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Coexpression cluster:C1721: Difference between revisions

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|full_id=C1721_Mast_CD14_Eosinophils_Natural_Peripheral_Basophils_Neutrophils
|full_id=C1721_Mast_CD14_Eosinophils_Natural_Peripheral_Basophils_Neutrophils
|id=C1721
|id=C1721
|ontology_enrichment_celltype=CL:0002057!1.79e-26!42;CL:0000860!4.44e-25!45;CL:0000766!6.17e-23!76;CL:0000738!1.24e-19!140;CL:0000557!1.68e-18!71;CL:0000839!4.12e-18!70;CL:0002009!1.83e-16!65;CL:0002031!2.04e-16!124;CL:0002194!1.52e-15!63;CL:0000576!1.52e-15!63;CL:0000040!1.52e-15!63;CL:0000559!1.52e-15!63;CL:0002087!1.27e-14!119;CL:0000037!4.68e-12!172;CL:0000566!4.68e-12!172;CL:0002032!1.23e-11!165;CL:0000837!1.23e-11!165;CL:0000763!1.97e-11!112;CL:0000049!1.97e-11!112;CL:0000988!3.81e-11!182
|ontology_enrichment_celltype=CL:0000860!2.95e-39!42;CL:0002057!2.95e-39!42;CL:0000766!7.19e-35!72;CL:0000738!3.85e-34!136;CL:0000473!1.90e-32!48;CL:0000234!1.90e-32!48;CL:0000557!2.24e-29!67;CL:0002031!9.95e-28!120;CL:0000839!6.76e-27!66;CL:0002009!8.40e-25!61;CL:0002087!9.66e-25!115;CL:0000037!1.45e-23!168;CL:0000566!1.45e-23!168;CL:0002194!4.84e-23!59;CL:0000576!4.84e-23!59;CL:0000040!4.84e-23!59;CL:0000559!4.84e-23!59;CL:0002032!1.74e-22!161;CL:0000837!1.74e-22!161;CL:0000988!5.43e-22!177;CL:0000763!3.59e-20!108;CL:0000049!3.59e-20!108;CL:0000325!2.75e-15!87;CL:0000094!2.52e-08!8;CL:0002274!9.62e-08!5;CL:0000457!9.62e-08!5;CL:0002191!9.62e-08!5;CL:0000097!9.62e-08!5;CL:0000831!9.62e-08!5;CL:0002028!9.62e-08!5
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!1.31e-19!112;UBERON:0002390!1.90e-19!102;UBERON:0003061!1.90e-19!102;UBERON:0002371!4.98e-16!80;UBERON:0002405!7.60e-15!115;UBERON:0001474!1.16e-14!86;UBERON:0007023!7.30e-12!115;UBERON:0004765!7.36e-11!101;UBERON:0001434!7.36e-11!101
|ontology_enrichment_uberon=UBERON:0002390!1.47e-25!98;UBERON:0003061!1.47e-25!98;UBERON:0002405!9.72e-25!93;UBERON:0002193!1.58e-24!108;UBERON:0002371!5.70e-24!76;UBERON:0001474!4.89e-22!82;UBERON:0004765!1.22e-19!90;UBERON:0001434!5.54e-17!100
|tf_chipseq_enrich=BCL11A#53335;2:11.3477820414428:0.0115705693374132:0.0422864083364278!BCL3#602;2:13.8188411214953:0.00790282333228084:0.032439687379636!CHD2#1106;3:6.20641370047011:0.00777455012627559:0.0319495648319075!CTBP2#1488;2:25.0868001357313:0.00246143859967838:0.0138477798918235!CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239302359804554!EBF1#1879;3:5.3438801079414:0.0118761556386811:0.0432307629133952!ELF1#1997;4:3.40647836704603:0.0123506610529955:0.0447319562253362!GATA3#2625;2:10.8946065428824:0.012515829121883:0.045279918167533!HNF4G#3174;2:11.5013690105787:0.0112743830492105:0.0413733412254565!IRF4#3662;3:13.1487076120465:0.000886046932280843:0.00660277242671987!MEF2C#4208;2:16.5245417970496:0.00557985007798205:0.0252427428872203!NFKB1#4790;4:4.39045073935507:0.00470773269252496:0.0222013408595057!RAD21#5885;3:6.2130203372738:0.00775105506881164:0.031890657119903!SMC3#9126;3:9.0269597069597:0.00265096444946755:0.0146357285054682!SRF#6722;3:8.27830695730069:0.00340484607377615:0.0173572860398842!TCF7L2#6934;3:6.46210593788241:0.00693010875568919:0.0293168190349734
