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Coexpression cluster:C1631: Difference between revisions

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{{Coexpression_clusters
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of neurons!0.000345141160614551!4155;3073$GO:0008366!axon ensheathment!0.000345141160614551!4155;3073$GO:0001508!regulation of action potential!0.000361727870421891!4155;3073$GO:0043209!myelin sheath!0.00716883192883501!4155$GO:0003008!system process!0.00716883192883501!4155;3073;5002$GO:0050884!neuromuscular process controlling posture!0.00716883192883501!3073$GO:0004563!beta-N-acetylhexosaminidase activity!0.00716883192883501!3073$GO:0006689!ganglioside catabolic process!0.00716883192883501!3073$GO:0019226!transmission of nerve impulse!0.00716883192883501!4155;3073$GO:0046479!glycosphingolipid catabolic process!0.00716883192883501!3073$GO:0019377!glycolipid catabolic process!0.00716883192883501!3073$GO:0019915!sequestering of lipid!0.00716883192883501!3073$GO:0001573!ganglioside metabolic process!0.00716883192883501!3073$GO:0007628!adult walking behavior!0.00716883192883501!3073$GO:0015904!tetracycline transport!0.00716883192883501!5002$GO:0015520!tetracycline:hydrogen antiporter activity!0.00716883192883501!5002$GO:0015307!drug:hydrogen antiporter activity!0.00716883192883501!5002$GO:0044459!plasma membrane part!0.00716883192883501!4155;7106;5002$GO:0015101!organic cation transmembrane transporter activity!0.00716883192883501!5002$GO:0042895!antibiotic transporter activity!0.00716883192883501!5002$GO:0046677!response to antibiotic!0.00716883192883501!5002$GO:0008493!tetracycline transporter activity!0.00716883192883501!5002$GO:0019911!structural constituent of myelin sheath!0.00754252487059236!4155$GO:0008344!adult locomotory behavior!0.00919837608377269!3073$GO:0030149!sphingolipid catabolic process!0.00946076904077037!3073$GO:0015929!hexosaminidase activity!0.00978570597354006!3073$GO:0015893!drug transport!0.00978570597354006!5002$GO:0007267!cell-cell signaling!0.00978570597354006!4155;3073$GO:0050885!neuromuscular process controlling balance!0.00978570597354006!3073$GO:0006687!glycosphingolipid metabolic process!0.00998460349909566!3073$GO:0007040!lysosome organization and biogenesis!0.0101706240274497!3073$GO:0007399!nervous system development!0.0101996367455477!4155;3073$GO:0007033!vacuole organization and biogenesis!0.0101996367455477!3073$GO:0015238!drug transporter activity!0.0101996367455477!5002$GO:0050905!neuromuscular process!0.0103581346894914!3073$GO:0046466!membrane lipid catabolic process!0.0105077885383775!3073$GO:0042552!myelination!0.0109104886857533!3073$GO:0015299!solute:hydrogen antiporter activity!0.0109104886857533!5002$GO:0030534!adult behavior!0.0109104886857533!3073$GO:0006664!glycolipid metabolic process!0.0114246970871211!3073$GO:0006672!ceramide metabolic process!0.0122974558044596!3073$GO:0046519!sphingoid metabolic process!0.0131283565550644!3073$GO:0065008!regulation of biological quality!0.0141560905259556!4155;3073$GO:0007588!excretion!0.0150332874311201!5002$GO:0005886!plasma membrane!0.0151829793304564!4155;7106;5002$GO:0032501!multicellular organismal process!0.0151829793304564!4155;3073;5002$GO:0015298!solute:cation antiporter activity!0.0154113469493529!5002$GO:0044242!cellular lipid catabolic process!0.0157428993076182!3073$GO:0030203!glycosaminoglycan metabolic process!0.0157428993076182!3073$GO:0006022!aminoglycan metabolic process!0.0157428993076182!3073$GO:0015300!solute:solute antiporter activity!0.0157428993076182!5002$GO:0016020!membrane!0.0174546116642479!4155;7106;3073;5002$GO:0042493!response to drug!0.0187033419075893!5002$GO:0050877!neurological system process!0.0191020292066077!4155;3073$GO:0016324!apical plasma membrane!0.0191020292066077!5002$GO:0006665!sphingolipid metabolic process!0.0191020292066077!3073$GO:0045177!apical part of cell!0.0237157522220542!5002$GO:0015297!antiporter activity!0.0246564633342525!5002$GO:0046982!protein heterodimerization activity!0.0279502739579866!3073$GO:0048731!system development!0.028044494614052!4155;3073$GO:0050954!sensory perception of mechanical stimulus!0.0333974226952198!3073$GO:0007605!sensory perception of sound!0.0333974226952198!3073$GO:0016042!lipid catabolic process!0.0363307499073583!3073$GO:0048856!anatomical structure development!0.0403753673555447!4155;3073$GO:0007626!locomotory behavior!0.0435868571927119!3073$GO:0004553!hydrolase activity, hydrolyzing O-glycosyl compounds!0.045042994673342!3073$GO:0005764!lysosome!0.0464547052074452!3073$GO:0000323!lytic vacuole!0.0464547052074452!3073$GO:0001501!skeletal development!0.0473532810576143!3073$GO:0007275!multicellular organismal development!0.0479593152336682!4155;3073$GO:0016798!hydrolase activity, acting on glycosyl 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|full_id=C1631_Monocytederived_Melanocyte_CD14_Macrophage_Mast_Mesenchymal_Fibroblast
|id=C1631
}}

