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Difference between revisions of "Coexpression cluster:C2235"

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{{Coexpression_clusters
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{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0.0673047577016915,0.149853777506208,0.028634144538123,0,0,0,0,0,0.1007790131153,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.027856248390591,0.0256809761409315,0.030882034193267,0.0171338168051181,0.0164525096832193,0.252058577919365,0.356327201340532,0.455392631826673,0,0,0,0,0,0.055900077197111,0.530544361108161,0.0396891217357494,0.359414903389598,0.12423464073344,0.255868905356769,0.0995340912392844,0.37660857544823,0.326696618564906,0.41059844509359,0.505959479630032,0.564291093123967,0.67267933679854,0.495275958056512,0.533003808885093,0.470038286495479,0.664323449656838,0.647965381297658,0.755863185864514,0.506451608479406,0.346013698674655,0.54057450405078,0.530699532335688,0.488813472853896,0.622906437711325,0.298755709453128,0.321117114611533,0.312714311311476,0.361986747347441,0.262263465458381,0.376628376434988,0.522197346206348,0.538241253660198,0.684119863191457,0.275066192297334,0.388374097289529,0.507212952056032,0,0.0837191039350518,0.117371163682316,0.107070693635831,0.0874130823459109,0.0323647790038062,0,0.0393945006861718,0,0,0,0,0,0,0,0,0,0.097840944397814,0.100320915279728,0.070296948342049,0,0.0966330780564035,0.0507677008280515,0,0,0.0812037792923173,0,0,0,0,0,0.0560687922176245,0,0,0.0261721287455008,0.0531012520152427,0,0,0,0,0,0,0,0.0704457073800035,0,0,0,0,0,0.0304574891363872,0,0,0,0,0.147123750097248,0.179379759914676,0.0587388785772559,0,0,0,0,0,0,0,0,0.0572184347821852,0,0,0.0534545700183436,0,0,0,0.129773480880396,0.102404861888327,0.046446361606319,0,0.120638104118337,0,0,0,0,0,0,0.0412122463733808,0,0,0.111285566928017,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0588362978411115,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0479797036867934,0,0,0.033783900598984,0,0,0,0,0.0303938666854821,0,0.0358286534697011,0,0,0,0,0,0,0.0338657042689512,0,0.0488773853372077,0,0,0,0,0,0,0,0,0,0,0,0.0214178589168123,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.100806413395318,0,0.0477549913674189,0,0,0,0,0,0,0,0,0,0,0.0843640151307332,0,0.107839364342942,0,0,0.134744405676195,0,0.0601805944860265,0,0,0,0,0,0,0.29783193426097,0.25133755598819,0.826121558382811,1.13628617955926,0.618481448081118,0.0834631698541397,0,0,0,0.0212537921102839,0,0,0,0,0.0153683104289607,0,0,0,0.051206238195096,0,0,0,0,0,0,0,0,0,0,0,0,0.0206910107952029,0.172808179578577,0,0,0.0466451378069441,0,0,0,0.0405793422855208,0.0357681304161639,0,0.249744764170801,0.288605840312286,0.188807407019751,0,0,0,0,0,0,0.300574300797821,0,0.0476514636743252,0,0,0.0410282292166428,0,0,0,0,0,0,0,0,0.0180915207549932,0.0388294847274804,0,0.104798262569204,0.212974551107957,0.228947097395951,0,0,0,0,0.0310016407534881,0,0,0,0,0,0,0,0.0342782958079773,0,0,0,0,0.0191274234626113,0,0,0.0267551882976717,0,0.0161109439295801,0,0,0,0,0,0,0,0,0,0,0.131353186234183,0,0,0,0.089905147355422,0,0,0.0813768443325499,0.0190256891830726,0.0331665040796858,0,0,0,0,0,0.0310094911974069,0.0280399444016552,0,0,0.0177602205939906,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.061810668115653,0,0,0,0,0,0.05699798491772,0,0,0,0,0.089121113667536,0,0,0,0,0,0,0,0,0,0.0475916898912054,0,0,0,0,0.0395144944032282,0,0,0,0,0,0,0,0,0,0,0.0770363470064715,0,0,0,0.0670147110949639,0.0387544632396516,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0436452879209715,0,0,0,0,0,0.0211437342385579,0.0252062757946575,0,0