946227,0.824083,0.826168,0.86619,0.907239,0.840056,0.522566,0.713328,0.614579,0.658377,0.531553,0.419963,0.247784,0.381339,0.616573,0.657327,0.943928,0.992561,0.919971,0.686986,0.57955,0.513213,0.815469,0.861963,0.840688,0.824756,0.941554,0.936092,0.485214,0.63127,0.811103,0.90435,0.71734,0.264362,0.932266,0.691651,0.874537,0.898952,0.400685,0.615629,0.61212,0.742356,0.995081,0.480745,0.704871,0.45751,0.776874,0.523748,0.845785,0.935266,0.884522,0.954462,0.998614,0.795723,0.735559,0.849754,0.895267,0.728478,0.837205,0.99362,0.851683,0.92978,0.820781,0.609707,0.794433,0.794646,0.930572,0.824375,1.57475e-07,0.669081,0.955997,0.62474,0.947742,0.757652,0.877767,0.416407,0.371874,0.726903,0.772575,0.854366,0.700002,0.875517,0.265179,0.988991,0.999886,0.404278,0.448303,0.882159,0.479817,0.90721,0.992677,0.971067,0.936758,0.839522,0.999995,0.870944,0.999824,0.842516,0.55276,0.993739,0.921725,0.992115,0.997881,0.999559,0.984491,0.999345,0.955519,0.863667,0.968503,0.996929,0.98347,0.999213,0.994247,0.958377,0.818649,0.811781,0.969005,0.533176,0.862606,0.890642,0.853342,0.994162,0.735367,0.995971,0.989418,0.987495,0.836251,0.988584,0.997572,0.655051,0.872771,0.97362,0.972214,0.98016,0.979323,0.998481,0.971266,0.404497,0.979333,0.951771,0.897635,0.994312,0.556527,0.317205,0.612591,0.98913,0.940793,0.999238,0.999114,0.37025,0.954375,0.990018,0.999992,0.994172,0.548626,0.984029,0.0996943,0.633679,0.138788,0.992142,0.992737,0.955763,0.92378,0.933645,0.987515,0.396438,0.925123,0.93496,0.654994,0.324265,0.819831,0.994169,0.985375,0.991573,0.999715,0.974723,0.769326,0.782599,0.980395,0.328796,0.978556,0.999985,0.507241,0.696179,0.981459,0.999915,0.799652,0.981459,0.781116,0.770494,0.98926,0.766341,0.997699,0.766325,0.237155,0.915958,0.929248,0.906179,0.949635,0.965822,0.926186,0.998818,0.967544,0.990436,0.840281,0.865719,1,0.870371,0.909155,0.910336,0.939556,0.99928,0.980117,0.984554,0.821506,0.921165,0.518695,0.895749,0.837479,0.891388,0.79637,0.981083,0.900639,0.582899,0.988309,0.975868,0.808954,0.970156,0.838008,0.999854,0.583029,0.990624,0.966327,0.903406,0.899541,0.997637,0.914598,0.996121,0.99522,0.868409,0.971018,0.817515,0.999851,0.952634,0.952101,0.993942,0.961784,0.415593,0.71196,0.999844,0.9305,0.787043,0.999207,0.912193,0.96012,0.76107,0.610001,0.58858,0.963553,0.89099,0.991774,0.989684,0.999444,0.956162,0.999881,0.98448,0.92988,0.670089,0.584597,0.962345,0.712114,0.597125,0.908358,0.743244,0.46159,0.993615,0.977826,0.961793,0.543134,0.766714,0.494679,0.914201,0.874243,0.89151,0.517046,0.992521,0.630045,0.977522,0.242032,0.804516,0.739534,0.999494,0.51801,0.94214,0.845262,0.816106,0.764329,0.751058,0.93077,0.82398,0.497308,0.0580206,0.86772,0.880027,0.973259,0.963145,0.889519,0.544388,0.73469,0.652976,0.813027,0.836161,0.526027,0.985452,0.964465,0.886299,0.959496,0.530995,0.967319,0.899628,0.349259,0.568765,0.381205,0.776127,0.754983,0.784439,0.159339,0.978882,0.517849,0.957364,0.0713107,0.946374,0.902955,0.494391,0.373831,0.884987,0.502601,0.561619,0.972468,0.921883,0.720573,0.792299,0.931171,0.867567,0.427685,0.585421,0.99386,0.995714,0.896182,0.201895,0.647242,0.70572,0.73437,0.72224,0.701357,0.933218,0.962822,0.579304,0.711986,0.587959,0.480107,0.416672,0.455538,0.939249,0.779389,0.857781,0.536371,0.792985,0.999171,0.402912,0.893277,0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 }}

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Coexpression cluster:C282: Difference between revisions

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Revision as of 18:38, 8 August 2012

Phase1 CAGE Peaks

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