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Coexpression cluster:C874: Difference between revisions

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{{Coexpression_clusters
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genome replication!0.0261202502901549!6347$GO:0007259!JAK-STAT cascade!0.0261202502901549!6347$GO:0019058!viral infectious cycle!0.0261202502901549!6347$GO:0022415!viral reproductive process!0.0261202502901549!6347$GO:0006959!humoral immune response!0.0261202502901549!6347$GO:0008009!chemokine activity!0.0261202502901549!6347$GO:0042379!chemokine receptor binding!0.0261202502901549!6347$GO:0001664!G-protein-coupled receptor binding!0.0261202502901549!6347$GO:0055074!calcium ion homeostasis!0.0261202502901549!6347$GO:0006874!cellular calcium ion homeostasis!0.0261202502901549!6347$GO:0007187!G-protein signaling, coupled to cyclic nucleotide second messenger!0.0261202502901549!6347$GO:0019935!cyclic-nucleotide-mediated signaling!0.0261202502901549!6347$GO:0006875!cellular metal ion homeostasis!0.0261202502901549!6347$GO:0055065!metal ion homeostasis!0.0261202502901549!6347$GO:0042330!taxis!0.0267573295655245!6347$GO:0006935!chemotaxis!0.0267573295655245!6347$GO:0006916!anti-apoptosis!0.027100372252262!6347$GO:0030005!cellular di-, tri-valent inorganic cation homeostasis!0.027100372252262!6347$GO:0007626!locomotory behavior!0.027100372252262!6347$GO:0055066!di-, tri-valent inorganic cation homeostasis!0.027100372252262!6347$GO:0030003!cellular cation homeostasis!0.027100372252262!6347$GO:0055080!cation homeostasis!0.027100372252262!6347$GO:0043066!negative regulation of apoptosis!0.027100372252262!6347$GO:0043069!negative regulation of programmed cell death!0.027100372252262!6347$GO:0055082!cellular chemical homeostasis!0.027100372252262!6347$GO:0006873!cellular ion homeostasis!0.027100372252262!6347$GO:0050801!ion homeostasis!0.0279285258091334!6347$GO:0019932!second-messenger-mediated signaling!0.0279285258091334!6347$GO:0006954!inflammatory response!0.0279285258091334!6347$GO:0007610!behavior!0.0279285258091334!6347$GO:0048878!chemical homeostasis!0.0279285258091334!6347$GO:0022414!reproductive process!0.0279285258091334!6347$GO:0005125!cytokine activity!0.0279285258091334!6347$GO:0009887!organ morphogenesis!0.0310517157920902!6347$GO:0019725!cellular homeostasis!0.0310517157920902!6347$GO:0007243!protein kinase cascade!0.0310517157920902!6347$GO:0009611!response to wounding!0.0339890402589095!6347$GO:0042592!homeostatic process!0.0375541467586309!6347$GO:0005615!extracellular space!0.0402503419105326!6347$GO:0042981!regulation of apoptosis!0.0407236876333177!6347$GO:0043067!regulation of programmed cell death!0.0407236876333177!6347$GO:0006952!defense response!0.0407236876333177!6347$GO:0042221!response to chemical stimulus!0.0407236876333177!6347$GO:0009605!response to external stimulus!0.0422831874615696!6347$GO:0007267!cell-cell 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|full_id=C874_Monocytederived_CD14_Mast_Lymphatic_Smooth_Neurons_Fibroblast
|id=C874
}}

Latest revision as of 11:32, 17 September 2013


Full id: C874_Monocytederived_CD14_Mast_Lymphatic_Smooth_Neurons_Fibroblast



Phase1 CAGE Peaks

Hg19::chr10:64575696..64575711,-p1@CU690136
Hg19::chr17:32583229..32583324,+p2@CCL2
Hg19::chr17:32583293..32583323,-p@chr17:32583293..32583323
-
Hg19::chr17:32583753..32583906,+p@chr17:32583753..32583906
+
Hg19::chr17:32583823..32583891,-p@chr17:32583823..32583891
-
Hg19::chr17:32584045..32584055,+p@chr17:32584045..32584055
+
Hg19::chr17:32584062..32584073,+p@chr17:32584062..32584073
+
Hg19::chr17:32584096..32584112,+p@chr17:32584096..32584112
+
Hg19::chr8:15997784..15997797,-p@chr8:15997784..15997797
-