|tf_chipseq_enrich=BCL11A#53335;2:11.3477820414428:0.0115705693374132:0.0422864083364278!BCL3#602;2:13.8188411214953:0.00790282333228084:0.032439687379636!CHD2#1106;3:6.20641370047011:0.00777455012627559:0.0319495648319075!CTBP2#1488;2:25.0868001357313:0.00246143859967838:0.0138477798918235!CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239302359804554!EBF1#1879;3:5.3438801079414:0.0118761556386811:0.0432307629133952!ELF1#1997;4:3.40647836704603:0.0123506610529955:0.0447319562253362!GATA3#2625;2:10.8946065428824:0.012515829121883:0.045279918167533!HNF4G#3174;2:11.5013690105787:0.0112743830492105:0.0413733412254565!IRF4#3662;3:13.1487076120465:0.000886046932280843:0.00660277242671987!MEF2C#4208;2:16.5245417970496:0.00557985007798205:0.0252427428872203!NFKB1#4790;4:4.39045073935507:0.00470773269252496:0.0222013408595057!RAD21#5885;3:6.2130203372738:0.00775105506881164:0.031890657119903!SMC3#9126;3:9.0269597069597:0.00265096444946755:0.0146357285054682!SRF#6722;3:8.27830695730069:0.00340484607377615:0.0173572860398842!TCF7L2#6934;3:6.46210593788241:0.00693010875568919:0.0293168190349734
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242146,0.10708,0.327369,0.339826,0.12998,0.123097,0.254847,0.300809,0.0898207,0.126545,0.0918749,0.0686325,0.0569043,0.0639461,0.0871536,0.267408,0.312064,0.080156,0.274185,0.53753,0.0545112,0.0359652,0.0651134,0.0649137,0.0974216,0.0638093,0.195675,0.174786,0.176557,0.396547,0.0472148,0.735114,0.229138,0.0639045,0.141461,0.0900204,0.228387,0.385962,0.000833826,0.00556522,0.00179772,0.203834,6.37823e-11,0.430936,0.123626,0.270619,0.132705,0.285556,0.493429,0.0297611,0.224471,0.00377097,0.223204,0.143824,0.460679,0.11021,0.0775891,0.153079,0.62577,0.211515,0.125701,0.175283,0.0226059,0.209341,0.0144211,0.0789618,0.084895,0.160115,0.0819954,0.10091,0.122658,0.151161,0.228398,0.056055,0.120552,0.41771,0.655862,0.104741,0.0637856,0.020181,0.190688,0.299739,0.278645,0.733648,0.0940982,0.00312866,0.202744,0.0993772,0.274769,0.00327734,0.11602,0.344528,0.436413,0.0585992,0.20045,0.274438,0.114625,0.180484,0.319826,0.336512,0.0160761,0.109708,0.174594,0.0809806,0.154589,0.00709017,0.122767,0.0749261,0.176858,0.114361,0.347759,0.242462,0.0620267,0.211111,0.0738743,0.00401232,0.183058,0.150073,0.270522,0.16872,0.341388,0.0934526,0.359135,0.123404,0.430769,0.240825,0.3033,0.0643653,0.163542,0.483244,0.040684,0.500871,0.239667,0.10226,0.29809,0.235147,0.32673,0.245965,0.116923,0.148426,0.0983658,0.228743,0.238223,0.156976,0.244789,0.267391,0.301441,0.21807,0.0702189,0.382904,0.432408,0.0194011,0.135865,0.488841,0.18137,0.180609,0.291283,0.273972,0.153023,0.400137,0.37958,0.22307,0.160699,0.0891264,0.166736,0.181253,0.0422294,0.263877,0.146486,0.183121,0.262486,0.000465485,0.131936,0.288826,0.246621,0.463617,0.119485,0.0965376,0.377203,0.279263,0.336564,0.00108243,0.581771,0.47901,0.0594155,0.587524,0.00179791,0.0713793,0.212621,0.594469,0.53612,0.629713,0.581874,0.355154,0.730614,0.0739871,0.180545,0.0147743,0.629445,4.07471e-05,0.206