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Coexpression cluster:C3806: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.338474986694436,0.404032369974143,0.248973350862402,0,0,0,0,0,0,0,0.204563101265448,0.0852944574994353,0.160717855764157,0.121853104351623,0.248641786604834,0.901954749556652,0.847943569502966,0.849087671020411,0.604396440243365,0.260628401312869,0.406290066269433,0.197386646657653,0.247600673195823,0.289126972412746,0.435163799767044,0.467823209448954,0.569201765171362,0.890796698373783,0.630923298369189,0.511513698530816,0.60861576320791,0.65611922575131,0.551126413850657,0.298755709453128,0.254754572975711,0.357682244950033,0.271987364718628,0.329351182440039,0.351341005362286,0.353385934656962,0.182267080928499,0.271552455695895,0.205583124092593,0,0.212966178241721,0.493116736157158,0.464405884733206,0.546036977007646,0.428932881317029,0.423564647270572,0.327375101464831,0.64543729498012,0.641631093701747,0.632250195478005,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0609149782727745,0.0523039447392876,0,0.168366204242204,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0779013103271332,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.560577092055277,0.688224224545008,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.201612826790636,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0955936734149088,0,0.0601805944860265,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.399114709370023,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.511485107029086,0.601148601595643,0.635013419473632,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.350365912650083,0.270179472213526,0.0840237168815831,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0425916600387234,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.401804113981,0.246655432029025,0.33027054911511,0.340673868673579,0.14963850419244,0.217081920302005,0.187529586342753,0.412670562882006,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0593771573651105,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0385280079017836,0,0,0,0,0,0,0,0,0,0,0,0.0494492378997174,0,0,0,0.0861409897892114,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0978631351411755,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.204234048342335,0,0,0,0,0.106966425460878,0,0,0.0790650569133411,0,0.0874873383132558,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0329432353726146,0,0,0,0,0.234186964128339,0,0,0,0,0,0,0,0,0,0,0,0.0528027736253869,0,0,0,0.0440642112897698,0,0.150522826464445,0.174979787616842,0,0,0,0,0,0,0,0,0,0.0500030232022126,0.0512262229954782,0,0,0.0261639379934246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.031493427513643,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0369091684033041,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0322859259446875,0,0,0,0,0,0,0,0,0.138598130132424,0.121326529566266,0,0,0,0,0,0,0.0581752393062885,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0769194708595365,0,0,0,0,0,0,0,0.0582150559773052,0,0,0,0,0,0,0,0,0,0,0|full_id=C3806_CD14_Eosinophils_CD14CD16_Neutrophils_Whole_lymph_Basophils|gostat_on_coexpression_clusters=GO:0001816!cytokine production!0.00103446535802594!58484;943$GO:0043065!positive regulation of apoptosis!0.00103446535802594!58484;943$GO:0043068!positive regulation of programmed cell death!0.00103446535802594!58484;943$GO:0045554!regulation of TRAIL biosynthetic process!0.00103446535802594!943$GO:0032639!TRAIL production!0.00103446535802594!943$GO:0045556!positive regulation of TRAIL biosynthetic process!0.00103446535802594!943$GO:0045553!TRAIL biosynthetic process!0.00103446535802594!943$GO:0042981!regulation of apoptosis!0.00362041559311593!58484;943$GO:0043067!regulation of programmed cell death!0.00362041559311593!58484;943$GO:0042535!positive regulation of tumor necrosis factor biosynthetic process!0.00362041559311593!943$GO:0042533!tumor necrosis factor biosynthetic process!0.00445569935155049!943$GO:0042534!regulation