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Difference between revisions of "Coexpression cluster:C392"

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|tf_chipseq_enrich=BATF#10538;5:4.51070403561178:0.00441220021019274:0.0209020129616402!BCL11A#53335;4:4.20288223757142:0.0141559221446243:0.0496667569073946!CTCF#10664;12:2.38233616581112:0.00186858308648917:0.0110212316580924!EBF1#1879;12:3.95842970958622:1.36112426091127e-05:0.00032974821778082!MEF2A#4205;6:4.16516242436535:0.00257954572908317:0.0142700978017754!POLR2A#5430;21:1.67024135954517:0.0009506830914421:0.00684511488363472!SPI1#6688;10:3.0386383364899:0.000844402612671174:0.00636694566924877!STAT1#6772;5:3.83455324022207:0.00869107245088687:0.0330236089535827!TBP#6908;15:2.05931704838688:0.00158410807947826:0.00998266238536352!USF2#7392;8:3.84953996594655:0.00071937991693606:0.00574662070864962!ZNF143#7702;7:3.50022725428131:0.00288584518373218:0.015613074240769!ZNF263#10127;8:2.43610122578094:0.0125167901394377:0.0452755531248133
 
|tf_chipseq_enrich=BATF#10538;5:4.51070403561178:0.00441220021019274:0.0209020129616402!BCL11A#53335;4:4.20288223757142:0.0141559221446243:0.0496667569073946!CTCF#10664;12:2.38233616581112:0.00186858308648917:0.0110212316580924!EBF1#1879;12:3.95842970958622:1.36112426091127e-05:0.00032974821778082!MEF2A#4205;6:4.16516242436535:0.00257954572908317:0.0142700978017754!POLR2A#5430;21:1.67024135954517:0.0009506830914421:0.00684511488363472!SPI1#6688;10:3.0386383364899:0.000844402612671174:0.00636694566924877!STAT1#6772;5:3.83455324022207:0.00869107245088687:0.0330236089535827!TBP#6908;15:2.05931704838688:0.00158410807947826:0.00998266238536352!USF2#7392;8:3.84953996594655:0.00071937991693606:0.00574662070864962!ZNF143#7702;7:3.50022725428131:0.00288584518373218:0.015613074240769!ZNF263#10127;8:2.43610122578094:0.0125167901394377:0.0452755531248133
 
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 +
|tfbs_overrepresentation_for_novel_motifs=0.842038,0.232343,0.059802,0.407729,0.169673,1.89882,0.175095,0.1716,0.845954,0.236052,0.36231,0.203538,0.232225,0.501974,0.679085,0.193751,0.33472,0.278637,0.696397,0.774334,0.817929,0.826358,0.124907,1.46965,0.0793696,0.625087,0.3399,0.781813,0.390789,0.472041,0.679821,0.363981,0.692711,0.237227,0.576985,0.407307,0.310398,0.407022,1.16254,0.290004,0.313801,0.310187,0.526516,0.378645,0.114392,0.919739,0.521477,0.347224,0.650702,1.07146,0.648329,0.183375,0.702527,0.427029,0.558863,0.506501,0.177677,1.43474,0.0699846,0.148912,0.397292,0.525166,1.1876,0.841377,0.553355,1.42621,1.54105,0.983449,0.355656,0.828977,0.292832,0.354898,0.478217,0.557091,0.392971,0.0902157,0.0043264,0.300172,0.353062,0.264612,0.719426,0.312308,0.188707,0.872997,0.511911,0.16518,0.0242141,0.0655331,0.691411,1.07932,0.723727,0.488513,0.377556,2.39169,2.00286,0.0246063,0.983712,0.412519,0.250711,2.16387,0.111393,0.372975,1.0509,0.337605,0.762448,0.110252,0.325192,0.96047,0.573573,0.63374,0.496755,0.405608,0.460391,0.375574,0.679489,0.562692,0.0833136,0.330496,0.285144,0.238729,0.549768,0.245647,0.127707,0.196148,0.782053,0.813472,0.171066,0.993409,0.587649,1.13546,0.489108,0.102719,0.600533,0.56539,0.735665,0.257438,0.665613,0.391857,0.696441,1.52541,1.13019,0.662221,0.987058,0.409595,0.279588,0.443961,0.26723,1.36826,0.0914794,1.04292,0.424756,0.484758,0.489437,0.313905,0.176994,0.857896,0.235846,0.639911,0.0793963,0.236668,0.661111,0.47352,0.352434,0.516622,0.291674,0.18819,0.208206,0.174248,1.77108
 