759,0.172506,0.580285,0.550495,0.764863,0.248142,0.0700912,0.167927,0.00161135,0.0269405,0.111362,0.00330321,0.127834,0.139489,0.663441,0.349068,0.0353848,0.0792617,0.196345,0.427789,0.689998,0.737642,0.176145,0.111685,0.258394,0.644878,0.432123,0.759415,0.09639,0.494975,0.28382,0.392155,0.626931,0.371758,0.0422618,0.20076,0.183098,0.128028,0.254547,0.00974547,0.249366,0.316342,0.0197008,0.00831689,0.0463311,0.660884,0.253789,0.401389,0.446908,0.0560233,0.311289,0.318577,0.4488,0.389888,0.603509,0.161355,0.553178,0.246387,0.224252,0.587237,0.155054,0.466978,0.166402,0.257848,0.353942,0.192234,0.427276,0.747776,0.131598,2.61152e-05,0.002511,0.111989,0.797471,0.218352,0.702164,0.138015,0.0349115,0.498956,0.209091,0.55798,0.349033,0.286029,0.139363,0.34194,0.0625602,0.592314,0.0869207,0.182727,0.423117,0.317485,0.633504,0.220564,0.286976,0.262394,0.307462,0.135076,0.469588,0.664443,0.274593,0.0311407,0.183857,0.128394,0.218812,0.176255,0.137231,0.200667,0.174119,0.361524,0.31558,0.412744,0.54408,0.018149,0.513592,0.415367,0.815658,0.45585,0.36864,0.00811127,0.456862,0.453004,0.680686,0.557093,0.330982,0.382214,0.193207,0.639572,0.11429,0.339393,0.117434,0.306231,0.298354,0.646049,0.0701109,0.457741,0.641611,0.10749,0.0517097,0.289012,0.0549063,0.412586,0.0425269,0.41502,0.55475,0.66153,0.00702347,0.499347,0.307426,0.0736126,0.049727,6.9963e-06,0.132075,0.44799,0.499536,0.0070566,0.276338,0.126433,0.000245277,0.318174,0.0555558,0.048795,0.393022,0.293641,0.116969,0.401231,0.0359836,0.0494979,0.256708,0.338258,0.322052,0.145568,0.153833,0.261242,0.38389,0.188453,0.388459,0.321362,0.627637,0.280757,0.301366,0.340343,0.343265,0.154685,0.128553,0.336254,0.000576219,0.291523,0.0208148,0.309816,0.0537285,0.15063,0.0210584,0.281455,0.348739,0.419895,0.138495,0.0235054,0.32256,0.082459,0.342366,0.109684,0.00738257,0.0156813,0.181288,0.230841,0.352328,0.255358,0.351665,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.406458,0.312881,0.512825,0.244656,0.192188,0.158985,0.174153,0.0972854,0.333309,0.034215,0.339517,0.303699,0.198326,0.0905116,0.458518,0.0443031,0.252005,0.390891,0.238377,0.063694,0.197875,0.287909,0.289389,0.117618,0.392533,0.396962,0.000641077,0.0618069,0.321404,0.0274786,0.050521,0.0127373,0.185715,0.345505,0.0814929,0.271405,0.00654668,0.221943,0.0526496,0.367733,0.246925,0.208775,0.390438,7.69637e-05,0.0402908,0.276922,0.156279,0.313647,0.128336,0.422872,0.336468,0.13327,0.313545,0.17149,0.0877361,0.00399146,0.00018643,0.0083772,0.00229268,0.0879453,0.474066,0.00182507,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.00268881,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.430541,0.159424,0.224871,0.092937,0.389061,0.310732,0.0698238,0.0221952,0.0134421,0.278202,0.426488,0.0938069,0.209809,0.253154,0.0575641,0.309489,0.110045,0.362154,0.140472,0.185476,0.336314,0.344469,0.184651,0.303359,0.297596,0.42392,0.107309,0.0128718,0.259046,0.00922992,0.151046,0.142558,0.347171,0.321735,0.15463,0.13907,0.470121,0.269432,0.250466,0.0165533,0.115686,0.0981568,0.0140064,0.342661,0.27567,0.248127,0.0628839,0.0858973,0.319112,0.00721116
}}
}}

