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Coexpression cluster:C294: Difference between revisions

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{{Coexpression_clusters
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828130386425,0.054407660998573,0.210353308343831,0.350479829061732,0.261586685319474,0.092743246865863,0.140845366054086,0.19275485324392,0,0.0758904199370637,0.079946807131842,0.156983076262146,0.127828009549688,0.273134826423806,0.286094482485878,0.124719478691449,0,0,0,0,0,0.20715139958257,0.14826204992358,0,0.321762975806487,0|full_id=C294_CD14_Macrophage_Monocytederived_CD14CD16_Neutrophils_Basophils_Peripheral|gostat_on_coexpression_clusters=GO:0006952!defense response!0.000349565744672719!4688;4048;1536;929;6280;10871$GO:0006954!inflammatory response!0.00448776427999258!4048;1536;929;6280$GO:0009611!response to wounding!0.0127504247667843!4048;1536;929;6280$GO:0009605!response to external stimulus!0.0246489756269869!4048;1536;929;6280$GO:0045113!regulation of integrin biosynthetic process!0.0246489756269869!6280$GO:0004218!cathepsin S activity!0.0246489756269869!1520$GO:0008747!N-acetylneuraminate lyase activity!0.0246489756269869!80896$GO:0045112!integrin biosynthetic process!0.0246489756269869!6280$GO:0006950!response to stress!0.026619015725701!23678;4048;1536;929;6280$GO:0006968!cellular defense response!0.0289096751976543!4688;10871$GO:0005011!macrophage colony stimulating factor receptor activity!0.0358425014391679!1436|id=C294|ontology_enrichment_celltype=CL:0000766!1.74e-60!72;CL:0002009!6.60e-59!61;CL:0002194!6.04e-58!59;CL:0000576!6.04e-58!59;CL:0000040!6.04e-58!59;CL:0000559!6.04e-58!59;CL:0000557!7.19e-53!67;CL:0000473!2.78e-52!48;CL:0000234!2.78e-52!48;CL:0000839!1.12e-50!66;CL:0000763!3.34e-45!108;CL:0000049!3.34e-45!108;CL:0000860!4.15e-45!42;CL:0002057!4.15e-45!42;CL:0000738!3.62e-36!136;CL:0000037!1.59e-32!168;CL:0000566!1.59e-32!168;CL:0002087!1.92e-31!115;CL:0000988!3.17e-29!177;CL:0002032!3.40e-29!161;CL:0000837!3.40e-29!161;CL:0002031!3.88e-28!120;CL:0000325!7.18e-20!87;CL:0002393!2.37e-11!9;CL:0002397!2.37e-11!9;CL:0000235!2.12e-08!6;CL:0000094!2.58e-08!8|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002390!4.26e-54!98;UBERON:0003061!4.26e-54!98;UBERON:0002193!2.31e-49!108;UBERON:0007023!1.49e-45!114;UBERON:0002371!4.89e-45!76;UBERON:0002405!1.35e-40!93;UBERON:0001474!6.08e-40!82;UBERON:0004765!3.04e-34!90;UBERON:0001434!1.62e-29!100;UBERON:0003081!7.33e-20!203;UBERON:0002204!9.01e-12!167;UBERON:0001049!1.19e-11!56;UBERON:0005068!1.19e-11!56;UBERON:0006241!1.19e-11!56;UBERON:0007135!1.19e-11!56;UBERON:0000073!4.17e-10!53;UBERON:0002616!4.17e-10!53;UBERON:0000479!3.91e-09!773;UBERON:0000178!4.08e-09!15;UBERON:0000179!4.08e-09!15;UBERON:0000463!4.08e-09!15;UBERON:0000062!1.12e-08!503;UBERON:0002780!1.19e-08!41;UBERON:0001890!1.19e-08!41;UBERON:0003080!1.19e-08!41;UBERON:0006240!1.19e-08!41;UBERON:0000926!1.24e-08!315;UBERON:0004120!1.24e-08!315;UBERON:0006603!1.24e-08!315;UBERON:0000923!4.82e-08!560;UBERON:0010316!4.82e-08!560;UBERON:0005291!4.82e-08!560;UBERON:0006598!4.82e-08!560;UBERON:0010317!4.82e-08!560;UBERON:0002532!4.82e-08!560;UBERON:0002050!4.99e-08!564;UBERON:0005423!2.90e-07!581;UBERON:0003528!4.07e-07!34;UBERON:0002020!4.07e-07!34;UBERON:0001893!4.69e-07!34;UBERON:0003075!5.10e-07!82;UBERON:0007284!5.10e-07!82;UBERON:0000922!5.50e-07!592;UBERON:0001017!5.87e-07!81|pathway_enrichment=8.37369675774424e-06;0.0053005500476521;4;156;Phagosome 