}}
 
}}

Revision as of 05:11, 26 November 2012


Full id: C392_Monocytederived_CD14_Macrophage_CD14CD16_Dendritic_Eosinophils_migratory



Phase1 CAGE Peaks

Hg19::chr11:124932955..124932970,+p3@SLC37A2
Hg19::chr12:8218926..8218980,-p1@C3AR1
Hg19::chr13:44453688..44453795,+p1@LACC1
Hg19::chr13:50018402..50018469,+p1@SETDB2
Hg19::chr17:4642690..4642701,-p9@CXCL16
Hg19::chr17:55055472..55055522,+p1@SCPEP1
Hg19::chr18:74824549..74824569,+p1@AK097116
Hg19::chr19:18284561..18284667,+p1@IFI30
Hg19::chr19:54876531..54876549,-p1@LAIR1
Hg19::chr19:7587555..7587570,+p2@MCOLN1
Hg19::chr1:17944806..17944819,+p10@ARHGEF10L
Hg19::chr1:17944832..17944849,+p2@ARHGEF10L
Hg19::chr1:228870893..228870910,+p3@RHOU
Hg19::chr3:46249843..46249846,-p6@CCR1
Hg19::chr3:46249859..46249874,-p4@CCR1
Hg19::chr3:46249878..46249905,-p2@CCR1
Hg19::chr3:46412794..46412814,-p@chr3:46412794..46412814
-
Hg19::chr3:46412829..46412861,-p@chr3:46412829..46412861
-
Hg19::chr5:156536036..156536065,-p2@HAVCR2
Hg19::chr5:156536071..156536082,-p9@HAVCR2
Hg19::chr5:156536090..156536106,-p8@HAVCR2
Hg19::chr5:180257951..180257966,+p1@ENST00000501855
Hg19::chr5:180257974..180258065,+p1@ENST00000502162
p1@ENST00000508309
p1@ENST00000509921
Hg19::chr5:77806227..77806251,-p6@LHFPL2
Hg19::chr5:77806360..77806396,-p9@LHFPL2
Hg19::chr8:17941575..17941642,-p1@ASAH1
Hg19::chr9:115983665..115983682,-p5@FKBP15


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:0042330taxis0.00405379739799262
GO:0006935chemotaxis0.00405379739799262
GO:0007626locomotory behavior0.00433475631325112
GO:0005764lysosome0.00433475631325112
GO:0000323lytic vacuole0.00433475631325112
GO:0042221response to chemical stimulus0.00433475631325112
GO:0005773vacuole0.0048306998448887
GO:0007610behavior0.00837779738250679
GO:0051480cytosolic calcium ion homeostasis0.00912516189803368
GO:0007204elevation of cytosolic calcium ion concentration0.00912516189803368
GO:0004943C3a anaphylatoxin receptor activity0.00912516189803368
GO:0004876complement component C3a receptor activity0.00912516189803368
GO:0006874cellular calcium ion homeostasis0.0193159095894078
GO:0055074calcium ion homeostasis0.0193159095894078
GO:0006875cellular metal ion homeostasis0.0193159095894078
GO:0055065metal ion homeostasis0.0193159095894078
GO:0004875complement receptor activity0.0193159095894078
GO:0004942anaphylatoxin receptor activity0.0225218536178917
GO:0048247lymphocyte chemotaxis0.0225218536178917
GO:0001653peptide receptor activity0.0225218536178917
GO:0008528peptide receptor activity, G-protein coupled0.0225218536178917
GO:0009605response to external stimulus0.0279409002264544
GO:0001848complement binding0.02853630822038
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0287048152723536
GO:0055066di-, tri-valent inorganic cation homeostasis0.0287048152723536
GO:0030003cellular cation homeostasis0.0325569677870366
GO:0055080cation homeostasis0.0325569677870366
GO:0042277peptide binding0.0329217591962625
GO:0016021integral to membrane0.0329326172035117
GO:0031224intrinsic to membrane0.0329326172035117
GO:0055082cellular chemical homeostasis0.0343440629744898
GO:0006873cellular ion homeostasis0.0343440629744898
GO:0005041low-density lipoprotein receptor activity0.0343440629744898
GO:0030228lipoprotein receptor activity0.0343440629744898
GO:0004185serine carboxypeptidase activity0.0343440629744898
GO:0017040ceramidase activity0.0364180192480767
GO:0050801ion homeostasis0.0404833389821219
GO:0006954inflammatory response0.0465522445284474
GO:0030169low-density lipoprotein binding0.0475041394165519
GO:0048878chemical homeostasis0.0475041394165519