Latest revision as of 11:48, 17 September 2013


Full id: C1631_Monocytederived_Melanocyte_CD14_Macrophage_Mast_Mesenchymal_Fibroblast



Phase1 CAGE Peaks

Hg19::chr11:2920913..2920942,+p4@SLC22A18
Hg19::chr11:844067..844158,+p2@TSPAN4
Hg19::chr15:72668805..72668860,-p4@HEXA
Hg19::chr18:74845649..74845670,-p10@MBP
Hg19::chr18:74845672..74845681,-p42@MBP


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:0007272ensheathment of neurons0.000345141160614551
GO:0008366axon ensheathment0.000345141160614551
GO:0001508regulation of action potential0.000361727870421891
GO:0043209myelin sheath0.00716883192883501
GO:0003008system process0.00716883192883501
GO:0050884neuromuscular process controlling posture0.00716883192883501
GO:0004563beta-N-acetylhexosaminidase activity0.00716883192883501
GO:0006689ganglioside catabolic process0.00716883192883501
GO:0019226transmission of nerve impulse0.00716883192883501
GO:0046479glycosphingolipid catabolic process0.00716883192883501
GO:0019377glycolipid catabolic process0.00716883192883501
GO:0019915sequestering of lipid0.00716883192883501
GO:0001573ganglioside metabolic process0.00716883192883501
GO:0007628adult walking behavior0.00716883192883501
GO:0015904tetracycline transport0.00716883192883501
GO:0015520tetracycline:hydrogen antiporter activity0.00716883192883501
GO:0015307drug:hydrogen antiporter activity0.00716883192883501
GO:0044459plasma membrane part0.00716883192883501
GO:0015101organic cation transmembrane transporter activity0.00716883192883501
GO:0042895antibiotic transporter activity0.00716883192883501
GO:0046677response to antibiotic0.00716883192883501
GO:0008493tetracycline transporter activity0.00716883192883501
GO:0019911structural constituent of myelin sheath0.00754252487059236
GO:0008344adult locomotory behavior0.00919837608377269
GO:0030149sphingolipid catabolic process0.00946076904077037
GO:0015929hexosaminidase activity0.00978570597354006
GO:0015893drug transport0.00978570597354006
GO:0007267cell-cell signaling0.00978570597354006
GO:0050885neuromuscular process controlling balance0.00978570597354006
GO:0006687glycosphingolipid metabolic process0.00998460349909566
GO:0007040lysosome organization and biogenesis0.0101706240274497
GO:0007399nervous system development0.0101996367455477
GO:0007033vacuole organization and biogenesis0.0101996367455477
GO:0015238drug transporter activity0.0101996367455477
GO:0050905neuromuscular process0.0103581346894914
GO:0046466membrane lipid catabolic process0.0105077885383775
GO:0042552myelination0.0109104886857533
GO:0015299solute:hydrogen antiporter activity0.0109104886857533
GO:0030534adult behavior0.0109104886857533
GO:0006664glycolipid metabolic process0.0114246970871211
GO:0006672ceramide metabolic process0.0122974558044596
GO:0046519sphingoid metabolic process0.0131283565550644
GO:0065008regulation of biological quality0.0141560905259556
GO:0007588excretion0.0150332874311201
GO:0005886plasma membrane0.0151829793304564
GO:0032501multicellular organismal process0.0151829793304564
GO:0015298solute:cation antiporter activity0.0154113469493529
GO:0044242cellular lipid catabolic process0.0157428993076182
GO:0030203glycosaminoglycan metabolic process0.0157428993076182
GO:0006022aminoglycan metabolic process0.0157428993076182
GO:0015300solute:solute antiporter activity0.0157428993076182
GO:0016020membrane0.0174546116642479
GO:0042493response to drug0.0187033419075893
GO:0050877neurological system process0.0191020292066077
GO:0016324apical plasma membrane0.0191020292066077
GO:0006665sphingolipid metabolic process0.0191020292066077
GO:0045177apical part of cell0.0237157522220542
GO:0015297antiporter activity0.0246564633342525
GO:0046982protein heterodimerization activity0.0279502739579866
GO:0048731system development0.028044494614052
GO:0050954sensory perception of mechanical stimulus0.0333974226952198
GO:0007605sensory perception of sound0.0333974226952198
GO:0016042lipid catabolic process0.0363307499073583
GO:0048856anatomical structure development0.0403753673555447
GO:0007626locomotory behavior0.0435868571927119
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds0.045042994673342
GO:0005764lysosome0.0464547052074452
GO:0000323lytic vacuole0.0464547052074452
GO:0001501skeletal development0.0473532810576143
GO:0007275multicellular organismal development0.0479593152336682
GO:0016798hydrolase activity, acting on glycosyl bonds0.0484179111847522