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267003,0.142821,0.0650927,0.201939,0.086913,0.99733,0.191982,1.31238,1.88142,0.0505631,0.138453,0.495902,0.362758,0.751018,0.416755,0.299755,0.6423,0.340619,0.225942,0.0600724,0.328492,0.00692154,1.035,0.103223,0.437709,0.52089,0.15016,0.617465,0.132827,0.149896,1.06471,0.235065,0.242544,0.0827325,0.15691,1.21596,0.300024,0.381461,0.0878499,0.942108,0.279152,0.395448,0.570568,0.308932,0.0656157,0.202462,0.0652342,0.253821,0.0837482,0.953215,0.184561,0.306237,0.163857,0.467759,0.795125,0.219064,0.646807,0.121914,0.744365,0.0550238,0.39385,0.458046,0.572422,1.42757,0.995643,1.81872,0.104726,1.03421,0.541181,0.0914916,0.0996242,0.353377,0.000535795,1.3595,0.610297,0.133659,0.888194,1.35011,0.8851,0.237235,0.451424,0.145317,0.169396,0.741921,1.3523,0.136147,0.147753,1.39269,0.233414,0.26281,0.590138,0.157159,0.0421223,1.07567,0.557273,0.0258187,0.261173,0.213865,0.260865,0.0736769,0.176012,0.506054,1.18878,0.200363,0.338538,0.162487,0.283914,0.38725,0.132357,1.15422,0.319719,0.602275,0.174728,0.273004,0.240631,0.42154,0.0769737,0.333187,0.149525,0.433284,0.650802,0.558549,2.48176,0.141697,0.187224,0.521838,1.32718,0.937823,0.49003,0.578841,0.264254,0.929508,0.839352,0.148664,1.17173,0.562385,0.143958,0.628215,0.129752,0.333478,1.17352,0.0835396,0.674386,0.787941,0.00904583,0.109448,0.222198,0.489002,0.319485,0.618918,0.226888,0.167587,0.304838,0.240338,0.0817006,0.164689|tfbs_overrepresentation_jaspar=MA0003.1;0.525553,MA0004.1;0.171976,MA0006.1;0.142277,MA0007.1;0.154321,MA0009.1;0.302111,MA0014.1;0.00352503,MA0017.1;0.929101,MA0019.1;0.340017,MA0024.1;0.227674,MA0025.1;0.406058,MA0027.1;1.80451,MA0028.1;0.16205,MA0029.1;0.240834,MA0030.1;0.232995,MA0031.1;0.190676,MA0038.1;0.0834613,MA0040.1;0.244872,MA0041.1;0.423736,MA0042.1;0.364423,MA0043.1;0.817071,MA0046.1;0.798301,MA0048.1;0.425649,MA0050.1;3.69445,MA0051.1;2.02366,MA0052.1;0.247554,MA0055.1;0.937823,MA0056.1;0,MA0057.1;0.392862,MA0058.1;0.0208353,MA0059.1;0.226987,MA0060.1;0.0382043,MA0061.1;0.0640719,MA0063.1;0,MA0066.1;0.0836468,MA0067.1;0.561712,MA0068.1;0.00276632,MA0069.1;0.291208,MA0070.1;0.283018,MA0071.1;0.23879,MA0072.1;0.279748,MA0073.1;1.77931e-05,MA0074.1;0.277824,MA0076.1;0.0241147,MA0077.1;0.274171,MA0078.1;0.129652,MA0081.1;1.03959,MA0083.1;0.307714,MA0084.1;0.730117,MA0087.1;0.277975,MA0088.1;0.911218,MA0089.1;0,MA0090.1;0.0273569,MA0091.1;0.174518,MA0092.1;0.325996,MA0093.1;0.145919,MA0095.1;0,MA0098.1;0,MA0100.1;0.0895989,MA0101.1;0.0553842,MA0103.1;0.131452,MA0105.1;0.0794316,MA0106.1;0.335022,MA0107.1;0.0238439,MA0108.2;0.552897,MA0109.1;0,MA0111.1;0.298254,MA0113.1;0.721891,MA0114.1;0.965766,MA0115.1;1.24016,MA0116.1;3.002,MA0117.1;0.33048,MA0119.1;0.96476,MA0122.1;0.350462,MA0124.1;0.460583,MA0125.1;0.391616,MA0130.1;0,MA0131.1;0.431527,MA0132.1;0,MA0133.1;0,MA0135.1;0.867887,MA0136.1;3.39332,MA0139.1;0.112225,MA0140.1;0.235818,MA0141.1;0.0894989,MA0142.1;0.98257,MA0143.1;0.356524,MA0144.1;0.627221,MA0145.1;0.389091,MA0146.1;0.371633,MA0147.1;0.079656,MA0148.1;1.16607,MA0149.1;0.0627813,MA0062.2;0.12378,MA0035.2;0.0661931,MA0039.2;0.00606129,MA0138.2;0.130311,MA0002.2;0.87215,MA0137.2;1.58519,MA0104.2;0.0927552,MA0047.2;0.096586,MA0112.2;1.18443,MA0065.2;0.292302,MA0150.1;0.26659,MA0151.1;0,MA0152.1;0.891699,MA0153.1;0.378142,MA0154.1;0.310931,MA0155.1;0.143139,MA0156.1;2.03861,MA0157.1;0.915699,MA0158.1;0,MA0159.1;0.0263735,MA0160.1;0.0585812,MA0161.1;0,MA0162.1;0.00786188,MA0163.1;0.345103,MA0164.1;0.372716,MA0080.2;6.40107,MA0018.2;0.103006,MA0099.2;0.0691713,MA0079.2;9.95326e-06,MA0102.2;0.764449,MA0258.1;1.10297,MA0259.1;0.342985,MA0442.1;0}}
|full_id=C294_CD14_Macrophage_Monocytederived_CD14CD16_Neutrophils_Basophils_Peripheral
|id=C294
}}