of tumor necrosis factor biosynthetic process!0.00445569935155049!943$GO:0016045!detection of bacterium!0.00445569935155049!58484$GO:0050702!interleukin-1 beta secretion!0.00460719125131041!58484$GO:0006915!apoptosis!0.00460719125131041!58484;943$GO:0012501!programmed cell death!0.00460719125131041!58484;943$GO:0050701!interleukin-1 secretion!0.00460719125131041!58484$GO:0016265!death!0.00460719125131041!58484;943$GO:0008219!cell death!0.00460719125131041!58484;943$GO:0032640!tumor necrosis factor production!0.00460719125131041!943$GO:0048522!positive regulation of cellular process!0.00460719125131041!58484;943$GO:0009595!detection of biotic stimulus!0.00460719125131041!58484$GO:0048518!positive regulation of biological process!0.0052214091912989!58484;943$GO:0050663!cytokine secretion!0.00603269373868363!58484$GO:0048468!cell development!0.00657096317561614!58484;943$GO:0042108!positive regulation of cytokine biosynthetic process!0.0114121833297713!943$GO:0006919!caspase activation!0.0116710243335441!58484$GO:0048869!cellular developmental process!0.0116710243335441!58484;943$GO:0030154!cell differentiation!0.0116710243335441!58484;943$GO:0009581!detection of external stimulus!0.0116710243335441!58484$GO:0043280!positive regulation of caspase activity!0.0116710243335441!58484$GO:0045727!positive regulation of translation!0.0119841535431956!943$GO:0009306!protein secretion!0.0120582821448717!58484$GO:0042035!regulation of cytokine biosynthetic process!0.0120582821448717!943$GO:0043281!regulation of caspase activity!0.0120582821448717!58484$GO:0031328!positive regulation of cellular biosynthetic process!0.0120582821448717!943$GO:0042089!cytokine biosynthetic process!0.012945261368358!943$GO:0042107!cytokine metabolic process!0.012945261368358!943$GO:0009891!positive regulation of biosynthetic process!0.0129839293357284!943$GO:0051345!positive regulation of hydrolase activity!0.0137432016135358!58484$GO:0051606!detection of stimulus!0.0141128540237549!58484$GO:0051247!positive regulation of protein metabolic process!0.0146368073075038!943$GO:0008632!apoptotic program!0.0149683065950834!58484$GO:0042742!defense response to bacterium!0.0156129023590789!58484$GO:0009617!response to bacterium!0.0170308235643359!58484$GO:0042803!protein homodimerization activity!0.0248146709306179!58484$GO:0032502!developmental process!0.0253956571749537!58484;943$GO:0006417!regulation of translation!0.0276833879125117!943$GO:0031326!regulation of cellular biosynthetic process!0.0293226689605162!943$GO:0051707!response to other organism!0.0297439634680821!58484$GO:0032501!multicellular organismal process!0.0301222550321238!58484;943$GO:0009889!regulation of biosynthetic process!0.0301222550321238!943$GO:0008285!negative regulation of cell proliferation!0.0306398359910231!943$GO:0043085!positive regulation of catalytic activity!0.0342000811111639!58484$GO:0009607!response to biotic stimulus!0.037888228250408!58484$GO:0032940!secretion by cell!0.0382372110621555!58484$GO:0051336!regulation of hydrolase activity!0.0388255038108474!58484$GO:0051704!multi-organism process!0.0413716498701346!58484$GO:0042802!identical protein binding!0.0432141348646109!58484$GO:0031325!positive regulation of cellular metabolic process!0.0432141348646109!943$GO:0046983!protein dimerization activity!0.0432141348646109!58484$GO:0046903!secretion!0.0440225673836635!58484$GO:0009893!positive regulation of metabolic process!0.0440225673836635!943$GO:0007165!signal transduction!0.0440225673836635!58484;943$GO:0051246!regulation of protein metabolic process!0.0467211608289428!943$GO:0000287!magnesium ion binding!0.0487211228152806!58484$GO:0007154!cell communication!0.0491668435042182!58484;943$GO:0042127!regulation of cell 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MA0099.2;0.902716,MA0079.2;0.0107199,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3806_CD14_Eosinophils_CD14CD16_Neutrophils_Whole_lymph_Basophils
|id=C3806
}}