.0545795660013852,0,0,0.0204283766509788,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0861409897892114,0,0,0.0321956448428329,0,0,0,0.0223967159144265,0,0.0190312847642998,0,0,0.0316629739392048,0,0,0,0,0,0,0,0.0328333213282965,0,0,0,0.0368115019473605,0,0,0,0.0215675146547342,0.0283276594447047,0,0,0,0.0388046890849592,0,0.0722224018548135,0,0,0.0133047429825382,0,0,0,0,0,0,0.054385572482455,0,0,0,0.0348559494732584,0.0699368280688007,0,0,0,0.0171368002956374,0.0201011396294926,0,0.0442418239009707,0,0,0.0266602233572113,0.0387841230400532,0.016743808154486,0.0420114789121791,0,0,0,0,0,0,0,0,0,0,0,0.102117024171167,0,0,0,0,0,0.0448042842895513,0,0,0,0,0.0141195453442412,0,0,0,0,0,0,0,0,0,0.0323699351672233,0.055966461856338,0,0,0,0,0,0.0164716176863073,0.0327649730749157,0,0,0,0,0,0,0,0,0,0,0.0342643952743103,0,0,0.0296969223726757,0,0,0,0,0,0.0220321056448849,0.0634100406668813,0,0,0,0,0,0.094326151840709,0.121775687313253,0.116058079104876,0,0,0,0,0,0,0.0456863240084368,0.0130819689967123,0,0,0,0,0,0,0,0,0.083278196541229,0,0,0,0.138209211739092,0.0447476819101155,0.057382505275071,0,0,0,0.080654513839309,0,0,0,0,0,0,0,0,0.0644104954448837,0,0.145536958608929,0,0.064101977765766,0,0,0,0,0,0,0.0452211708913631,0,0.035773264607702,0,0,0,0.0383045747062242,0,0,0.114053912936646,0,0,0.0386585674343867,0.0270890491031128,0,0,0,0,0.0395883422157288,0.0419990352144489,0.0345036334513385,0,0,0,0,0,0,0,0,0,0,0.0507414909260677,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0393944182617646,0.031493427513643,0,0,0,0,0.0562542693604755,0,0,0,0.0259295126815682,0,0,0,0,0,0,0,0,0,0,0.0236829981957466,0,0.027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serine/threonine kinase activity!0.0117724961403574!11214;10783$GO:0004691!cAMP-dependent protein kinase activity!0.0117724961403574!11214$GO:0009966!regulation of signal transduction!0.0117724961403574!11214;10783$GO:0030071!regulation of mitotic metaphase/anaphase transition!0.0117724961403574!10783$GO:0007091!mitotic metaphase/anaphase transition!0.0117724961403574!10783$GO:0004690!cyclic nucleotide-dependent protein kinase activity!0.0117724961403574!11214$GO:0004672!protein kinase activity!0.0165849601211184!11214;10783$GO:0016773!phosphotransferase activity, alcohol group as acceptor!0.0211838772948868!11214;10783$GO:0016301!kinase activity!0.02669602727628!11214;10783$GO:0016772!transferase activity, transferring phosphorus-containing groups!0.02669602727628!11214;10783$GO:0007242!intracellular signaling cascade!0.02669602727628!11214;10783$GO:0007059!chromosome segregation!0.02669602727628!10783$GO:0019992!diacylglycerol binding!0.02669602727628!11214$GO:0007088!regulation of mitosis!0.0281470938565469!10783$GO:0043123!positive regulation of I-kappaB kinase/NF-kappaB cascade!0.0387994826056314!10783$GO:0043122!regulation of I-kappaB kinase/NF-kappaB cascade!0.0396760250169122!10783$GO:0007249!I-kappaB kinase/NF-kappaB cascade!0.0440474291966009!10783$GO:0005089!Rho guanyl-nucleotide exchange factor activity!0.0440474291966009!11214$GO:0009967!positive regulation of signal transduction!0.0440474291966009!10783$GO:0016740!transferase activity!0.0440474291966009!11214;10783$GO:0035023!regulation of Rho protein signal transduction!0.0440474291966009!11214$GO:0005088!Ras guanyl-nucleotide exchange factor activity!0.0440474291966009!11214$GO:0007266!Rho protein signal transduction!0.0477194477002178!11214$GO:0060089!molecular transducer activity!0.0477194477002178!11214;10783$GO:0004871!signal transducer 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|full_id=C2235_Mast_CD14_Basophils_immature_Neutrophils_Monocytederived_mature
 