Latest revision as of 11:15, 17 September 2013


Full id: C294_CD14_Macrophage_Monocytederived_CD14CD16_Neutrophils_Basophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr11:117059709..117059733,+p11@SIDT2
Hg19::chr11:59950486..59950515,-p2@MS4A6A
Hg19::chr11:59950519..59950605,-p1@MS4A6A
Hg19::chr11:72433267..72433292,-p4@ARAP1
Hg19::chr11:72433293..72433345,-p3@ARAP1
Hg19::chr12:111127201..111127221,-p3@HVCN1
Hg19::chr12:96429349..96429381,-p1@LTA4H
Hg19::chr14:103587794..103587823,+p@chr14:103587794..103587823
+
Hg19::chr16:50308028..50308093,+p2@ADCY7
Hg19::chr17:29248896..29248906,+p5@ADAP2
Hg19::chr17:29248918..29248949,+p2@ADAP2
Hg19::chr17:29248955..29248978,+p1@ADAP2
Hg19::chr17:72542265..72542277,-p4@CD300C
Hg19::chr17:7462261..7462266,+p13@TNFSF13
Hg19::chr17:7462268..7462279,+p7@TNFSF13
Hg19::chr17:7462297..7462342,+p1@TNFSF13
Hg19::chr1:150738211..150738260,-p1@CTSS
Hg19::chr1:153330728..153330829,+p2@S100A9
Hg19::chr1:182758900..182758918,+p1@NPL
Hg19::chr1:182767386..182767390,+p@chr1:182767386..182767390
+
Hg19::chr1:183559693..183559704,-p5@NCF2
Hg19::chr20:1517945..1517963,-p@chr20:1517945..1517963
-
Hg19::chr22:17700260..17700331,-p1@CECR1
Hg19::chr2:68962023..68962095,+p5@ARHGAP25
Hg19::chr2:68962229..68962279,+p6@ARHGAP25
Hg19::chr2:74782818..74782845,-p3@LOXL3
Hg19::chr5:140012392..140012432,-p5@CD14
Hg19::chr5:140013191..140013202,-p10@CD14
Hg19::chr5:140013224..140013235,-p12@CD14
Hg19::chr5:140013241..140013270,-p3@CD14
Hg19::chr5:140013275..140013296,-p4@CD14
Hg19::chr5:149466042..149466143,-p1@CSF1R
Hg19::chr5:180230830..180230903,-p2@MGAT1
Hg19::chr5:39274617..39274636,-p7@FYB
Hg19::chr5:39274655..39274666,-p12@FYB
Hg19::chr6:25452404..25452424,-p@chr6:25452404..25452424
-
Hg19::chr7:157647472..157647497,+p1@ENST00000443338
Hg19::chr8:67624963..67625045,+p3@SGK3
Hg19::chr9:115983523..115983565,-p1@FKBP15
Hg19::chrX:37639279..37639290,+p2@CYBB
Hg19::chrX:80457922..80457946,+p4@SH3BGRL
Hg19::chrX:80457962..80457977,+p6@SH3BGRL
Hg19::chrX:80458001..80458016,+p8@SH3BGRL