Latest revision as of 12:33, 17 September 2013


Full id: C3806_CD14_Eosinophils_CD14CD16_Neutrophils_Whole_lymph_Basophils



Phase1 CAGE Peaks

Hg19::chr19:47234972..47234989,-p@chr19:47234972..47234989
-
Hg19::chr1:12185978..12185991,+p9@TNFRSF8
Hg19::chr2:32490833..32490846,-p3@NLRC4


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

GO IDGO nameFDR corrected p-value
GO:0001816cytokine production0.00103446535802594
GO:0043065positive regulation of apoptosis0.00103446535802594
GO:0043068positive regulation of programmed cell death0.00103446535802594
GO:0045554regulation of TRAIL biosynthetic process0.00103446535802594
GO:0032639TRAIL production0.00103446535802594
GO:0045556positive regulation of TRAIL biosynthetic process0.00103446535802594
GO:0045553TRAIL biosynthetic process0.00103446535802594
GO:0042981regulation of apoptosis0.00362041559311593
GO:0043067regulation of programmed cell death0.00362041559311593
GO:0042535positive regulation of tumor necrosis factor biosynthetic process0.00362041559311593
GO:0042533tumor necrosis factor biosynthetic process0.00445569935155049
GO:0042534regulation of tumor necrosis factor biosynthetic process0.00445569935155049
GO:0016045detection of bacterium0.00445569935155049
GO:0050702interleukin-1 beta secretion0.00460719125131041
GO:0006915apoptosis0.00460719125131041
GO:0012501programmed cell death0.00460719125131041
GO:0050701interleukin-1 secretion0.00460719125131041
GO:0016265death0.00460719125131041
GO:0008219cell death0.00460719125131041
GO:0032640tumor necrosis factor production0.00460719125131041
GO:0048522positive regulation of cellular process0.00460719125131041
GO:0009595detection of biotic stimulus0.00460719125131041
GO:0048518positive regulation of biological process0.0052214091912989
GO:0050663cytokine secretion0.00603269373868363
GO:0048468cell development0.00657096317561614
GO:0042108positive regulation of cytokine biosynthetic process0.0114121833297713
GO:0006919caspase activation0.0116710243335441
GO:0048869cellular developmental process0.0116710243335441
GO:0030154cell differentiation0.0116710243335441
GO:0009581detection of external stimulus0.0116710243335441
GO:0043280positive regulation of caspase activity0.0116710243335441
GO:0045727positive regulation of translation0.0119841535431956
GO:0009306protein secretion0.0120582821448717
GO:0042035regulation of cytokine biosynthetic process0.0120582821448717
GO:0043281regulation of caspase activity0.0120582821448717
GO:0031328positive regulation of cellular biosynthetic process0.0120582821448717
GO:0042089cytokine biosynthetic process0.012945261368358
GO:0042107cytokine metabolic process0.012945261368358
GO:0009891positive regulation of biosynthetic process0.0129839293357284
GO:0051345positive regulation of hydrolase activity0.0137432016135358
GO:0051606detection of stimulus0.0141128540237549
GO:0051247positive regulation of protein metabolic process0.0146368073075038
GO:0008632apoptotic program0.0149683065950834
GO:0042742defense response to bacterium0.0156129023590789
GO:0009617response to bacterium0.0170308235643359
GO:0042803protein homodimerization activity0.0248146709306179
GO:0032502developmental process0.0253956571749537
GO:0006417regulation of translation0.0276833879125117
GO:0031326regulation of cellular biosynthetic process0.0293226689605162
GO:0051707response to other organism0.0297439634680821
GO:0032501multicellular organismal process0.0301222550321238
GO:0009889regulation of biosynthetic process0.0301222550321238
GO:0008285negative regulation of cell proliferation0.0306398359910231
GO:0043085positive regulation of catalytic activity0.0342000811111639
GO:0009607response to biotic stimulus0.037888228250408
GO:0032940secretion by cell0.0382372110621555
GO:0051336regulation of hydrolase activity0.0388255038108474
GO:0051704multi-organism process0.0413716498701346
GO:0042802identical protein binding0.0432141348646109
GO:0031325positive regulation of cellular metabolic process0.0432141348646109
GO:0046983protein dimerization activity0.0432141348646109
GO:0046903secretion0.0440225673836635
GO:0009893positive regulation of metabolic process0.0440225673836635
GO:0007165signal transduction0.0440225673836635
GO:0051246regulation of protein metabolic process0.0467211608289428
GO:0000287magnesium ion binding0.0487211228152806
GO:0007154cell communication0.0491668435042182
GO:0042127regulation of cell proliferation0.0495993575852572



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
myeloid leukocyte3.07e-7972
classical monocyte3.10e-7942
CD14-positive, CD16-negative classical monocyte3.10e-7942
defensive cell1.36e-7848
phagocyte1.36e-7848
monopoietic cell2.27e-6959
monocyte2.27e-6959
monoblast2.27e-6959
promonocyte2.27e-6959
macrophage dendritic cell progenitor1.14e-6661
myeloid lineage restricted progenitor cell1.27e-6066
granulocyte monocyte progenitor cell1.61e-5967
myeloid cell1.07e-47108
common myeloid progenitor1.07e-47108
leukocyte1.56e-44136
nongranular leukocyte7.71e-39115
stuff accumulating cell2.55e-3787
hematopoietic stem cell7.32e-33168
angioblastic mesenchymal cell7.32e-33168
hematopoietic lineage restricted progenitor cell1.15e-31120
hematopoietic oligopotent progenitor cell1.03e-30161
hematopoietic multipotent progenitor cell1.03e-30161
hematopoietic cell2.41e-30177
granulocyte2.77e-188
intermediate monocyte1.02e-159
CD14-positive, CD16-positive monocyte1.02e-159
blood cell8.05e-1311
non-classical monocyte2.53e-083
CD14-low, CD16-positive monocyte2.53e-083
neutrophil3.84e-083
mesenchymal cell6.15e-08354
connective tissue cell1.65e-07361
basophil1.90e-073
single nucleate cell4.69e-073
mononuclear cell4.69e-073
adult endothelial progenitor cell7.92e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.53e-6798
blood island2.53e-6798
hemolymphoid system8.09e-62108
bone marrow6.74e-5176
immune system4.09e-4793
bone element3.40e-4682
skeletal element6.73e-4190
skeletal system1.80e-35100
lateral plate mesoderm3.20e-27203
musculoskeletal system6.54e-17167
blood2.27e-1515
haemolymphatic fluid2.27e-1515
organism substance2.27e-1515
mesoderm1.30e-13315
mesoderm-derived structure1.30e-13315
presumptive mesoderm1.30e-13315
adult organism4.09e-09114
connective tissue2.22e-07371


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.20.0107199
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



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
ESRRA#21011161.2801047120420.006187620080219560.0273501292347236



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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