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
granulocyte monocyte progenitor cell1.67e-5567
myeloid lineage restricted progenitor cell9.80e-5566
monopoietic cell3.02e-5259
monocyte3.02e-5259
monoblast3.02e-5259
promonocyte3.02e-5259
myeloid leukocyte1.74e-5172
macrophage dendritic cell progenitor8.89e-5061
defensive cell3.35e-4348
phagocyte3.35e-4348
myeloid cell5.36e-42108
common myeloid progenitor5.36e-42108
stuff accumulating cell4.05e-3887
classical monocyte3.96e-3642
CD14-positive, CD16-negative classical monocyte3.96e-3642
hematopoietic stem cell1.84e-22168
angioblastic mesenchymal cell1.84e-22168
hematopoietic lineage restricted progenitor cell3.79e-21120
leukocyte9.36e-21136
hematopoietic oligopotent progenitor cell1.26e-20161
hematopoietic multipotent progenitor cell1.26e-20161
nongranular leukocyte1.90e-20115
hematopoietic cell6.33e-20177
motile cell1.04e-10386
mesenchymal cell1.59e-10354
connective tissue cell9.91e-10361
macrophage1.70e-086
Uber Anatomy
Ontology termp-valuen
bone marrow6.18e-5176
hematopoietic system4.90e-4798
blood island4.90e-4798
immune system3.58e-4693
bone element2.68e-4582
hemolymphoid system1.05e-43108
skeletal element5.52e-3990
skeletal system1.14e-34100
lateral plate mesoderm1.56e-23203
musculoskeletal system9.14e-18167
mesoderm4.87e-16315
mesoderm-derived structure4.87e-16315
presumptive mesoderm4.87e-16315
connective tissue1.49e-09371


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)
MA0003.10.136928
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.10.554727
MA0058.11.29981
MA0059.11.29682
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.551452
MA0074.10.730989
MA0076.11.33654
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.11.77562
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.11.39943
MA0146.10.143081
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.20.15493
MA0138.21.95446
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.425004
MA0065.21.41695
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.813062
MA0156.11.20729
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.11.49262
MA0164.10.810347
MA0080.22.01584
MA0018.20.781393
MA0099.20.699641
MA0079.20.823998
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
REST#597835.790017229676810.009468788694433940.0356878680064232



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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