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

p.valueFDRnGenesnPathwayName
8.37369675774424e-060.00530055004765214156Phagosome (KEGG):04145



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:0006952defense response0.000349565744672719
GO:0006954inflammatory response0.00448776427999258
GO:0009611response to wounding0.0127504247667843
GO:0009605response to external stimulus0.0246489756269869
GO:0045113regulation of integrin biosynthetic process0.0246489756269869
GO:0004218cathepsin S activity0.0246489756269869
GO:0008747N-acetylneuraminate lyase activity0.0246489756269869
GO:0045112integrin biosynthetic process0.0246489756269869
GO:0006950response to stress0.026619015725701
GO:0006968cellular defense response0.0289096751976543
GO:0005011macrophage colony stimulating factor receptor activity0.0358425014391679



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 leukocyte1.74e-6072
macrophage dendritic cell progenitor6.60e-5961
monopoietic cell6.04e-5859
monocyte6.04e-5859
monoblast6.04e-5859
promonocyte6.04e-5859
granulocyte monocyte progenitor cell7.19e-5367
defensive cell2.78e-5248
phagocyte2.78e-5248
myeloid lineage restricted progenitor cell1.12e-5066
myeloid cell3.34e-45108
common myeloid progenitor3.34e-45108
classical monocyte4.15e-4542
CD14-positive, CD16-negative classical monocyte4.15e-4542
leukocyte3.62e-36136
hematopoietic stem cell1.59e-32168
angioblastic mesenchymal cell1.59e-32168
nongranular leukocyte1.92e-31115
hematopoietic cell3.17e-29177
hematopoietic oligopotent progenitor cell3.40e-29161
hematopoietic multipotent progenitor cell3.40e-29161
hematopoietic lineage restricted progenitor cell3.88e-28120
stuff accumulating cell7.18e-2087
intermediate monocyte2.37e-119
CD14-positive, CD16-positive monocyte2.37e-119
macrophage2.12e-086
granulocyte2.58e-088
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.26e-5498
blood island4.26e-5498
hemolymphoid system2.31e-49108
adult organism1.49e-45114
bone marrow4.89e-4576
immune system1.35e-4093
bone element6.08e-4082
skeletal element3.04e-3490
skeletal system1.62e-29100
lateral plate mesoderm7.33e-20203
musculoskeletal system9.01e-12167
neural tube1.19e-1156
neural rod1.19e-1156
future spinal cord1.19e-1156
neural keel1.19e-1156
regional part of nervous system4.17e-1053
regional part of brain4.17e-1053
tissue3.91e-09773
blood4.08e-0915
haemolymphatic fluid4.08e-0915
organism substance4.08e-0915
organ1.12e-08503
regional part of forebrain1.19e-0841
forebrain1.19e-0841
anterior neural tube1.19e-0841
future forebrain1.19e-0841
mesoderm1.24e-08315
mesoderm-derived structure1.24e-08315
presumptive mesoderm1.24e-08315
germ layer4.82e-08560
germ layer / neural crest4.82e-08560
embryonic tissue4.82e-08560
presumptive structure4.82e-08560
germ layer / neural crest derived structure4.82e-08560
epiblast (generic)4.82e-08560
embryonic structure4.99e-08564
developing anatomical structure2.90e-07581
brain grey matter4.07e-0734
gray matter4.07e-0734
telencephalon4.69e-0734
neural plate5.10e-0782
presumptive neural plate5.10e-0782
embryo5.50e-07592
central nervous system5.87e-0781