|gostat_on_coexpression_clusters=GO:0004674!protein serine/threonine kinase activity!0.0117724961403574!11214;10783$GO:0004691!cAMP-dependent protein kinase activity!0.0117724961403574!11214$GO:0009966!regulation of signal transduction!0.0117724961403574!11214;10783$GO:0030071!regulation of mitotic metaphase/anaphase transition!0.0117724961403574!10783$GO:0007091!mitotic metaphase/anaphase transition!0.0117724961403574!10783$GO:0004690!cyclic nucleotide-dependent protein kinase activity!0.0117724961403574!11214$GO:0004672!protein kinase activity!0.0165849601211184!11214;10783$GO:0016773!phosphotransferase activity, alcohol group as acceptor!0.0211838772948868!11214;10783$GO:0016301!kinase activity!0.02669602727628!11214;10783$GO:0016772!transferase activity, transferring phosphorus-containing groups!0.02669602727628!11214;10783$GO:0007242!intracellular signaling cascade!0.02669602727628!11214;10783$GO:0007059!chromosome segregation!0.02669602727628!10783$GO:0019992!diacylglycerol binding!0.02669602727628!11214$GO:0007088!regulation of mitosis!0.0281470938565469!10783$GO:0043123!positive regulation of I-kappaB kinase/NF-kappaB cascade!0.0387994826056314!10783$GO:0043122!regulation of I-kappaB kinase/NF-kappaB cascade!0.0396760250169122!10783$GO:0007249!I-kappaB kinase/NF-kappaB cascade!0.0440474291966009!10783$GO:0005089!Rho guanyl-nucleotide exchange factor activity!0.0440474291966009!11214$GO:0009967!positive regulation of signal transduction!0.0440474291966009!10783$GO:0016740!transferase activity!0.0440474291966009!11214;10783$GO:0035023!regulation of Rho protein signal transduction!0.0440474291966009!11214$GO:0005088!Ras guanyl-nucleotide exchange factor activity!0.0440474291966009!11214$GO:0007266!Rho protein signal transduction!0.0477194477002178!11214$GO:0060089!molecular transducer activity!0.0477194477002178!11214;10783$GO:0004871!signal transducer activity!0.0477194477002178!11214;10783
 
|id=C2235
 
|ontology_enrichment_celltype=CL:0000766!1.51e-26!76;CL:0000557!1.77e-26!71;CL:0000839!1.17e-24!70;CL:0002009!4.25e-24!65;CL:0002057!1.34e-23!42;CL:0002194!3.29e-23!63;CL:0000576!3.29e-23!63;CL:0000040!3.29e-23!63;CL:0000559!3.29e-23!63;CL:0000860!1.02e-22!45;CL:0000738!8.48e-21!140;CL:0002031!8.42e-18!124;CL:0000763!4.97e-17!112;CL:0000049!4.97e-17!112;CL:0002087!2.36e-16!119;CL:0000037!3.48e-15!172;CL:0000566!3.48e-15!172;CL:0000988!3.08e-14!182;CL:0002032!1.62e-13!165;CL:0000837!1.62e-13!165;CL:0000134!1.68e-10!358;CL:0002320!8.02e-10!365;CL:0000219!2.20e-08!390
 
|ontology_enrichment_disease=
 
|ontology_enrichment_uberon=UBERON:0002390!4.54e-25!102;UBERON:0003061!4.54e-25!102;UBERON:0002193!2.29e-24!112;UBERON:0002371!3.08e-24!80;UBERON:0001474!1.58e-23!86;UBERON:0004765!1.01e-21!101;UBERON:0001434!1.01e-21!101;UBERON:0002405!2.39e-20!115;UBERON:0002384!7.03e-10!375;UBERON:0002204!3.26e-07!167
 