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:0019079viral genome replication0.0261202502901549
GO:0007259JAK-STAT cascade0.0261202502901549
GO:0019058viral infectious cycle0.0261202502901549
GO:0022415viral reproductive process0.0261202502901549
GO:0006959humoral immune response0.0261202502901549
GO:0008009chemokine activity0.0261202502901549
GO:0042379chemokine receptor binding0.0261202502901549
GO:0001664G-protein-coupled receptor binding0.0261202502901549
GO:0055074calcium ion homeostasis0.0261202502901549
GO:0006874cellular calcium ion homeostasis0.0261202502901549
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0261202502901549
GO:0019935cyclic-nucleotide-mediated signaling0.0261202502901549
GO:0006875cellular metal ion homeostasis0.0261202502901549
GO:0055065metal ion homeostasis0.0261202502901549
GO:0042330taxis0.0267573295655245
GO:0006935chemotaxis0.0267573295655245
GO:0006916anti-apoptosis0.027100372252262
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.027100372252262
GO:0007626locomotory behavior0.027100372252262
GO:0055066di-, tri-valent inorganic cation homeostasis0.027100372252262
GO:0030003cellular cation homeostasis0.027100372252262
GO:0055080cation homeostasis0.027100372252262
GO:0043066negative regulation of apoptosis0.027100372252262
GO:0043069negative regulation of programmed cell death0.027100372252262
GO:0055082cellular chemical homeostasis0.027100372252262
GO:0006873cellular ion homeostasis0.027100372252262
GO:0050801ion homeostasis0.0279285258091334
GO:0019932second-messenger-mediated signaling0.0279285258091334
GO:0006954inflammatory response0.0279285258091334
GO:0007610behavior0.0279285258091334
GO:0048878chemical homeostasis0.0279285258091334
GO:0022414reproductive process0.0279285258091334
GO:0005125cytokine activity0.0279285258091334
GO:0009887organ morphogenesis0.0310517157920902
GO:0019725cellular homeostasis0.0310517157920902
GO:0007243protein kinase cascade0.0310517157920902
GO:0009611response to wounding0.0339890402589095
GO:0042592homeostatic process0.0375541467586309
GO:0005615extracellular space0.0402503419105326
GO:0042981regulation of apoptosis0.0407236876333177
GO:0043067regulation of programmed cell death0.0407236876333177
GO:0006952defense response0.0407236876333177
GO:0042221response to chemical stimulus0.0407236876333177
GO:0009605response to external stimulus0.0422831874615696
GO:0007267cell-cell signaling0.0422831874615696



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
defensive cell1.06e-3248
phagocyte1.06e-3248
monopoietic cell2.69e-2559
monocyte2.69e-2559
monoblast2.69e-2559
promonocyte2.69e-2559
classical monocyte2.53e-2442
CD14-positive, CD16-negative classical monocyte2.53e-2442
macrophage dendritic cell progenitor4.19e-2461
myeloid lineage restricted progenitor cell1.91e-2166
granulocyte monocyte progenitor cell5.82e-2167
myeloid leukocyte9.39e-1972
stuff accumulating cell4.30e-1487
multi fate stem cell3.53e-12427
vascular associated smooth muscle cell3.65e-1232
somatic stem cell1.17e-11433
macrophage3.54e-116
stem cell5.42e-11441
smooth muscle cell7.28e-1043
smooth muscle myoblast7.28e-1043
myeloid cell7.78e-10108
common myeloid progenitor7.78e-10108
electrically responsive cell1.69e-0961
electrically active cell1.69e-0961
nongranular leukocyte1.27e-08115
muscle precursor cell3.65e-0858
myoblast3.65e-0858
multi-potent skeletal muscle stem cell3.65e-0858
muscle cell4.40e-0855
hematopoietic lineage restricted progenitor cell6.99e-08120
cardiocyte1.26e-0716
aortic smooth muscle cell1.88e-0710
contractile cell3.71e-0759
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm1.50e-21203
musculoskeletal system3.90e-20167
mesoderm3.87e-18315
mesoderm-derived structure3.87e-18315
presumptive mesoderm3.87e-18315
immune system1.84e-1793
bone marrow3.33e-1776
bone element3.54e-1582
hemolymphoid system2.12e-13108
skeletal system3.94e-13100
splanchnic layer of lateral plate mesoderm4.69e-1383
skeletal element6.43e-1390
systemic artery6.61e-1333
systemic arterial system6.61e-1333
artery9.21e-1342
arterial blood vessel9.21e-1342
arterial system9.21e-1342
vessel4.52e-1268
hematopoietic system8.63e-1298
blood island8.63e-1298
cardiovascular system2.54e-10109
vasculature2.58e-1078
vascular system2.58e-1078
epithelial tube open at both ends3.25e-1059
blood vessel3.25e-1059
blood vasculature3.25e-1059
vascular cord3.25e-1059
circulatory system8.92e-10112
epithelial tube6.08e-08117
germ layer1.85e-07560
germ layer / neural crest1.85e-07560
embryonic tissue1.85e-07560
presumptive structure1.85e-07560
germ layer / neural crest derived structure1.85e-07560
epiblast (generic)1.85e-07560
blood vessel smooth muscle1.88e-0710
arterial system smooth muscle1.88e-0710
artery smooth muscle tissue1.88e-0710
aorta smooth muscle tissue1.88e-0710
skeletal muscle tissue2.91e-0762
striated muscle tissue2.91e-0762
myotome2.91e-0762
embryonic structure3.19e-07564
anatomical system6.25e-07624
anatomical group7.11e-07625
muscle tissue7.38e-0764
musculature7.38e-0764
musculature of body7.38e-0764


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)
MA0003.10.000472949
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.00594475
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.11.03929
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.22215
MA0056.10
MA0057.10.253359
MA0058.10.325084
MA0059.10.865474
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.354973
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.000336275
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.865814
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.0408613
MA0089.10
MA0090.10.931587
MA0091.11.07263
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.11.31682
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.582067
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.046841
MA0146.10.0260584
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.0006485
MA0138.20.608783
MA0002.20.46405
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.0433683
MA0065.20.182082
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.11.27456
MA0155.10.645215
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.00648562
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.23.89582e-07
MA0102.21.41188
MA0258.10.532421
MA0259.10.218904
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

No analysis results for this cluster

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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