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)
MA0003.10.525553
MA0004.10.171976
MA0006.10.142277
MA0007.10.154321
MA0009.10.302111
MA0014.10.00352503
MA0017.10.929101
MA0019.10.340017
MA0024.10.227674
MA0025.10.406058
MA0027.11.80451
MA0028.10.16205
MA0029.10.240834
MA0030.10.232995
MA0031.10.190676
MA0038.10.0834613
MA0040.10.244872
MA0041.10.423736
MA0042.10.364423
MA0043.10.817071
MA0046.10.798301
MA0048.10.425649
MA0050.13.69445
MA0051.12.02366
MA0052.10.247554
MA0055.10.937823
MA0056.10
MA0057.10.392862
MA0058.10.0208353
MA0059.10.226987
MA0060.10.0382043
MA0061.10.0640719
MA0063.10
MA0066.10.0836468
MA0067.10.561712
MA0068.10.00276632
MA0069.10.291208
MA0070.10.283018
MA0071.10.23879
MA0072.10.279748
MA0073.11.77931e-05
MA0074.10.277824
MA0076.10.0241147
MA0077.10.274171
MA0078.10.129652
MA0081.11.03959
MA0083.10.307714
MA0084.10.730117
MA0087.10.277975
MA0088.10.911218
MA0089.10
MA0090.10.0273569
MA0091.10.174518
MA0092.10.325996
MA0093.10.145919
MA0095.10
MA0098.10
MA0100.10.0895989
MA0101.10.0553842
MA0103.10.131452
MA0105.10.0794316
MA0106.10.335022
MA0107.10.0238439
MA0108.20.552897
MA0109.10
MA0111.10.298254
MA0113.10.721891
MA0114.10.965766
MA0115.11.24016
MA0116.13.002
MA0117.10.33048
MA0119.10.96476
MA0122.10.350462
MA0124.10.460583
MA0125.10.391616
MA0130.10
MA0131.10.431527
MA0132.10
MA0133.10
MA0135.10.867887
MA0136.13.39332
MA0139.10.112225
MA0140.10.235818
MA0141.10.0894989
MA0142.10.98257
MA0143.10.356524
MA0144.10.627221
MA0145.10.389091
MA0146.10.371633
MA0147.10.079656
MA0148.11.16607
MA0149.10.0627813
MA0062.20.12378
MA0035.20.0661931
MA0039.20.00606129
MA0138.20.130311
MA0002.20.87215
MA0137.21.58519
MA0104.20.0927552
MA0047.20.096586
MA0112.21.18443
MA0065.20.292302
MA0150.10.26659
MA0151.10
MA0152.10.891699
MA0153.10.378142
MA0154.10.310931
MA0155.10.143139
MA0156.12.03861
MA0157.10.915699
MA0158.10
MA0159.10.0263735
MA0160.10.0585812
MA0161.10
MA0162.10.00786188
MA0163.10.345103
MA0164.10.372716
MA0080.26.40107
MA0018.20.103006
MA0099.20.0691713
MA0079.29.95326e-06
MA0102.20.764449
MA0258.11.10297
MA0259.10.342985
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
SPI1#6688193.625166201440271.80912235243461e-079.89748189449547e-06



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

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