Revision as of 11:37, 19 October 2012


Full id: C1721_Mast_CD14_Eosinophils_Natural_Peripheral_Basophils_Neutrophils



Phase1 CAGE Peaks

Hg19::chr14:35874092..35874103,-p16@NFKBIA
Hg19::chr14:35874125..35874149,-p11@NFKBIA
Hg19::chr14:93121971..93122003,+p@chr14:93121971..93122003
+
Hg19::chr1:228297188..228297205,+p@chr1:228297188..228297205
+
Hg19::chr7:129592344..129592375,+p@chr7:129592344..129592375
+


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 monocyte2.95e-3942
CD14-positive, CD16-negative classical monocyte2.95e-3942
myeloid leukocyte7.19e-3572
leukocyte3.85e-34136
defensive cell1.90e-3248
phagocyte1.90e-3248
granulocyte monocyte progenitor cell2.24e-2967
hematopoietic lineage restricted progenitor cell9.95e-28120
myeloid lineage restricted progenitor cell6.76e-2766
macrophage dendritic cell progenitor8.40e-2561
nongranular leukocyte9.66e-25115
hematopoietic stem cell1.45e-23168
angioblastic mesenchymal cell1.45e-23168
monopoietic cell4.84e-2359
monocyte4.84e-2359
monoblast4.84e-2359
promonocyte4.84e-2359
hematopoietic oligopotent progenitor cell1.74e-22161
hematopoietic multipotent progenitor cell1.74e-22161
hematopoietic cell5.43e-22177
myeloid cell3.59e-20108
common myeloid progenitor3.59e-20108
stuff accumulating cell2.75e-1587
granulocyte2.52e-088
histamine secreting cell9.62e-085
biogenic amine secreting cell9.62e-085
granulocytopoietic cell9.62e-085
mast cell9.62e-085
mast cell progenitor9.62e-085
basophil mast progenitor cell9.62e-085
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.47e-2598
blood island1.47e-2598
immune system9.72e-2593
hemolymphoid system1.58e-24108
bone marrow5.70e-2476
bone element4.89e-2282
skeletal element1.22e-1990
skeletal system5.54e-17100


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
BCL11A#53335211.34778204144280.01157056933741320.0422864083364278
BCL3#602213.81884112149530.007902823332280840.032439687379636
CHD2#110636.206413700470110.007774550126275590.0319495648319075
CTBP2#1488225.08680013573130.002461438599678380.0138477798918235
CTCF#1066444.288205098460020.005152015588243280.0239302359804554
EBF1#187935.34388010794140.01187615563868110.0432307629133952
ELF1#199743.406478367046030.01235066105299550.0447319562253362
GATA3#2625210.89460654288240.0125158291218830.045279918167533
HNF4G#3174211.50136901057870.01127438304921050.0413733412254565
IRF4#3662313.14870761204650.0008860469322808430.00660277242671987
MEF2C#4208216.52454179704960.005579850077982050.0252427428872203
NFKB1#479044.390450739355070.004707732692524960.0222013408595057
RAD21#588536.21302033727380.007751055068811640.031890657119903
SMC3#912639.02695970695970.002650964449467550.0146357285054682
SRF#672238.278306957300690.003404846073776150.0173572860398842
TCF7L2#693436.462105937882410.006930108755689190.0293168190349734



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.