}}
 

Latest revision as of 03:01, 17 September 2013


Full id: C2235_Mast_CD14_Basophils_immature_Neutrophils_Monocytederived_mature



Phase1 CAGE Peaks

  Short description
Hg19::chr12:69327112..69327126,+ p@chr12:69327112..69327126
+
Hg19::chr15:86124881..86124895,+ p35@AKAP13
Hg19::chr19:13947099..13947104,- p1@LOC284454
Hg19::chr9:127048437..127048462,+ p10@NEK6


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 IDGO nameFDR corrected p-value
GO:0004674protein serine/threonine kinase activity0.0117724961403574
GO:0004691cAMP-dependent protein kinase activity0.0117724961403574
GO:0009966regulation of signal transduction0.0117724961403574
GO:0030071regulation of mitotic metaphase/anaphase transition0.0117724961403574
GO:0007091mitotic metaphase/anaphase transition0.0117724961403574
GO:0004690cyclic nucleotide-dependent protein kinase activity0.0117724961403574
GO:0004672protein kinase activity0.0165849601211184
GO:0016773phosphotransferase activity, alcohol group as acceptor0.0211838772948868
GO:0016301kinase activity0.02669602727628
GO:0016772transferase activity, transferring phosphorus-containing groups0.02669602727628
GO:0007242intracellular signaling cascade0.02669602727628
GO:0007059chromosome segregation0.02669602727628
GO:0019992diacylglycerol binding0.02669602727628
GO:0007088regulation of mitosis0.0281470938565469
GO:0043123positive regulation of I-kappaB kinase/NF-kappaB cascade0.0387994826056314
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.0396760250169122
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0440474291966009
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0440474291966009
GO:0009967positive regulation of signal transduction0.0440474291966009
GO:0016740transferase activity0.0440474291966009
GO:0035023regulation of Rho protein signal transduction0.0440474291966009
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0440474291966009
GO:0007266Rho protein signal transduction0.0477194477002178
GO:0060089molecular transducer activity0.0477194477002178
GO:0004871signal transducer activity0.0477194477002178



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 termp-valuen
myeloid leukocyte6.81e-4272
myeloid lineage restricted progenitor cell1.08e-3966
granulocyte monocyte progenitor cell9.07e-3967
classical monocyte2.04e-3642
CD14-positive, CD16-negative classical monocyte2.04e-3642
monopoietic cell2.81e-3659
monocyte2.81e-3659
monoblast2.81e-3659
promonocyte2.81e-3659
defensive cell1.84e-3548
phagocyte1.84e-3548
leukocyte3.34e-35136
macrophage dendritic cell progenitor1.94e-3461
hematopoietic lineage restricted progenitor cell1.24e-30120
nongranular leukocyte4.15e-30115
hematopoietic stem cell9.52e-28168
angioblastic mesenchymal cell9.52e-28168
hematopoietic cell4.23e-27177
myeloid cell7.60e-27108
common myeloid progenitor7.60e-27108
hematopoietic oligopotent progenitor cell3.65e-25161
hematopoietic multipotent progenitor cell3.65e-25161
stuff accumulating cell8.17e-2487
mesenchymal cell7.11e-12354
connective tissue cell7.37e-12361
motile cell2.05e-10386
multi fate stem cell8.29e-08427
stem cell1.49e-07441
somatic stem cell2.87e-07433
histamine secreting cell5.84e-075
biogenic amine secreting cell5.84e-075
granulocytopoietic cell5.84e-075
mast cell5.84e-075
mast cell progenitor5.84e-075
basophil mast progenitor cell5.84e-075
Uber Anatomy
Ontology termp-valuen
immune system8.67e-3793
bone marrow6.71e-3676
bone element3.87e-3582
hematopoietic system8.94e-3598
blood island8.94e-3598
hemolymphoid system2.35e-34108
skeletal element3.68e-3190
skeletal system7.52e-29100
musculoskeletal system2.76e-13167
connective tissue1.22e-10371
lateral plate mesoderm1.75e-10203


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)
MA0003.11.45381
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.8712
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.599068
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.11.25938
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.657636
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
MA0442.10



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


This analysis result is provided for C0 - C305 clusters.