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 leukocyte2.54e-6072
granulocyte monocyte progenitor cell4.67e-5767
macrophage dendritic cell progenitor5.44e-5761
monopoietic cell7.90e-5659
monocyte7.90e-5659
monoblast7.90e-5659
promonocyte7.90e-5659
myeloid lineage restricted progenitor cell1.23e-5466
defensive cell4.53e-5448
phagocyte4.53e-5448
classical monocyte7.48e-4742
CD14-positive, CD16-negative classical monocyte7.48e-4742
myeloid cell2.32e-38108
common myeloid progenitor2.32e-38108
leukocyte1.08e-33136
hematopoietic lineage restricted progenitor cell3.16e-29120
nongranular leukocyte5.24e-29115
hematopoietic stem cell1.03e-25168
angioblastic mesenchymal cell1.03e-25168
hematopoietic oligopotent progenitor cell1.36e-23161
hematopoietic multipotent progenitor cell1.36e-23161
hematopoietic cell5.88e-23177
stuff accumulating cell1.05e-2287
intermediate monocyte2.75e-109
CD14-positive, CD16-positive monocyte2.75e-109
macrophage2.01e-086
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.84e-6398
blood island2.84e-6398
hemolymphoid system9.92e-58108
bone marrow2.78e-5576
immune system5.94e-5193
bone element2.64e-4982
adult organism2.50e-46114
skeletal element1.32e-4290
skeletal system5.12e-37100
lateral plate mesoderm1.01e-24203
neural tube6.12e-1556
neural rod6.12e-1556
future spinal cord6.12e-1556
neural keel6.12e-1556
musculoskeletal system1.87e-14167
regional part of nervous system4.85e-1353
regional part of brain4.85e-1353
organ2.23e-12503
regional part of forebrain2.62e-1141
forebrain2.62e-1141
anterior neural tube2.62e-1141
future forebrain2.62e-1141
mesoderm3.56e-11315
mesoderm-derived structure3.56e-11315
presumptive mesoderm3.56e-11315
germ layer7.24e-11560
germ layer / neural crest7.24e-11560
embryonic tissue7.24e-11560
presumptive structure7.24e-11560
germ layer / neural crest derived structure7.24e-11560
epiblast (generic)7.24e-11560
embryonic structure1.78e-10564
central nervous system9.03e-1081
developing anatomical structure9.45e-10581
brain grey matter1.37e-0934
gray matter1.37e-0934
telencephalon1.65e-0934
embryo1.88e-09592
neural plate4.05e-0982
presumptive neural plate4.05e-0982
brain5.70e-0968
future brain5.70e-0968
regional part of telencephalon2.23e-0832
anatomical system2.28e-08624
anatomical group2.77e-08625
cerebral hemisphere3.20e-0832
neurectoderm3.42e-0886
tissue8.39e-08773
nervous system1.03e-0789
neural nucleus1.33e-079
nucleus of brain1.33e-079
multi-cellular organism1.55e-07656
blood3.94e-0715
haemolymphatic fluid3.94e-0715
organism substance3.94e-0715
basal ganglion4.81e-079
nuclear complex of neuraxis4.81e-079
aggregate regional part of brain4.81e-079
collection of basal ganglia4.81e-079
cerebral subcortex4.81e-079


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
BATF#1053854.510704035611780.004412200210192740.0209020129616402
BCL11A#5333544.202882237571420.01415592214462430.0496667569073946
CTCF#10664122.382336165811120.001868583086489170.0110212316580924
EBF1#1879123.958429709586221.36112426091127e-050.00032974821778082
MEF2A#420564.165162424365350.002579545729083170.0142700978017754
POLR2A#5430211.670241359545170.00095068309144210.00684511488363472
SPI1#6688103.03863833648990.0008444026126711740.00636694566924877
STAT1#677253.834553240222070.008691072450886870.0330236089535827
TBP#6908152.059317048386880.001584108079478260.00998266238536352
USF2#739283.849539965946550.000719379916936060.00574662070864962
ZNF143#770273.500227254281310.002885845183732180.015613074240769
ZNF263#1012782.436101225780940.01251679013943770.0452755531248133



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.